Starting phenix.real_space_refine on Mon Nov 18 22:12:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm3_41377/11_2024/8tm3_41377.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm3_41377/11_2024/8tm3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm3_41377/11_2024/8tm3_41377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm3_41377/11_2024/8tm3_41377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm3_41377/11_2024/8tm3_41377.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm3_41377/11_2024/8tm3_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-5513/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: 10.89, per 1000 atoms: 0.62 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: 5.09 Conformation dependent library (CDL) restraints added in 2.4 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: 1.70 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: 5.43 Time building geometry restraints manager: 5.77 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.850 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.220 ------------------------------------------------------------------------------- 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 17893 Z= 0.188 Angle : 0.559 14.928 24353 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 *********************** 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 : 2.179 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: 1.2151 time to fit residues: 563.2279 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 : 2.061 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 17893 Z= 0.218 Angle : 0.600 10.394 24353 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 *********************** 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 : 2.270 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: 0.7910 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: A 189 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7302 (m170) REVERT: B 17 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7231 (ptm160) REVERT: B 57 ASP cc_start: 0.7008 (t0) cc_final: 0.6745 (t0) REVERT: B 139 TRP cc_start: 0.8661 (t60) cc_final: 0.8317 (t60) REVERT: C 166 LYS cc_start: 0.8511 (mptt) cc_final: 0.8175 (mppt) REVERT: C 205 ASN cc_start: 0.8477 (m110) cc_final: 0.8045 (p0) REVERT: D 110 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8003 (tm-30) REVERT: E 82 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8468 (ttt-90) REVERT: E 86 ASN cc_start: 0.9156 (m-40) cc_final: 0.8836 (m110) REVERT: E 125 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8021 (mmm-85) REVERT: E 226 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7055 (t70) REVERT: F 153 ASP cc_start: 0.8305 (t0) cc_final: 0.8020 (t0) REVERT: G 21 ARG cc_start: 0.8870 (ptm160) cc_final: 0.8536 (mtp-110) REVERT: G 159 TYR cc_start: 0.7303 (t80) cc_final: 0.6967 (t80) REVERT: c 133 PHE cc_start: 0.7651 (m-80) cc_final: 0.6901 (m-80) REVERT: c 163 GLN cc_start: 0.8377 (mp10) cc_final: 0.7510 (mp10) REVERT: c 198 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7101 (tmmt) REVERT: c 248 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7736 (tt0) REVERT: c 277 MET cc_start: 0.8366 (mpt) cc_final: 0.8117 (mpt) REVERT: d 40 ASN cc_start: 0.9208 (t0) cc_final: 0.8688 (t0) REVERT: d 152 GLN cc_start: 0.7698 (mt0) cc_final: 0.7060 (mp-120) REVERT: d 193 GLU cc_start: 0.8438 (tp30) cc_final: 0.8089 (mm-30) REVERT: d 200 GLN cc_start: 0.7771 (mp10) cc_final: 0.7520 (tm-30) REVERT: j 66 SER cc_start: 0.9286 (p) cc_final: 0.9044 (p) outliers start: 63 outliers final: 22 residues processed: 421 average time/residue: 1.2020 time to fit residues: 571.9773 Evaluate side-chains 359 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 332 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 82 ARG 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 176 optimal weight: 0.0030 chunk 144 optimal weight: 0.0170 chunk 58 optimal weight: 0.0570 chunk 212 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.3948 ------------------------------------------------------------------------------- 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** D 118 ASN E 5 GLN E 65 HIS E 152 ASN c 283 GLN d 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17893 Z= 0.179 Angle : 0.593 11.204 24353 Z= 0.307 Chirality : 0.042 0.315 2881 Planarity : 0.005 0.061 3113 Dihedral : 4.060 19.173 2545 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 3.76 % Allowed : 23.80 % Favored : 72.44 % 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: -0.05 (0.18), residues: 2351 helix: 1.82 (0.18), residues: 905 sheet: -1.44 (0.22), residues: 517 loop : -0.99 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 160 HIS 0.003 0.001 HIS F 121 PHE 0.010 0.001 PHE d 102 TYR 0.014 0.001 TYR c 222 ARG 0.009 0.001 ARG j 57 *********************** 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 447 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 382 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7319 (m-80) cc_final: 0.6987 (m-80) REVERT: A 49 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 50 LYS cc_start: 0.7340 (tptp) cc_final: 0.6808 (tptp) REVERT: A 92 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8597 (mmmm) REVERT: A 189 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7317 (m170) REVERT: B 17 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7337 (ptm160) REVERT: B 139 TRP cc_start: 0.8689 (t60) cc_final: 0.8336 (t60) REVERT: B 151 ASP cc_start: 0.7559 (t0) cc_final: 0.7045 (t70) REVERT: C 166 LYS cc_start: 0.8478 (mptt) cc_final: 0.8123 (mppt) REVERT: C 205 ASN cc_start: 0.8366 (m110) cc_final: 0.7985 (p0) REVERT: D 29 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8117 (mm-30) REVERT: D 110 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7875 (tm-30) REVERT: D 118 ASN cc_start: 0.8246 (m-40) cc_final: 0.8043 (m110) REVERT: E 19 ILE cc_start: 0.8894 (mp) cc_final: 0.8502 (mt) REVERT: E 82 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8492 (ttt-90) REVERT: E 86 ASN cc_start: 0.9141 (m-40) cc_final: 0.8862 (m110) REVERT: E 91 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7891 (mp0) REVERT: E 125 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: F 153 ASP cc_start: 0.8143 (t0) cc_final: 0.7760 (t0) REVERT: G 21 ARG cc_start: 0.8828 (ptm160) cc_final: 0.8445 (mtp-110) REVERT: G 236 ASP cc_start: 0.8327 (p0) cc_final: 0.8120 (p0) REVERT: c 133 PHE cc_start: 0.7649 (m-80) cc_final: 0.6886 (m-80) REVERT: c 163 GLN cc_start: 0.8191 (mp10) cc_final: 0.7356 (mp10) REVERT: c 198 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7075 (tmmt) REVERT: c 251 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8318 (tmmt) REVERT: d 40 ASN cc_start: 0.9240 (t0) cc_final: 0.8733 (t0) REVERT: d 141 TYR cc_start: 0.7669 (p90) cc_final: 0.7444 (p90) REVERT: d 152 GLN cc_start: 0.7730 (mt0) cc_final: 0.7135 (mp-120) REVERT: d 193 GLU cc_start: 0.8419 (tp30) cc_final: 0.8068 (mm-30) REVERT: d 200 GLN cc_start: 0.7723 (mp10) cc_final: 0.7506 (tm-30) REVERT: i 31 HIS cc_start: 0.7696 (m90) cc_final: 0.7451 (m90) REVERT: j 116 MET cc_start: 0.8807 (mtm) cc_final: 0.8573 (mtm) outliers start: 65 outliers final: 30 residues processed: 424 average time/residue: 1.2094 time to fit residues: 579.7732 Evaluate side-chains 358 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain C residue 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 82 ARG Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 21 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 66 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 256 THR 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 189 THR Chi-restraints excluded: chain i residue 74 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain j residue 52 VAL 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 210 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 C 85 ASN D 118 ASN D 204 GLN E 5 GLN E 90 GLN c 283 GLN d 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17893 Z= 0.321 Angle : 0.652 12.974 24353 Z= 0.340 Chirality : 0.044 0.340 2881 Planarity : 0.005 0.065 3113 Dihedral : 4.293 19.678 2545 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 5.39 % Allowed : 23.45 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2351 helix: 1.62 (0.17), residues: 904 sheet: -1.43 (0.22), residues: 519 loop : -0.96 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 160 HIS 0.003 0.001 HIS F 121 PHE 0.018 0.002 PHE j 92 TYR 0.018 0.002 TYR F 123 ARG 0.011 0.001 ARG j 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 337 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7729 (m-80) cc_final: 0.7178 (m-80) REVERT: A 49 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: A 50 LYS cc_start: 0.7438 (tptp) cc_final: 0.6897 (tptp) REVERT: A 92 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8668 (mmmm) REVERT: A 185 GLU cc_start: 0.7654 (mp0) cc_final: 0.7360 (pm20) REVERT: B 9 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7513 (m) REVERT: B 17 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7566 (ptm160) REVERT: B 57 ASP cc_start: 0.7384 (t0) cc_final: 0.6972 (t0) REVERT: B 139 TRP cc_start: 0.8696 (t60) cc_final: 0.8361 (t60) REVERT: C 166 LYS cc_start: 0.8611 (mptt) cc_final: 0.8293 (mppt) REVERT: C 205 ASN cc_start: 0.8518 (m110) cc_final: 0.8055 (p0) REVERT: D 53 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8275 (ptt180) REVERT: D 110 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 118 ASN cc_start: 0.8400 (m110) cc_final: 0.8121 (m110) REVERT: E 19 ILE cc_start: 0.9092 (mp) cc_final: 0.8756 (mt) REVERT: E 82 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8437 (ttt-90) REVERT: E 86 ASN cc_start: 0.9158 (m-40) cc_final: 0.8826 (m110) REVERT: E 91 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8048 (mp0) REVERT: E 226 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7291 (t70) REVERT: G 11 ARG cc_start: 0.7887 (ptp90) cc_final: 0.7645 (ptp90) REVERT: G 19 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: G 21 ARG cc_start: 0.8841 (ptm160) cc_final: 0.8539 (mtp-110) REVERT: G 159 TYR cc_start: 0.7714 (t80) cc_final: 0.7413 (t80) REVERT: G 236 ASP cc_start: 0.8387 (p0) cc_final: 0.8180 (p0) REVERT: c 46 GLU cc_start: 0.7597 (pp20) cc_final: 0.6851 (pm20) REVERT: c 133 PHE cc_start: 0.7710 (m-80) cc_final: 0.6936 (m-80) REVERT: c 163 GLN cc_start: 0.8379 (mp10) cc_final: 0.8170 (mp10) REVERT: c 198 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7149 (tmmt) REVERT: c 256 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8625 (p) REVERT: c 277 MET cc_start: 0.8499 (mpt) cc_final: 0.8287 (mpt) REVERT: d 152 GLN cc_start: 0.7824 (mt0) cc_final: 0.7576 (mp10) REVERT: d 200 GLN cc_start: 0.7860 (mp10) cc_final: 0.7622 (tm-30) REVERT: j 59 ASP cc_start: 0.7357 (t0) cc_final: 0.7120 (t0) outliers start: 93 outliers final: 38 residues processed: 401 average time/residue: 1.1855 time to fit residues: 537.6583 Evaluate side-chains 368 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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 B residue 9 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG 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 82 ARG 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 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 13 ILE Chi-restraints excluded: chain G residue 15 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 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 169 CYS Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 74 LEU Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 186 HIS ** c 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 153 ASN i 31 HIS i 92 ASN j 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17893 Z= 0.366 Angle : 0.687 13.395 24353 Z= 0.359 Chirality : 0.045 0.349 2881 Planarity : 0.005 0.069 3113 Dihedral : 4.513 20.796 2545 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 6.37 % Allowed : 24.20 % Favored : 69.43 % 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: -0.29 (0.18), residues: 2351 helix: 1.49 (0.17), residues: 898 sheet: -1.41 (0.22), residues: 521 loop : -1.07 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP d 109 HIS 0.003 0.001 HIS E 190 PHE 0.018 0.002 PHE j 104 TYR 0.025 0.002 TYR A 167 ARG 0.009 0.001 ARG E 51 *********************** 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 446 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 336 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7782 (m-80) cc_final: 0.7374 (m-80) REVERT: A 50 LYS cc_start: 0.7663 (tptp) cc_final: 0.6987 (tptp) REVERT: A 189 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7392 (m-70) REVERT: B 17 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7704 (ptm160) REVERT: B 57 ASP cc_start: 0.7574 (t0) cc_final: 0.7199 (t0) REVERT: B 139 TRP cc_start: 0.8695 (t60) cc_final: 0.8340 (t60) REVERT: C 166 LYS cc_start: 0.8653 (mptt) cc_final: 0.8387 (mppt) REVERT: C 205 ASN cc_start: 0.8682 (m110) cc_final: 0.8188 (p0) REVERT: D 20 ARG cc_start: 0.8774 (mtp180) cc_final: 0.8415 (mmm-85) REVERT: D 110 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 118 ASN cc_start: 0.8401 (m110) cc_final: 0.8030 (m110) REVERT: E 86 ASN cc_start: 0.9153 (m-40) cc_final: 0.8927 (m-40) REVERT: E 226 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7388 (t70) REVERT: F 28 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7857 (mmm) REVERT: G 11 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7624 (ptp90) REVERT: G 19 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: G 21 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8476 (mtp-110) REVERT: G 70 PHE cc_start: 0.8321 (m-80) cc_final: 0.8114 (m-80) REVERT: G 159 TYR cc_start: 0.7770 (t80) cc_final: 0.7488 (t80) REVERT: c 46 GLU cc_start: 0.7794 (pp20) cc_final: 0.7056 (pm20) REVERT: c 120 PHE cc_start: 0.7827 (p90) cc_final: 0.7295 (p90) REVERT: c 133 PHE cc_start: 0.7737 (m-80) cc_final: 0.7387 (m-80) REVERT: c 163 GLN cc_start: 0.8385 (mp10) cc_final: 0.8167 (mp10) REVERT: c 256 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8720 (p) REVERT: c 277 MET cc_start: 0.8509 (mpt) cc_final: 0.8299 (mpt) REVERT: c 283 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: d 40 ASN cc_start: 0.9343 (t0) cc_final: 0.8853 (t0) REVERT: d 96 LYS cc_start: 0.9309 (tttm) cc_final: 0.8851 (tttp) REVERT: d 141 TYR cc_start: 0.7905 (p90) cc_final: 0.7652 (p90) REVERT: d 152 GLN cc_start: 0.7877 (mt0) cc_final: 0.7658 (mp10) REVERT: d 200 GLN cc_start: 0.7968 (mp10) cc_final: 0.7573 (tm-30) REVERT: d 218 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9137 (mm) REVERT: i 48 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7024 (mp) REVERT: j 54 MET cc_start: 0.8765 (ptp) cc_final: 0.8449 (ptt) REVERT: j 59 ASP cc_start: 0.7426 (t0) cc_final: 0.7120 (t0) REVERT: j 113 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (ttmm) outliers start: 110 outliers final: 58 residues processed: 406 average time/residue: 1.1678 time to fit residues: 537.4541 Evaluate side-chains 376 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 76 LEU 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 191 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 182 CYS 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 28 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 161 CYS Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL 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 53 VAL Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 218 LEU Chi-restraints excluded: chain i residue 35 VAL 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 92 ASN Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 86 LYS Chi-restraints excluded: chain j residue 113 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN G 12 HIS c 283 GLN d 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17893 Z= 0.222 Angle : 0.652 13.537 24353 Z= 0.337 Chirality : 0.044 0.364 2881 Planarity : 0.005 0.069 3113 Dihedral : 4.392 20.316 2545 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 4.57 % Allowed : 26.81 % Favored : 68.62 % 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: -0.18 (0.18), residues: 2351 helix: 1.63 (0.18), residues: 895 sheet: -1.33 (0.22), residues: 523 loop : -1.04 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 160 HIS 0.004 0.001 HIS F 121 PHE 0.014 0.001 PHE d 94 TYR 0.020 0.002 TYR A 167 ARG 0.012 0.001 ARG j 57 *********************** 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 431 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 352 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7832 (m-80) cc_final: 0.7403 (m-80) REVERT: A 50 LYS cc_start: 0.7647 (tptp) cc_final: 0.6891 (tptp) REVERT: A 185 GLU cc_start: 0.7547 (mp0) cc_final: 0.7293 (pm20) REVERT: A 189 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7282 (m-70) REVERT: A 203 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7837 (mtt) REVERT: B 17 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7768 (ptm160) REVERT: B 57 ASP cc_start: 0.7519 (t0) cc_final: 0.7162 (t0) REVERT: B 139 TRP cc_start: 0.8667 (t60) cc_final: 0.8171 (t60) REVERT: C 85 ASN cc_start: 0.8774 (m-40) cc_final: 0.8509 (m110) REVERT: C 120 GLN cc_start: 0.8264 (tt0) cc_final: 0.8015 (tt0) REVERT: C 166 LYS cc_start: 0.8581 (mptt) cc_final: 0.8228 (mppt) REVERT: C 205 ASN cc_start: 0.8658 (m110) cc_final: 0.8194 (p0) REVERT: D 20 ARG cc_start: 0.8763 (mtp180) cc_final: 0.8413 (mmm-85) REVERT: D 53 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8324 (ptt180) REVERT: D 118 ASN cc_start: 0.8490 (m110) cc_final: 0.8152 (m110) REVERT: E 19 ILE cc_start: 0.8969 (mp) cc_final: 0.8617 (mt) REVERT: E 27 GLU cc_start: 0.8764 (tp30) cc_final: 0.8414 (mm-30) REVERT: E 61 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8516 (mmmt) REVERT: G 11 ARG cc_start: 0.7979 (ptp90) cc_final: 0.7598 (ptp90) REVERT: G 19 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: G 21 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8500 (mtp-110) REVERT: G 159 TYR cc_start: 0.7648 (t80) cc_final: 0.7300 (t80) REVERT: c 46 GLU cc_start: 0.7793 (pp20) cc_final: 0.7028 (pm20) REVERT: c 120 PHE cc_start: 0.7877 (p90) cc_final: 0.7233 (p90) REVERT: c 123 PHE cc_start: 0.7986 (m-80) cc_final: 0.7134 (m-80) REVERT: c 133 PHE cc_start: 0.7708 (m-80) cc_final: 0.7407 (m-80) REVERT: c 163 GLN cc_start: 0.8288 (mp10) cc_final: 0.8049 (mp10) REVERT: c 256 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8824 (p) REVERT: d 40 ASN cc_start: 0.9323 (t0) cc_final: 0.8844 (t0) REVERT: d 97 TYR cc_start: 0.8245 (m-80) cc_final: 0.7915 (m-10) REVERT: d 141 TYR cc_start: 0.7851 (p90) cc_final: 0.7615 (p90) REVERT: d 200 GLN cc_start: 0.7891 (mp10) cc_final: 0.7685 (tm-30) REVERT: j 59 ASP cc_start: 0.7482 (t0) cc_final: 0.7209 (t0) REVERT: j 102 SER cc_start: 0.7615 (p) cc_final: 0.7216 (t) REVERT: j 113 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8441 (ttmm) outliers start: 79 outliers final: 46 residues processed: 402 average time/residue: 1.1533 time to fit residues: 527.8258 Evaluate side-chains 369 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 51 ASN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 224 VAL 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 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 182 CYS 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 110 LYS Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL 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 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 33 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 j residue 52 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 0.0040 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN E 86 ASN c 283 GLN d 153 ASN i 31 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17893 Z= 0.206 Angle : 0.662 13.569 24353 Z= 0.340 Chirality : 0.044 0.365 2881 Planarity : 0.005 0.067 3113 Dihedral : 4.325 19.985 2545 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 4.98 % Allowed : 27.62 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.18), residues: 2351 helix: 1.59 (0.18), residues: 903 sheet: -1.29 (0.22), residues: 525 loop : -0.97 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 160 HIS 0.005 0.001 HIS i 31 PHE 0.012 0.001 PHE d 94 TYR 0.020 0.001 TYR A 167 ARG 0.013 0.001 ARG E 51 *********************** 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 432 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 346 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7891 (m-80) cc_final: 0.7578 (m-80) REVERT: A 50 LYS cc_start: 0.7630 (tptp) cc_final: 0.6936 (tptp) REVERT: A 51 LYS cc_start: 0.7016 (tmtt) cc_final: 0.6732 (tmtt) REVERT: A 53 LYS cc_start: 0.7062 (mppt) cc_final: 0.6691 (tptp) REVERT: A 120 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8865 (tm-30) REVERT: A 189 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7380 (m-70) REVERT: A 203 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7809 (mtt) REVERT: B 57 ASP cc_start: 0.7518 (t0) cc_final: 0.7137 (t0) REVERT: B 139 TRP cc_start: 0.8613 (t60) cc_final: 0.8197 (t60) REVERT: C 166 LYS cc_start: 0.8559 (mptt) cc_final: 0.8258 (mppt) REVERT: C 205 ASN cc_start: 0.8590 (m110) cc_final: 0.8108 (p0) REVERT: D 20 ARG cc_start: 0.8734 (mtp180) cc_final: 0.8399 (mmm-85) REVERT: D 29 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8193 (mm-30) REVERT: D 53 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8307 (ptt180) REVERT: D 118 ASN cc_start: 0.8570 (m110) cc_final: 0.8245 (m110) REVERT: E 19 ILE cc_start: 0.8930 (mp) cc_final: 0.8588 (mt) REVERT: E 27 GLU cc_start: 0.8761 (tp30) cc_final: 0.8418 (mm-30) REVERT: E 61 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8513 (mmmt) REVERT: E 91 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7945 (mp0) REVERT: F 28 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8559 (mpp) REVERT: G 19 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: G 21 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8480 (mtp-110) REVERT: G 159 TYR cc_start: 0.7552 (t80) cc_final: 0.7157 (t80) REVERT: c 46 GLU cc_start: 0.7809 (pp20) cc_final: 0.7029 (pm20) REVERT: c 120 PHE cc_start: 0.7949 (p90) cc_final: 0.7310 (p90) REVERT: c 123 PHE cc_start: 0.7947 (m-80) cc_final: 0.7043 (m-80) REVERT: c 133 PHE cc_start: 0.7675 (m-80) cc_final: 0.7369 (m-80) REVERT: c 163 GLN cc_start: 0.8237 (mp10) cc_final: 0.7990 (mp10) REVERT: c 256 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8924 (p) REVERT: c 277 MET cc_start: 0.8184 (mpm) cc_final: 0.7910 (mpt) REVERT: d 40 ASN cc_start: 0.9334 (t0) cc_final: 0.8818 (t0) REVERT: d 141 TYR cc_start: 0.7840 (p90) cc_final: 0.7620 (p90) REVERT: d 200 GLN cc_start: 0.7843 (mp10) cc_final: 0.7628 (tm-30) REVERT: d 218 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9145 (mm) REVERT: i 30 SER cc_start: 0.8550 (p) cc_final: 0.8297 (p) REVERT: i 31 HIS cc_start: 0.7837 (m90) cc_final: 0.7334 (m90) REVERT: j 59 ASP cc_start: 0.7414 (t0) cc_final: 0.7146 (t0) REVERT: j 102 SER cc_start: 0.7571 (p) cc_final: 0.7203 (t) REVERT: j 113 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8446 (ttmm) outliers start: 86 outliers final: 40 residues processed: 408 average time/residue: 1.0937 time to fit residues: 508.4872 Evaluate side-chains 372 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 A residue 209 GLU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 58 THR 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 2 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 256 THR 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 218 LEU Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain j residue 52 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 C 120 GLN D 13 ASN c 283 GLN d 153 ASN i 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17893 Z= 0.236 Angle : 0.677 14.051 24353 Z= 0.347 Chirality : 0.044 0.366 2881 Planarity : 0.005 0.066 3113 Dihedral : 4.332 20.417 2545 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 4.34 % Allowed : 28.78 % Favored : 66.88 % 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: 1.63 (0.18), residues: 902 sheet: -1.25 (0.22), residues: 533 loop : -0.94 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 160 HIS 0.009 0.001 HIS G 238 PHE 0.014 0.001 PHE E 179 TYR 0.021 0.001 TYR d 191 ARG 0.014 0.001 ARG E 51 *********************** 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 413 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 338 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7940 (m-80) cc_final: 0.7659 (m-80) REVERT: A 50 LYS cc_start: 0.7629 (tptp) cc_final: 0.7039 (tptp) REVERT: A 53 LYS cc_start: 0.7011 (mppt) cc_final: 0.6791 (tptp) REVERT: A 185 GLU cc_start: 0.7704 (mp0) cc_final: 0.7447 (pm20) REVERT: A 189 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7291 (m-70) REVERT: A 203 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7961 (mtt) REVERT: A 209 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: B 57 ASP cc_start: 0.7535 (t0) cc_final: 0.7152 (t0) REVERT: B 139 TRP cc_start: 0.8632 (t60) cc_final: 0.8163 (t60) REVERT: B 141 LYS cc_start: 0.8973 (tttm) cc_final: 0.8600 (ptmt) REVERT: C 166 LYS cc_start: 0.8569 (mptt) cc_final: 0.8270 (mppt) REVERT: C 205 ASN cc_start: 0.8597 (m110) cc_final: 0.8139 (p0) REVERT: D 20 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8448 (mmm-85) REVERT: D 29 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 53 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8329 (ptt180) REVERT: D 118 ASN cc_start: 0.8541 (m110) cc_final: 0.8185 (m110) REVERT: D 203 LYS cc_start: 0.9276 (ttmm) cc_final: 0.9013 (tppp) REVERT: E 19 ILE cc_start: 0.8982 (mp) cc_final: 0.8643 (mt) REVERT: E 30 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9084 (mtmm) REVERT: E 61 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8559 (mmmt) REVERT: E 91 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7955 (mp0) REVERT: E 226 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7295 (t70) REVERT: F 28 MET cc_start: 0.8968 (mmm) cc_final: 0.8590 (mpp) REVERT: F 206 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8998 (mmpt) REVERT: G 19 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8312 (mm-30) REVERT: G 21 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8418 (mtp-110) REVERT: c 46 GLU cc_start: 0.7831 (pp20) cc_final: 0.7042 (pm20) REVERT: c 120 PHE cc_start: 0.7947 (p90) cc_final: 0.7308 (p90) REVERT: c 123 PHE cc_start: 0.8019 (m-80) cc_final: 0.7056 (m-80) REVERT: c 133 PHE cc_start: 0.7676 (m-80) cc_final: 0.7407 (m-80) REVERT: c 256 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8892 (p) REVERT: d 40 ASN cc_start: 0.9298 (t0) cc_final: 0.8790 (t0) REVERT: d 96 LYS cc_start: 0.9394 (tttp) cc_final: 0.9086 (tttp) REVERT: d 141 TYR cc_start: 0.7871 (p90) cc_final: 0.7658 (p90) REVERT: d 200 GLN cc_start: 0.7841 (mp10) cc_final: 0.7621 (tm-30) REVERT: d 218 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9160 (mm) REVERT: i 31 HIS cc_start: 0.7747 (m90) cc_final: 0.7209 (m90) REVERT: i 82 LEU cc_start: 0.8636 (tm) cc_final: 0.8409 (tm) REVERT: i 87 SER cc_start: 0.7927 (t) cc_final: 0.7319 (p) REVERT: j 54 MET cc_start: 0.8481 (ptp) cc_final: 0.8269 (ptt) REVERT: j 59 ASP cc_start: 0.7501 (t0) cc_final: 0.7219 (t0) REVERT: j 102 SER cc_start: 0.7591 (p) cc_final: 0.7273 (t) REVERT: j 113 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8412 (ttmm) outliers start: 75 outliers final: 50 residues processed: 391 average time/residue: 1.1399 time to fit residues: 505.1705 Evaluate side-chains 379 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 51 ASN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 182 CYS 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 143 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL 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 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 92 ASN Chi-restraints excluded: chain j residue 52 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 210 optimal weight: 0.0980 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 283 GLN d 153 ASN i 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17893 Z= 0.216 Angle : 0.697 14.426 24353 Z= 0.353 Chirality : 0.044 0.371 2881 Planarity : 0.005 0.065 3113 Dihedral : 4.308 20.661 2545 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 4.00 % Allowed : 29.59 % Favored : 66.42 % 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: 1.65 (0.18), residues: 897 sheet: -1.22 (0.22), residues: 525 loop : -0.97 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP d 160 HIS 0.007 0.001 HIS G 238 PHE 0.017 0.001 PHE j 104 TYR 0.024 0.001 TYR A 57 ARG 0.014 0.001 ARG j 57 *********************** 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 406 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.8022 (m-80) cc_final: 0.7706 (m-80) REVERT: A 50 LYS cc_start: 0.7680 (tptp) cc_final: 0.7076 (tptp) REVERT: A 185 GLU cc_start: 0.7612 (mp0) cc_final: 0.7358 (pm20) REVERT: A 189 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7301 (m-70) REVERT: A 203 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8036 (mtt) REVERT: B 57 ASP cc_start: 0.7522 (t0) cc_final: 0.7156 (t0) REVERT: B 92 LEU cc_start: 0.9076 (mm) cc_final: 0.8837 (tt) REVERT: B 139 TRP cc_start: 0.8575 (t60) cc_final: 0.8151 (t60) REVERT: B 141 LYS cc_start: 0.8962 (tttm) cc_final: 0.8596 (ptmt) REVERT: C 166 LYS cc_start: 0.8557 (mptt) cc_final: 0.8267 (mppt) REVERT: C 205 ASN cc_start: 0.8495 (m110) cc_final: 0.8079 (p0) REVERT: D 20 ARG cc_start: 0.8768 (mtp180) cc_final: 0.8442 (mmm-85) REVERT: D 29 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 53 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8331 (ptt180) REVERT: D 118 ASN cc_start: 0.8579 (m110) cc_final: 0.8240 (m110) REVERT: D 133 MET cc_start: 0.8272 (tpp) cc_final: 0.8050 (tpp) REVERT: D 203 LYS cc_start: 0.9276 (ttmm) cc_final: 0.9018 (tppp) REVERT: E 19 ILE cc_start: 0.8951 (mp) cc_final: 0.8616 (mt) REVERT: E 27 GLU cc_start: 0.8756 (tp30) cc_final: 0.8426 (mm-30) REVERT: E 30 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9036 (mtmm) REVERT: E 61 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8536 (mmmt) REVERT: E 91 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7940 (mp0) REVERT: F 28 MET cc_start: 0.8975 (mmm) cc_final: 0.8599 (mpp) REVERT: F 196 LYS cc_start: 0.9553 (tptm) cc_final: 0.9335 (tptp) REVERT: F 206 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8969 (mmpt) REVERT: G 19 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: G 21 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8379 (mtp-110) REVERT: G 159 TYR cc_start: 0.7622 (t80) cc_final: 0.7158 (t80) REVERT: c 46 GLU cc_start: 0.7854 (pp20) cc_final: 0.7041 (pm20) REVERT: c 120 PHE cc_start: 0.7937 (p90) cc_final: 0.7296 (p90) REVERT: c 123 PHE cc_start: 0.8011 (m-80) cc_final: 0.7048 (m-80) REVERT: c 133 PHE cc_start: 0.7675 (m-80) cc_final: 0.7417 (m-80) REVERT: c 277 MET cc_start: 0.7896 (mpm) cc_final: 0.7478 (mtm) REVERT: d 40 ASN cc_start: 0.9227 (t0) cc_final: 0.8733 (t0) REVERT: d 96 LYS cc_start: 0.9413 (tttp) cc_final: 0.9185 (tttp) REVERT: d 218 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9139 (mm) REVERT: i 31 HIS cc_start: 0.7721 (m90) cc_final: 0.7316 (m90) REVERT: i 82 LEU cc_start: 0.8619 (tm) cc_final: 0.8403 (tm) REVERT: i 87 SER cc_start: 0.7909 (t) cc_final: 0.7275 (p) REVERT: j 52 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8736 (p) REVERT: j 59 ASP cc_start: 0.7517 (t0) cc_final: 0.7265 (t0) REVERT: j 102 SER cc_start: 0.7732 (p) cc_final: 0.7443 (t) REVERT: j 113 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8408 (ttmm) outliers start: 69 outliers final: 46 residues processed: 385 average time/residue: 1.1123 time to fit residues: 488.3703 Evaluate side-chains 376 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 320 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 51 ASN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 225 ILE 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 199 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 212 ILE 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 143 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 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL 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 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 j residue 52 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 147 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 198 ASN B 220 ASN c 283 GLN d 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17893 Z= 0.233 Angle : 0.713 14.554 24353 Z= 0.364 Chirality : 0.044 0.368 2881 Planarity : 0.005 0.065 3113 Dihedral : 4.305 20.581 2545 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.76 % Allowed : 30.23 % Favored : 66.01 % 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: -0.06 (0.18), residues: 2351 helix: 1.65 (0.18), residues: 897 sheet: -1.18 (0.22), residues: 524 loop : -0.97 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP d 160 HIS 0.003 0.001 HIS F 121 PHE 0.022 0.001 PHE E 179 TYR 0.027 0.002 TYR d 191 ARG 0.016 0.001 ARG E 51 ********************** 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 405 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 340 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.8132 (m-80) cc_final: 0.7803 (m-80) REVERT: A 50 LYS cc_start: 0.7829 (tptp) cc_final: 0.7273 (tptp) REVERT: A 92 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8265 (mmmt) REVERT: A 185 GLU cc_start: 0.7545 (mp0) cc_final: 0.7290 (pm20) REVERT: A 189 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7352 (m-70) REVERT: A 196 LYS cc_start: 0.8604 (tppt) cc_final: 0.8348 (tppt) REVERT: A 203 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7942 (mtt) REVERT: B 57 ASP cc_start: 0.7531 (t0) cc_final: 0.7154 (t0) REVERT: B 92 LEU cc_start: 0.9077 (mm) cc_final: 0.8845 (tt) REVERT: B 139 TRP cc_start: 0.8628 (t60) cc_final: 0.8217 (t60) REVERT: B 141 LYS cc_start: 0.8957 (tttm) cc_final: 0.8619 (ptmt) REVERT: C 166 LYS cc_start: 0.8559 (mptt) cc_final: 0.8271 (mppt) REVERT: C 205 ASN cc_start: 0.8465 (m110) cc_final: 0.8061 (p0) REVERT: D 29 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8168 (mm-30) REVERT: D 53 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8345 (ptt180) REVERT: D 59 MET cc_start: 0.8621 (tpt) cc_final: 0.7930 (tpt) REVERT: D 118 ASN cc_start: 0.8579 (m110) cc_final: 0.8220 (m110) REVERT: D 203 LYS cc_start: 0.9273 (ttmm) cc_final: 0.9018 (tppp) REVERT: E 19 ILE cc_start: 0.8971 (mp) cc_final: 0.8639 (mt) REVERT: E 30 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9053 (mtmm) REVERT: E 61 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8537 (mmmt) REVERT: F 196 LYS cc_start: 0.9551 (tptm) cc_final: 0.9346 (tptp) REVERT: F 206 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8953 (mmpt) REVERT: G 19 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: G 21 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8377 (mtp-110) REVERT: G 159 TYR cc_start: 0.7590 (t80) cc_final: 0.7168 (t80) REVERT: c 46 GLU cc_start: 0.7863 (pp20) cc_final: 0.7051 (pm20) REVERT: c 120 PHE cc_start: 0.7930 (p90) cc_final: 0.7291 (p90) REVERT: c 123 PHE cc_start: 0.8075 (m-80) cc_final: 0.7124 (m-80) REVERT: c 133 PHE cc_start: 0.7676 (m-80) cc_final: 0.7458 (m-80) REVERT: c 277 MET cc_start: 0.7893 (mpm) cc_final: 0.7490 (mtm) REVERT: d 40 ASN cc_start: 0.9224 (t0) cc_final: 0.8752 (OUTLIER) REVERT: d 96 LYS cc_start: 0.9378 (tttp) cc_final: 0.9156 (tttp) REVERT: d 152 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7307 (mp-120) REVERT: d 218 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9133 (mm) REVERT: i 31 HIS cc_start: 0.7691 (m90) cc_final: 0.7303 (m90) REVERT: i 80 LYS cc_start: 0.9077 (tppp) cc_final: 0.8666 (tptt) REVERT: i 87 SER cc_start: 0.7914 (t) cc_final: 0.7322 (p) REVERT: j 59 ASP cc_start: 0.7553 (t0) cc_final: 0.7292 (t0) REVERT: j 102 SER cc_start: 0.7742 (p) cc_final: 0.7488 (t) REVERT: j 113 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8468 (ttmm) outliers start: 65 outliers final: 49 residues processed: 388 average time/residue: 1.1513 time to fit residues: 505.9590 Evaluate side-chains 380 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 322 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 B residue 51 ASN Chi-restraints excluded: chain B residue 225 ILE 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 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 220 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 182 CYS Chi-restraints excluded: chain E residue 212 ILE 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 143 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 176 LYS Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 221 SER 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 152 GLN Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 218 LEU Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 163 optimal weight: 5.9990 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 198 ASN B 220 ASN E 20 HIS 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 = 0.3627 r_free = 0.3627 target = 0.094010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079094 restraints weight = 48969.417| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.52 r_work: 0.3223 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17893 Z= 0.219 Angle : 0.707 14.604 24353 Z= 0.358 Chirality : 0.044 0.368 2881 Planarity : 0.005 0.063 3113 Dihedral : 4.273 20.729 2545 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 4.00 % Allowed : 30.80 % Favored : 65.20 % 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: 1.68 (0.18), residues: 897 sheet: -1.05 (0.23), residues: 504 loop : -0.93 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP d 160 HIS 0.002 0.001 HIS F 121 PHE 0.012 0.001 PHE d 94 TYR 0.024 0.001 TYR d 141 ARG 0.017 0.001 ARG E 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7789.89 seconds wall clock time: 139 minutes 44.27 seconds (8384.27 seconds total)