Starting phenix.real_space_refine on Sun May 18 23:11:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm3_41377/05_2025/8tm3_41377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm3_41377/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tm3_41377/05_2025/8tm3_41377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm3_41377/05_2025/8tm3_41377.map" model { file = "/net/cci-nas-00/data/ceres_data/8tm3_41377/05_2025/8tm3_41377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm3_41377/05_2025/8tm3_41377.cif" } resolution = 3.0 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= 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG: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, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASN: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: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 10.12, per 1000 atoms: 0.58 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: 4.26 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.96 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: 5.27 Time building geometry restraints manager: 4.97 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: 4.530 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: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.110 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- 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 (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: -0.07 (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 TRP 0.005 0.001 TRP D 100 HIS 0.002 0.001 HIS C 154 PHE 0.015 0.001 PHE d 102 TYR 0.014 0.001 TYR c 66 ARG 0.008 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.17226 ( 925) hydrogen bonds : angle 7.62338 ( 2628) SS BOND : bond 0.00158 ( 1) SS BOND : angle 1.66482 ( 2) covalent geometry : bond 0.00289 (17893) covalent geometry : angle 0.55875 (24353) *********************** 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 : 2.169 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: A 120 GLU cc_start: 0.9128 (tt0) cc_final: 0.8890 (pt0) 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: 0.7405 (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: 1.1135 time to fit residues: 517.4270 Evaluate side-chains 325 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 D 98 ASN G 53 GLN c 103 ASN c 125 HIS c 145 GLN c 283 GLN d 29 GLN d 153 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081474 restraints weight = 49295.180| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.54 r_work: 0.3280 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17894 Z= 0.145 Angle : 0.600 10.394 24355 Z= 0.314 Chirality : 0.042 0.240 2881 Planarity : 0.005 0.082 3113 Dihedral : 4.055 18.046 2545 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 3.65 % Allowed : 22.29 % Favored : 74.06 % 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: -0.08 (0.18), residues: 2351 helix: 1.83 (0.18), residues: 902 sheet: -1.54 (0.22), residues: 501 loop : -1.01 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 139 HIS 0.006 0.001 HIS j 27 PHE 0.013 0.001 PHE F 99 TYR 0.020 0.001 TYR A 167 ARG 0.007 0.001 ARG i 93 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 925) hydrogen bonds : angle 5.63012 ( 2628) SS BOND : bond 0.00303 ( 1) SS BOND : angle 1.89309 ( 2) covalent geometry : bond 0.00332 (17893) covalent geometry : angle 0.59997 (24353) *********************** 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 447 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 384 time to evaluate : 2.157 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 49 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: A 118 MET cc_start: 0.7498 (mmm) cc_final: 0.7275 (mtm) REVERT: A 163 MET cc_start: 0.8677 (ptp) cc_final: 0.8453 (ptp) REVERT: A 189 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7658 (m170) REVERT: B 17 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7188 (ptm160) REVERT: B 57 ASP cc_start: 0.6940 (t0) cc_final: 0.6661 (t0) REVERT: B 66 TYR cc_start: 0.7755 (m-10) cc_final: 0.7552 (m-10) REVERT: B 139 TRP cc_start: 0.8830 (t60) cc_final: 0.8464 (t60) REVERT: C 166 LYS cc_start: 0.8687 (mptt) cc_final: 0.8226 (mppt) REVERT: C 205 ASN cc_start: 0.8721 (m110) cc_final: 0.8091 (p0) REVERT: D 110 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 189 MET cc_start: 0.8923 (mtp) cc_final: 0.8540 (mtt) REVERT: E 86 ASN cc_start: 0.9403 (m-40) cc_final: 0.9082 (m110) REVERT: E 125 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8193 (mmm-85) REVERT: E 226 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.7144 (t70) REVERT: F 153 ASP cc_start: 0.8449 (t0) cc_final: 0.8219 (t0) REVERT: F 182 MET cc_start: 0.8808 (pmm) cc_final: 0.8558 (pmm) REVERT: G 21 ARG cc_start: 0.9144 (ptm160) cc_final: 0.8852 (mtp-110) REVERT: G 159 TYR cc_start: 0.7843 (t80) cc_final: 0.7457 (t80) REVERT: c 133 PHE cc_start: 0.7753 (m-80) cc_final: 0.6962 (m-80) REVERT: c 157 CYS cc_start: 0.8369 (m) cc_final: 0.7981 (t) REVERT: c 163 GLN cc_start: 0.8387 (mp10) cc_final: 0.7590 (mp10) REVERT: c 198 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7245 (tmmt) REVERT: c 277 MET cc_start: 0.8481 (mpt) cc_final: 0.8206 (mpt) REVERT: d 40 ASN cc_start: 0.9280 (t0) cc_final: 0.8821 (t0) REVERT: d 141 TYR cc_start: 0.7814 (p90) cc_final: 0.7554 (p90) REVERT: d 152 GLN cc_start: 0.7857 (mt0) cc_final: 0.7133 (mp-120) REVERT: d 193 GLU cc_start: 0.8406 (tp30) cc_final: 0.7988 (mm-30) REVERT: d 200 GLN cc_start: 0.7977 (mp10) cc_final: 0.7517 (tm-30) REVERT: j 54 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.6211 (pmm) REVERT: j 59 ASP cc_start: 0.7870 (t0) cc_final: 0.7634 (t0) REVERT: j 66 SER cc_start: 0.9336 (p) cc_final: 0.9126 (p) outliers start: 63 outliers final: 22 residues processed: 421 average time/residue: 1.1285 time to fit residues: 537.8454 Evaluate side-chains 361 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS 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 25 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 161 CYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 177 THR 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 189 THR Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 74 LEU Chi-restraints excluded: chain j residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 174 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 163 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 220 ASN C 85 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN 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 = 0.3602 r_free = 0.3602 target = 0.092613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077560 restraints weight = 49749.772| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.51 r_work: 0.3206 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17894 Z= 0.202 Angle : 0.635 11.053 24355 Z= 0.334 Chirality : 0.044 0.309 2881 Planarity : 0.005 0.067 3113 Dihedral : 4.275 20.457 2545 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 5.10 % Allowed : 22.81 % Favored : 72.09 % 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: -0.11 (0.18), residues: 2351 helix: 1.74 (0.18), residues: 907 sheet: -1.50 (0.22), residues: 519 loop : -0.98 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP j 40 HIS 0.004 0.001 HIS E 65 PHE 0.015 0.002 PHE j 92 TYR 0.015 0.002 TYR F 123 ARG 0.009 0.001 ARG j 57 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 925) hydrogen bonds : angle 5.39713 ( 2628) SS BOND : bond 0.00714 ( 1) SS BOND : angle 3.98787 ( 2) covalent geometry : bond 0.00466 (17893) covalent geometry : angle 0.63416 (24353) *********************** 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 440 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 352 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7347 (m-80) cc_final: 0.6701 (m-80) REVERT: A 49 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: A 50 LYS cc_start: 0.7274 (tptp) cc_final: 0.6669 (tptp) REVERT: A 163 MET cc_start: 0.8789 (ptp) cc_final: 0.8469 (ptp) REVERT: A 189 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7863 (m170) REVERT: B 17 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7301 (ptm160) REVERT: B 20 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: B 57 ASP cc_start: 0.7158 (t0) cc_final: 0.6745 (t0) REVERT: B 139 TRP cc_start: 0.8879 (t60) cc_final: 0.8496 (t60) REVERT: C 166 LYS cc_start: 0.8758 (mptt) cc_final: 0.8289 (mppt) REVERT: C 205 ASN cc_start: 0.8792 (m110) cc_final: 0.8154 (p0) REVERT: D 110 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8563 (tm-30) REVERT: E 19 ILE cc_start: 0.9155 (mp) cc_final: 0.8790 (mt) REVERT: E 27 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8925 (mm-30) REVERT: E 86 ASN cc_start: 0.9400 (m-40) cc_final: 0.9022 (m-40) REVERT: E 226 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.7419 (t70) REVERT: F 153 ASP cc_start: 0.8510 (t0) cc_final: 0.8279 (t0) REVERT: G 19 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: G 21 ARG cc_start: 0.9123 (ptm160) cc_final: 0.8903 (mtp-110) REVERT: G 159 TYR cc_start: 0.8036 (t80) cc_final: 0.7727 (t80) REVERT: G 236 ASP cc_start: 0.8486 (p0) cc_final: 0.8257 (p0) REVERT: c 101 LEU cc_start: 0.8194 (pt) cc_final: 0.7992 (pt) REVERT: c 133 PHE cc_start: 0.7794 (m-80) cc_final: 0.6998 (m-80) REVERT: c 157 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8278 (t) REVERT: c 163 GLN cc_start: 0.8360 (mp10) cc_final: 0.7578 (mp10) REVERT: c 277 MET cc_start: 0.8530 (mpt) cc_final: 0.8221 (mpt) REVERT: c 283 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8231 (pp30) REVERT: d 152 GLN cc_start: 0.7972 (mt0) cc_final: 0.7620 (mp10) REVERT: d 200 GLN cc_start: 0.8103 (mp10) cc_final: 0.7627 (tm-30) REVERT: i 49 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8020 (tm-30) REVERT: j 54 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6688 (ptp) REVERT: j 59 ASP cc_start: 0.7998 (t0) cc_final: 0.7630 (t0) outliers start: 88 outliers final: 39 residues processed: 410 average time/residue: 1.1080 time to fit residues: 514.1958 Evaluate side-chains 368 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 HIS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain C residue 76 LEU 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 25 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 74 VAL 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 19 GLU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 161 CYS 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 c residue 285 ASN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 189 THR 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 54 MET Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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 20 GLN B 198 ASN B 220 ASN C 85 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN c 283 GLN d 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.093515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.078442 restraints weight = 49493.932| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.53 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17894 Z= 0.144 Angle : 0.613 13.376 24355 Z= 0.316 Chirality : 0.043 0.348 2881 Planarity : 0.005 0.059 3113 Dihedral : 4.218 19.606 2545 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 4.69 % Allowed : 23.97 % Favored : 71.34 % 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: -0.05 (0.18), residues: 2351 helix: 1.75 (0.18), residues: 907 sheet: -1.41 (0.22), residues: 516 loop : -0.94 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 160 HIS 0.004 0.001 HIS F 121 PHE 0.012 0.001 PHE D 143 TYR 0.021 0.001 TYR A 167 ARG 0.008 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 925) hydrogen bonds : angle 5.13165 ( 2628) SS BOND : bond 0.00416 ( 1) SS BOND : angle 3.22192 ( 2) covalent geometry : bond 0.00334 (17893) covalent geometry : angle 0.61260 (24353) *********************** 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 440 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 359 time to evaluate : 2.018 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: 0.7630 (m-80) cc_final: 0.7088 (m-80) REVERT: A 49 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: A 50 LYS cc_start: 0.7294 (tptp) cc_final: 0.6706 (tptp) REVERT: A 189 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7847 (m170) REVERT: B 17 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7409 (ptm160) REVERT: B 20 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: B 57 ASP cc_start: 0.7253 (t0) cc_final: 0.6823 (t0) REVERT: B 139 TRP cc_start: 0.8866 (t60) cc_final: 0.8399 (t60) REVERT: B 151 ASP cc_start: 0.8013 (t0) cc_final: 0.7525 (t0) REVERT: C 166 LYS cc_start: 0.8739 (mptt) cc_final: 0.8246 (mppt) REVERT: C 205 ASN cc_start: 0.8809 (m110) cc_final: 0.8129 (p0) REVERT: D 53 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8304 (ptt180) REVERT: D 110 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8508 (tm-30) REVERT: E 19 ILE cc_start: 0.9145 (mp) cc_final: 0.8795 (mt) REVERT: E 86 ASN cc_start: 0.9389 (m-40) cc_final: 0.9106 (m110) REVERT: E 91 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8406 (mp0) REVERT: F 144 ASN cc_start: 0.8819 (t0) cc_final: 0.8291 (t0) REVERT: F 153 ASP cc_start: 0.8559 (t0) cc_final: 0.8311 (t0) REVERT: F 182 MET cc_start: 0.8983 (pmm) cc_final: 0.8550 (pmm) REVERT: G 11 ARG cc_start: 0.8231 (pmt170) cc_final: 0.7807 (ptp90) REVERT: G 19 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8478 (mm-30) REVERT: G 21 ARG cc_start: 0.9115 (ptm160) cc_final: 0.8879 (mtp-110) REVERT: G 159 TYR cc_start: 0.8028 (t80) cc_final: 0.7682 (t80) REVERT: G 236 ASP cc_start: 0.8534 (p0) cc_final: 0.8266 (p0) REVERT: c 46 GLU cc_start: 0.7465 (pp20) cc_final: 0.6707 (pm20) REVERT: c 101 LEU cc_start: 0.8123 (pt) cc_final: 0.7902 (pt) REVERT: c 133 PHE cc_start: 0.7770 (m-80) cc_final: 0.7005 (m-80) REVERT: c 157 CYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8308 (t) REVERT: c 163 GLN cc_start: 0.8356 (mp10) cc_final: 0.8151 (mp10) REVERT: c 256 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8600 (p) REVERT: c 287 TYR cc_start: 0.9137 (m-80) cc_final: 0.8902 (m-80) REVERT: d 40 ASN cc_start: 0.9364 (t0) cc_final: 0.8952 (t0) REVERT: d 67 ASN cc_start: 0.9015 (m110) cc_final: 0.8613 (p0) REVERT: d 141 TYR cc_start: 0.7781 (p90) cc_final: 0.7386 (p90) REVERT: d 152 GLN cc_start: 0.7988 (mt0) cc_final: 0.7653 (mp10) REVERT: d 200 GLN cc_start: 0.8068 (mp10) cc_final: 0.7649 (tm-30) REVERT: j 54 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6528 (pmm) REVERT: j 59 ASP cc_start: 0.8052 (t0) cc_final: 0.7696 (t0) REVERT: j 113 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8280 (ttmm) outliers start: 81 outliers final: 38 residues processed: 412 average time/residue: 1.1107 time to fit residues: 519.2408 Evaluate side-chains 373 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain C residue 7 ILE 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 25 GLU 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 220 VAL Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 161 CYS 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 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 52 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 64 THR 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 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 55 optimal weight: 0.9990 chunk 209 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 220 ASN C 85 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN F 121 HIS 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 = 0.3624 r_free = 0.3624 target = 0.093673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078751 restraints weight = 49630.393| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.54 r_work: 0.3229 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17894 Z= 0.143 Angle : 0.623 12.932 24355 Z= 0.322 Chirality : 0.043 0.355 2881 Planarity : 0.005 0.061 3113 Dihedral : 4.224 19.532 2545 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 5.15 % Allowed : 24.90 % Favored : 69.95 % 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: -0.09 (0.18), residues: 2351 helix: 1.68 (0.18), residues: 902 sheet: -1.36 (0.22), residues: 520 loop : -0.94 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 160 HIS 0.004 0.001 HIS F 121 PHE 0.013 0.001 PHE d 94 TYR 0.023 0.001 TYR A 167 ARG 0.010 0.001 ARG j 57 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 925) hydrogen bonds : angle 4.99982 ( 2628) SS BOND : bond 0.00420 ( 1) SS BOND : angle 2.84610 ( 2) covalent geometry : bond 0.00334 (17893) covalent geometry : angle 0.62202 (24353) *********************** 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 441 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 352 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7652 (m-80) cc_final: 0.7092 (m-80) REVERT: A 7 SER cc_start: 0.7932 (m) cc_final: 0.7574 (p) REVERT: A 49 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: A 50 LYS cc_start: 0.7413 (tptp) cc_final: 0.6854 (tptp) REVERT: A 163 MET cc_start: 0.8875 (ptp) cc_final: 0.8553 (ptp) REVERT: A 173 PHE cc_start: 0.7795 (t80) cc_final: 0.7101 (t80) REVERT: A 185 GLU cc_start: 0.8087 (mp0) cc_final: 0.7813 (pm20) REVERT: A 189 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7851 (m170) REVERT: B 9 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7766 (m) REVERT: B 17 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7702 (ptm160) REVERT: B 57 ASP cc_start: 0.7290 (t0) cc_final: 0.6837 (t0) REVERT: B 139 TRP cc_start: 0.8852 (t60) cc_final: 0.8335 (t60) REVERT: B 141 LYS cc_start: 0.9031 (tttm) cc_final: 0.8623 (ptmt) REVERT: B 151 ASP cc_start: 0.7984 (t0) cc_final: 0.7493 (t0) REVERT: C 166 LYS cc_start: 0.8731 (mptt) cc_final: 0.8233 (mppt) REVERT: C 205 ASN cc_start: 0.8816 (m110) cc_final: 0.8125 (p0) REVERT: D 53 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8301 (ptt180) REVERT: D 110 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8476 (tm-30) REVERT: E 19 ILE cc_start: 0.9129 (mp) cc_final: 0.8787 (mt) REVERT: E 86 ASN cc_start: 0.9397 (m-40) cc_final: 0.9100 (m110) REVERT: E 91 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8374 (mp0) REVERT: E 226 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.7433 (t70) REVERT: F 144 ASN cc_start: 0.8838 (t0) cc_final: 0.8352 (t0) REVERT: F 206 LYS cc_start: 0.9308 (mmmm) cc_final: 0.9047 (mmpt) REVERT: G 11 ARG cc_start: 0.8229 (pmt170) cc_final: 0.7791 (ptp90) REVERT: G 19 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: G 21 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8849 (mtp-110) REVERT: G 93 ARG cc_start: 0.9237 (tpt-90) cc_final: 0.9018 (tpp80) REVERT: G 159 TYR cc_start: 0.7896 (t80) cc_final: 0.7539 (t80) REVERT: G 236 ASP cc_start: 0.8486 (p0) cc_final: 0.8234 (p0) REVERT: c 46 GLU cc_start: 0.7472 (pp20) cc_final: 0.6710 (pm20) REVERT: c 101 LEU cc_start: 0.8138 (pt) cc_final: 0.7926 (pt) REVERT: c 133 PHE cc_start: 0.7769 (m-80) cc_final: 0.7014 (m-80) REVERT: c 157 CYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8415 (t) REVERT: c 256 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8662 (p) REVERT: d 40 ASN cc_start: 0.9378 (t0) cc_final: 0.8961 (t0) REVERT: d 67 ASN cc_start: 0.9023 (m110) cc_final: 0.8623 (p0) REVERT: d 141 TYR cc_start: 0.7822 (p90) cc_final: 0.7421 (p90) REVERT: d 152 GLN cc_start: 0.8041 (mt0) cc_final: 0.7691 (mp10) REVERT: d 200 GLN cc_start: 0.8082 (mp10) cc_final: 0.7643 (tm-30) REVERT: d 218 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9069 (mm) REVERT: i 48 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.6923 (mp) REVERT: j 54 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6573 (pmm) REVERT: j 59 ASP cc_start: 0.8168 (t0) cc_final: 0.7785 (t0) outliers start: 89 outliers final: 49 residues processed: 407 average time/residue: 1.0507 time to fit residues: 486.1309 Evaluate side-chains 386 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 325 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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 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 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 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 61 LYS Chi-restraints excluded: chain E residue 161 ILE 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 21 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL 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 137 CYS Chi-restraints excluded: chain G residue 161 CYS 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 51 CYS Chi-restraints excluded: chain d residue 52 LEU 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 48 LEU 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 77 THR Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 84 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 20 GLN B 198 ASN C 85 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN c 283 GLN d 153 ASN i 31 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.092340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077370 restraints weight = 49385.573| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.52 r_work: 0.3204 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2728 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= 0.168 Angle : 0.635 13.271 24355 Z= 0.329 Chirality : 0.043 0.358 2881 Planarity : 0.005 0.064 3113 Dihedral : 4.250 19.789 2545 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 5.04 % Allowed : 26.00 % Favored : 68.96 % 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: -0.11 (0.18), residues: 2351 helix: 1.62 (0.18), residues: 908 sheet: -1.34 (0.22), residues: 526 loop : -0.94 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 160 HIS 0.006 0.001 HIS i 31 PHE 0.014 0.001 PHE d 94 TYR 0.031 0.001 TYR A 76 ARG 0.011 0.001 ARG j 57 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 925) hydrogen bonds : angle 4.99435 ( 2628) SS BOND : bond 0.00423 ( 1) SS BOND : angle 2.61776 ( 2) covalent geometry : bond 0.00391 (17893) covalent geometry : angle 0.63458 (24353) *********************** 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 430 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 343 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7729 (m-80) cc_final: 0.7207 (m-80) REVERT: A 7 SER cc_start: 0.8074 (m) cc_final: 0.7711 (p) REVERT: A 50 LYS cc_start: 0.7492 (tptp) cc_final: 0.6829 (tptp) REVERT: A 163 MET cc_start: 0.8896 (ptp) cc_final: 0.8616 (ptp) REVERT: A 177 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8358 (ptm-80) REVERT: A 203 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7745 (mtt) REVERT: B 17 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7681 (ptm160) REVERT: B 20 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: B 57 ASP cc_start: 0.7404 (t0) cc_final: 0.6988 (t0) REVERT: B 139 TRP cc_start: 0.8859 (t60) cc_final: 0.8350 (t60) REVERT: B 141 LYS cc_start: 0.9041 (tttm) cc_final: 0.8635 (ptmt) REVERT: B 151 ASP cc_start: 0.8191 (t0) cc_final: 0.7983 (t0) REVERT: C 166 LYS cc_start: 0.8760 (mptt) cc_final: 0.8326 (mppt) REVERT: C 205 ASN cc_start: 0.8823 (m110) cc_final: 0.8085 (p0) REVERT: D 53 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8333 (ptt180) REVERT: D 110 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8452 (tm-30) REVERT: D 122 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8745 (tm-30) REVERT: D 189 MET cc_start: 0.8936 (mtp) cc_final: 0.8552 (mtt) REVERT: E 61 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8581 (mmmt) REVERT: E 86 ASN cc_start: 0.9381 (m-40) cc_final: 0.9141 (m110) REVERT: E 226 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.7474 (t70) REVERT: F 206 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9030 (mmpt) REVERT: G 11 ARG cc_start: 0.8331 (pmt170) cc_final: 0.7891 (ptp90) REVERT: G 19 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8481 (mm-30) REVERT: G 21 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8780 (mtp-110) REVERT: G 93 ARG cc_start: 0.9246 (tpt-90) cc_final: 0.9018 (tpp80) REVERT: G 159 TYR cc_start: 0.7980 (t80) cc_final: 0.7658 (t80) REVERT: G 236 ASP cc_start: 0.8443 (p0) cc_final: 0.8197 (p0) REVERT: c 46 GLU cc_start: 0.7555 (pp20) cc_final: 0.6754 (pm20) REVERT: c 101 LEU cc_start: 0.8180 (pt) cc_final: 0.7966 (pt) REVERT: c 120 PHE cc_start: 0.7711 (p90) cc_final: 0.7049 (p90) REVERT: c 123 PHE cc_start: 0.7885 (m-80) cc_final: 0.7084 (m-80) REVERT: c 133 PHE cc_start: 0.7771 (m-80) cc_final: 0.7406 (m-80) REVERT: c 157 CYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8376 (t) REVERT: c 202 CYS cc_start: 0.8598 (p) cc_final: 0.8393 (p) REVERT: c 256 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8635 (p) REVERT: d 40 ASN cc_start: 0.9395 (t0) cc_final: 0.8976 (t0) REVERT: d 141 TYR cc_start: 0.7866 (p90) cc_final: 0.7517 (p90) REVERT: d 152 GLN cc_start: 0.8058 (mt0) cc_final: 0.7755 (mp10) REVERT: d 200 GLN cc_start: 0.8128 (mp10) cc_final: 0.7618 (tm-30) REVERT: d 218 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9088 (mm) REVERT: i 30 SER cc_start: 0.8396 (p) cc_final: 0.8191 (p) REVERT: i 31 HIS cc_start: 0.7950 (m90) cc_final: 0.7384 (m90) REVERT: j 54 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6672 (ptp) REVERT: j 59 ASP cc_start: 0.8239 (t0) cc_final: 0.7858 (t0) outliers start: 87 outliers final: 52 residues processed: 395 average time/residue: 1.0814 time to fit residues: 484.8457 Evaluate side-chains 389 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 20 GLN 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 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 122 GLN 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 61 LYS Chi-restraints excluded: chain E residue 161 ILE 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 21 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL 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 137 CYS Chi-restraints excluded: chain G residue 161 CYS 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 221 SER Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 285 ASN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 52 LEU 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 77 THR Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 180 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 232 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN B 198 ASN C 85 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 GLN d 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078302 restraints weight = 48990.223| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.52 r_work: 0.3206 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17894 Z= 0.138 Angle : 0.639 13.761 24355 Z= 0.328 Chirality : 0.043 0.359 2881 Planarity : 0.005 0.065 3113 Dihedral : 4.213 19.872 2545 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 5.10 % Allowed : 26.46 % Favored : 68.44 % 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: -0.03 (0.18), residues: 2351 helix: 1.64 (0.18), residues: 910 sheet: -1.24 (0.22), residues: 517 loop : -0.89 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 109 HIS 0.003 0.001 HIS F 121 PHE 0.012 0.001 PHE d 94 TYR 0.032 0.002 TYR A 76 ARG 0.012 0.000 ARG j 57 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 925) hydrogen bonds : angle 4.85867 ( 2628) SS BOND : bond 0.00408 ( 1) SS BOND : angle 2.46169 ( 2) covalent geometry : bond 0.00323 (17893) covalent geometry : angle 0.63904 (24353) *********************** REFINEMENT MACRO_CYCLE 7 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 434 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 346 time to evaluate : 1.936 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: A 6 TYR cc_start: 0.7837 (m-80) cc_final: 0.7303 (m-80) REVERT: A 7 SER cc_start: 0.8100 (m) cc_final: 0.7739 (p) REVERT: A 50 LYS cc_start: 0.7662 (tptp) cc_final: 0.6903 (tptp) REVERT: A 185 GLU cc_start: 0.8097 (mp0) cc_final: 0.7882 (pm20) REVERT: A 189 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7686 (m-70) REVERT: A 203 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7794 (mtt) REVERT: B 17 ARG cc_start: 0.8241 (mtm110) cc_final: 0.7885 (ptm160) REVERT: B 20 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: B 57 ASP cc_start: 0.7448 (t0) cc_final: 0.7063 (t0) REVERT: B 139 TRP cc_start: 0.8850 (t60) cc_final: 0.8373 (t60) REVERT: B 141 LYS cc_start: 0.9049 (tttm) cc_final: 0.8639 (ptmt) REVERT: B 151 ASP cc_start: 0.8201 (t0) cc_final: 0.7964 (t0) REVERT: C 166 LYS cc_start: 0.8732 (mptt) cc_final: 0.8307 (mppt) REVERT: C 205 ASN cc_start: 0.8830 (m110) cc_final: 0.8132 (p0) REVERT: D 29 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 110 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8440 (tm-30) REVERT: D 122 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8772 (tm-30) REVERT: D 133 MET cc_start: 0.8675 (tpp) cc_final: 0.8400 (tpp) REVERT: E 3 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.7633 (ptm-80) REVERT: E 19 ILE cc_start: 0.8977 (mp) cc_final: 0.8590 (mt) REVERT: E 61 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8583 (mmmt) REVERT: E 86 ASN cc_start: 0.9384 (m-40) cc_final: 0.9163 (m110) REVERT: E 91 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8417 (mp0) REVERT: E 226 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.7478 (t70) REVERT: F 182 MET cc_start: 0.9036 (pmm) cc_final: 0.8539 (pmm) REVERT: G 11 ARG cc_start: 0.8335 (pmt170) cc_final: 0.7990 (ptp90) REVERT: G 19 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: G 21 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8749 (mtp-110) REVERT: G 159 TYR cc_start: 0.7941 (t80) cc_final: 0.7537 (t80) REVERT: G 236 ASP cc_start: 0.8453 (p0) cc_final: 0.8204 (p0) REVERT: c 46 GLU cc_start: 0.7570 (pp20) cc_final: 0.6737 (pm20) REVERT: c 120 PHE cc_start: 0.7750 (p90) cc_final: 0.7089 (p90) REVERT: c 123 PHE cc_start: 0.7912 (m-80) cc_final: 0.7075 (m-80) REVERT: c 133 PHE cc_start: 0.7758 (m-80) cc_final: 0.7415 (m-80) REVERT: c 157 CYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8399 (t) REVERT: c 256 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8761 (p) REVERT: d 40 ASN cc_start: 0.9394 (t0) cc_final: 0.8936 (t0) REVERT: d 141 TYR cc_start: 0.7873 (p90) cc_final: 0.7519 (p90) REVERT: d 152 GLN cc_start: 0.8084 (mt0) cc_final: 0.7798 (mp10) REVERT: d 200 GLN cc_start: 0.8080 (mp10) cc_final: 0.7637 (tm-30) REVERT: d 218 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9078 (mm) REVERT: i 30 SER cc_start: 0.8473 (p) cc_final: 0.8269 (p) REVERT: i 31 HIS cc_start: 0.7942 (m90) cc_final: 0.7429 (m90) REVERT: j 54 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6606 (pmm) REVERT: j 59 ASP cc_start: 0.8232 (t0) cc_final: 0.7858 (t0) outliers start: 88 outliers final: 50 residues processed: 404 average time/residue: 1.0260 time to fit residues: 474.4019 Evaluate side-chains 386 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 51 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 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 122 GLN 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 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 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL 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 137 CYS Chi-restraints excluded: chain G residue 161 CYS 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 c residue 285 ASN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 52 LEU 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 74 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 54 MET Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 162 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN B 198 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 GLN d 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078873 restraints weight = 49157.739| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.53 r_work: 0.3234 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17894 Z= 0.135 Angle : 0.649 13.942 24355 Z= 0.333 Chirality : 0.043 0.369 2881 Planarity : 0.005 0.067 3113 Dihedral : 4.200 20.395 2545 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 4.34 % Allowed : 28.08 % Favored : 67.57 % 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: 0.01 (0.18), residues: 2351 helix: 1.65 (0.18), residues: 910 sheet: -1.24 (0.22), residues: 518 loop : -0.83 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 160 HIS 0.003 0.001 HIS F 121 PHE 0.019 0.001 PHE j 104 TYR 0.027 0.001 TYR A 76 ARG 0.014 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 925) hydrogen bonds : angle 4.80685 ( 2628) SS BOND : bond 0.00391 ( 1) SS BOND : angle 2.29793 ( 2) covalent geometry : bond 0.00322 (17893) covalent geometry : angle 0.64909 (24353) *********************** REFINEMENT MACRO_CYCLE 8 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 433 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 358 time to evaluate : 2.073 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: A 6 TYR cc_start: 0.7894 (m-80) cc_final: 0.7363 (m-80) REVERT: A 7 SER cc_start: 0.8127 (m) cc_final: 0.7762 (p) REVERT: A 50 LYS cc_start: 0.7672 (tptp) cc_final: 0.6982 (tptp) REVERT: A 185 GLU cc_start: 0.8075 (mp0) cc_final: 0.7785 (pm20) REVERT: A 189 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.7686 (m-70) REVERT: A 203 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7954 (mtt) REVERT: B 9 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7843 (m) REVERT: B 17 ARG cc_start: 0.8251 (mtm110) cc_final: 0.8039 (ptm-80) REVERT: B 20 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: B 57 ASP cc_start: 0.7425 (t0) cc_final: 0.7031 (t0) REVERT: B 92 LEU cc_start: 0.8989 (mm) cc_final: 0.8769 (tt) REVERT: B 139 TRP cc_start: 0.8836 (t60) cc_final: 0.8367 (t60) REVERT: B 141 LYS cc_start: 0.9049 (tttm) cc_final: 0.8636 (ptmt) REVERT: B 151 ASP cc_start: 0.8291 (t0) cc_final: 0.8013 (t0) REVERT: C 166 LYS cc_start: 0.8721 (mptt) cc_final: 0.8293 (mppt) REVERT: C 205 ASN cc_start: 0.8822 (m110) cc_final: 0.8117 (p0) REVERT: D 29 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8452 (mm-30) REVERT: D 122 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: E 19 ILE cc_start: 0.8984 (mp) cc_final: 0.8605 (mt) REVERT: E 49 LEU cc_start: 0.9265 (tp) cc_final: 0.9032 (tm) REVERT: E 61 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8584 (mmmt) REVERT: E 86 ASN cc_start: 0.9377 (m-40) cc_final: 0.9164 (m110) REVERT: E 91 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8374 (mp0) REVERT: E 226 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.7519 (t70) REVERT: F 182 MET cc_start: 0.9018 (pmm) cc_final: 0.8556 (pmm) REVERT: G 11 ARG cc_start: 0.8371 (pmt170) cc_final: 0.8069 (pmt170) REVERT: G 19 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: G 21 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8839 (mtp-110) REVERT: G 159 TYR cc_start: 0.7911 (t80) cc_final: 0.7556 (t80) REVERT: G 236 ASP cc_start: 0.8452 (p0) cc_final: 0.8206 (p0) REVERT: c 46 GLU cc_start: 0.7589 (pp20) cc_final: 0.6774 (pm20) REVERT: c 120 PHE cc_start: 0.7697 (p90) cc_final: 0.7046 (p90) REVERT: c 123 PHE cc_start: 0.7958 (m-80) cc_final: 0.7123 (m-80) REVERT: c 133 PHE cc_start: 0.7739 (m-80) cc_final: 0.7429 (m-80) REVERT: c 157 CYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8430 (t) REVERT: c 251 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8201 (tmmt) REVERT: c 256 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8800 (p) REVERT: d 40 ASN cc_start: 0.9372 (t0) cc_final: 0.8940 (t0) REVERT: d 141 TYR cc_start: 0.7868 (p90) cc_final: 0.7550 (p90) REVERT: d 152 GLN cc_start: 0.8103 (mt0) cc_final: 0.7822 (mp10) REVERT: d 200 GLN cc_start: 0.8125 (mp10) cc_final: 0.7645 (tm-30) REVERT: d 218 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9072 (mm) REVERT: i 31 HIS cc_start: 0.7932 (m90) cc_final: 0.7365 (m90) REVERT: i 87 SER cc_start: 0.8060 (t) cc_final: 0.7440 (p) REVERT: j 54 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6604 (pmm) REVERT: j 59 ASP cc_start: 0.8271 (t0) cc_final: 0.7903 (t0) outliers start: 75 outliers final: 46 residues processed: 408 average time/residue: 1.0931 time to fit residues: 507.2406 Evaluate side-chains 392 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 333 time to evaluate : 1.909 ------------------------------------------------------------------------------- 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 203 MET Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 51 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 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 122 GLN 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 61 LYS Chi-restraints excluded: chain E residue 161 ILE 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 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL 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 161 CYS 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 c residue 285 ASN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 67 ASN 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 74 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 54 MET Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 GLN d 153 ASN j 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078548 restraints weight = 49298.938| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.53 r_work: 0.3230 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17894 Z= 0.145 Angle : 0.679 14.298 24355 Z= 0.346 Chirality : 0.044 0.370 2881 Planarity : 0.005 0.068 3113 Dihedral : 4.234 20.759 2545 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 4.23 % Allowed : 28.78 % Favored : 66.99 % 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: 0.00 (0.18), residues: 2351 helix: 1.65 (0.18), residues: 903 sheet: -1.21 (0.22), residues: 524 loop : -0.84 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP d 160 HIS 0.003 0.001 HIS E 65 PHE 0.013 0.001 PHE d 94 TYR 0.027 0.002 TYR A 76 ARG 0.012 0.000 ARG j 57 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 925) hydrogen bonds : angle 4.79385 ( 2628) SS BOND : bond 0.00316 ( 1) SS BOND : angle 2.20877 ( 2) covalent geometry : bond 0.00344 (17893) covalent geometry : angle 0.67909 (24353) *********************** REFINEMENT MACRO_CYCLE 9 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 416 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 2.137 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: A 6 TYR cc_start: 0.7965 (m-80) cc_final: 0.7368 (m-80) REVERT: A 7 SER cc_start: 0.8142 (m) cc_final: 0.7778 (p) REVERT: A 50 LYS cc_start: 0.7676 (tptp) cc_final: 0.7065 (tptp) REVERT: A 185 GLU cc_start: 0.8049 (mp0) cc_final: 0.7756 (pm20) REVERT: A 189 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7735 (m-70) REVERT: B 9 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7885 (m) REVERT: B 17 ARG cc_start: 0.8293 (mtm110) cc_final: 0.8039 (ptm-80) REVERT: B 20 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: B 57 ASP cc_start: 0.7474 (t0) cc_final: 0.7068 (t0) REVERT: B 92 LEU cc_start: 0.9010 (mm) cc_final: 0.8799 (tt) REVERT: B 139 TRP cc_start: 0.8835 (t60) cc_final: 0.8400 (t60) REVERT: B 141 LYS cc_start: 0.9061 (tttm) cc_final: 0.8643 (ptmt) REVERT: B 151 ASP cc_start: 0.8292 (t0) cc_final: 0.8031 (t0) REVERT: C 166 LYS cc_start: 0.8729 (mptt) cc_final: 0.8302 (mppt) REVERT: C 205 ASN cc_start: 0.8795 (m110) cc_final: 0.8090 (p0) REVERT: D 29 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8464 (mm-30) REVERT: D 122 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: D 203 LYS cc_start: 0.9292 (ttmm) cc_final: 0.8942 (tppp) REVERT: E 19 ILE cc_start: 0.8997 (mp) cc_final: 0.8623 (mt) REVERT: E 49 LEU cc_start: 0.9270 (tp) cc_final: 0.9025 (tm) REVERT: E 61 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8574 (mmmt) REVERT: E 86 ASN cc_start: 0.9388 (m-40) cc_final: 0.9187 (m110) REVERT: E 91 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8310 (mp0) REVERT: E 197 GLU cc_start: 0.8952 (tt0) cc_final: 0.8482 (tt0) REVERT: E 226 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.7465 (t70) REVERT: F 182 MET cc_start: 0.9007 (pmm) cc_final: 0.8525 (pmm) REVERT: G 11 ARG cc_start: 0.8387 (pmt170) cc_final: 0.8094 (pmt170) REVERT: G 19 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8556 (mm-30) REVERT: G 21 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8778 (mtp-110) REVERT: G 159 TYR cc_start: 0.7960 (t80) cc_final: 0.7549 (t80) REVERT: G 236 ASP cc_start: 0.8455 (p0) cc_final: 0.8212 (p0) REVERT: c 46 GLU cc_start: 0.7606 (pp20) cc_final: 0.6785 (pm20) REVERT: c 120 PHE cc_start: 0.7683 (p90) cc_final: 0.7021 (p90) REVERT: c 133 PHE cc_start: 0.7729 (m-80) cc_final: 0.7456 (m-80) REVERT: c 157 CYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8459 (t) REVERT: c 251 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8173 (tmmt) REVERT: c 256 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8772 (p) REVERT: d 40 ASN cc_start: 0.9371 (t0) cc_final: 0.8946 (t0) REVERT: d 141 TYR cc_start: 0.7845 (p90) cc_final: 0.7559 (p90) REVERT: d 152 GLN cc_start: 0.8103 (mt0) cc_final: 0.7833 (mp10) REVERT: d 200 GLN cc_start: 0.8136 (mp10) cc_final: 0.7645 (tm-30) REVERT: d 218 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9074 (mm) REVERT: i 31 HIS cc_start: 0.7874 (m90) cc_final: 0.7344 (m90) REVERT: i 87 SER cc_start: 0.8094 (t) cc_final: 0.7460 (p) REVERT: j 54 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6639 (pmm) REVERT: j 59 ASP cc_start: 0.8300 (t0) cc_final: 0.7914 (t0) outliers start: 73 outliers final: 47 residues processed: 390 average time/residue: 1.0830 time to fit residues: 479.8257 Evaluate side-chains 386 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 327 time to evaluate : 1.960 ------------------------------------------------------------------------------- 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 B residue 9 THR Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 51 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 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 122 GLN 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 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 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL 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 161 CYS 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 285 ASN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 67 ASN 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 74 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 54 MET Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 179 optimal weight: 0.0050 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 176 optimal weight: 0.0030 chunk 145 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 209 optimal weight: 0.0470 chunk 74 optimal weight: 0.4980 chunk 232 optimal weight: 0.8980 overall best weight: 0.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN B 198 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080256 restraints weight = 49194.234| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.58 r_work: 0.3248 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17894 Z= 0.129 Angle : 0.694 14.379 24355 Z= 0.351 Chirality : 0.043 0.366 2881 Planarity : 0.005 0.069 3113 Dihedral : 4.173 20.810 2545 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 3.07 % Allowed : 29.99 % Favored : 66.94 % 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: 0.02 (0.18), residues: 2351 helix: 1.69 (0.18), residues: 904 sheet: -1.17 (0.22), residues: 512 loop : -0.89 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP d 160 HIS 0.003 0.000 HIS F 121 PHE 0.021 0.001 PHE E 179 TYR 0.026 0.001 TYR d 191 ARG 0.018 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 925) hydrogen bonds : angle 4.69103 ( 2628) SS BOND : bond 0.00404 ( 1) SS BOND : angle 3.92463 ( 2) covalent geometry : bond 0.00304 (17893) covalent geometry : angle 0.69361 (24353) ********************** REFINEMENT MACRO_CYCLE 10 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: 53 poor density : 377 time to evaluate : 2.006 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: A 6 TYR cc_start: 0.7976 (m-80) cc_final: 0.7453 (m-80) REVERT: A 7 SER cc_start: 0.8151 (m) cc_final: 0.7779 (p) REVERT: A 50 LYS cc_start: 0.7831 (tptp) cc_final: 0.7204 (tptp) REVERT: A 51 LYS cc_start: 0.7143 (tmtt) cc_final: 0.6763 (tmtt) REVERT: A 53 LYS cc_start: 0.7112 (mppt) cc_final: 0.6857 (tppp) REVERT: A 120 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8906 (tm-30) REVERT: A 185 GLU cc_start: 0.8041 (mp0) cc_final: 0.7747 (pm20) REVERT: B 9 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7935 (m) REVERT: B 20 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: B 57 ASP cc_start: 0.7472 (t0) cc_final: 0.7078 (t0) REVERT: B 92 LEU cc_start: 0.9046 (mm) cc_final: 0.8841 (tt) REVERT: B 139 TRP cc_start: 0.8808 (t60) cc_final: 0.8376 (t60) REVERT: B 141 LYS cc_start: 0.9110 (tttm) cc_final: 0.8683 (ptmt) REVERT: B 151 ASP cc_start: 0.8294 (t0) cc_final: 0.8031 (t0) REVERT: C 166 LYS cc_start: 0.8724 (mptt) cc_final: 0.8343 (mppt) REVERT: C 205 ASN cc_start: 0.8747 (m110) cc_final: 0.8014 (p0) REVERT: D 29 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8435 (mm-30) REVERT: D 122 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8677 (OUTLIER) REVERT: D 133 MET cc_start: 0.8855 (tpp) cc_final: 0.8631 (tpt) REVERT: D 189 MET cc_start: 0.8925 (mtp) cc_final: 0.8506 (mtt) REVERT: D 203 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8968 (tppp) REVERT: E 19 ILE cc_start: 0.8904 (mp) cc_final: 0.8431 (mt) REVERT: E 49 LEU cc_start: 0.9285 (tp) cc_final: 0.9073 (tm) REVERT: E 61 LYS cc_start: 0.8984 (mttt) cc_final: 0.8612 (mmmt) REVERT: E 179 PHE cc_start: 0.8333 (m-10) cc_final: 0.7890 (m-10) REVERT: E 197 GLU cc_start: 0.8919 (tt0) cc_final: 0.8449 (tt0) REVERT: F 182 MET cc_start: 0.9012 (pmm) cc_final: 0.8578 (pmm) REVERT: F 206 LYS cc_start: 0.9283 (mmmm) cc_final: 0.9066 (mmpt) REVERT: G 11 ARG cc_start: 0.8385 (pmt170) cc_final: 0.7945 (pmt170) REVERT: G 19 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8578 (mm-30) REVERT: G 21 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8788 (mtp-110) REVERT: G 159 TYR cc_start: 0.7967 (t80) cc_final: 0.7456 (t80) REVERT: G 236 ASP cc_start: 0.8435 (p0) cc_final: 0.8197 (p0) REVERT: c 46 GLU cc_start: 0.7553 (pp20) cc_final: 0.6759 (pm20) REVERT: c 120 PHE cc_start: 0.7701 (p90) cc_final: 0.7097 (p90) REVERT: c 133 PHE cc_start: 0.7714 (m-80) cc_final: 0.7498 (m-80) REVERT: c 157 CYS cc_start: 0.8653 (m) cc_final: 0.8422 (t) REVERT: c 162 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8192 (ptp) REVERT: c 256 THR cc_start: 0.9327 (t) cc_final: 0.9056 (p) REVERT: c 277 MET cc_start: 0.7909 (mpm) cc_final: 0.7448 (mtm) REVERT: d 40 ASN cc_start: 0.9319 (t0) cc_final: 0.8919 (OUTLIER) REVERT: d 141 TYR cc_start: 0.7805 (p90) cc_final: 0.7511 (p90) REVERT: d 152 GLN cc_start: 0.8144 (mt0) cc_final: 0.7885 (mp10) REVERT: d 200 GLN cc_start: 0.8052 (mp10) cc_final: 0.7562 (tm-30) REVERT: d 218 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9088 (mm) REVERT: i 13 THR cc_start: 0.8804 (t) cc_final: 0.8529 (m) REVERT: i 31 HIS cc_start: 0.7751 (m90) cc_final: 0.7239 (m90) REVERT: i 87 SER cc_start: 0.8220 (t) cc_final: 0.7615 (p) REVERT: j 59 ASP cc_start: 0.8324 (t0) cc_final: 0.7943 (t0) REVERT: j 102 SER cc_start: 0.8199 (p) cc_final: 0.7900 (t) outliers start: 53 outliers final: 33 residues processed: 415 average time/residue: 1.0188 time to fit residues: 482.3831 Evaluate side-chains 380 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 342 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 195 LEU 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 122 GLN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 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 c residue 96 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS 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 74 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 183 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN B 198 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN d 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079111 restraints weight = 49350.694| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.54 r_work: 0.3238 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17894 Z= 0.153 Angle : 0.717 14.363 24355 Z= 0.363 Chirality : 0.044 0.367 2881 Planarity : 0.005 0.071 3113 Dihedral : 4.206 21.662 2545 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 3.07 % Allowed : 31.21 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.18), residues: 2351 helix: 1.62 (0.18), residues: 904 sheet: -1.13 (0.22), residues: 523 loop : -0.84 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP d 160 HIS 0.003 0.001 HIS E 65 PHE 0.021 0.001 PHE E 179 TYR 0.025 0.002 TYR A 76 ARG 0.016 0.001 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 925) hydrogen bonds : angle 4.78756 ( 2628) SS BOND : bond 0.00443 ( 1) SS BOND : angle 3.80621 ( 2) covalent geometry : bond 0.00365 (17893) covalent geometry : angle 0.71582 (24353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12046.71 seconds wall clock time: 208 minutes 26.92 seconds (12506.92 seconds total)