Starting phenix.real_space_refine on Wed Jun 18 19:30:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm5_41379/06_2025/8tm5_41379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm5_41379/06_2025/8tm5_41379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tm5_41379/06_2025/8tm5_41379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm5_41379/06_2025/8tm5_41379.map" model { file = "/net/cci-nas-00/data/ceres_data/8tm5_41379/06_2025/8tm5_41379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm5_41379/06_2025/8tm5_41379.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 133 5.16 5 C 13829 2.51 5 N 3712 2.21 5 O 4015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21689 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1800 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 222} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1933 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 245} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1792 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1816 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1832 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1873 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 236} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1596 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1331 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1222 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 3 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "c" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2092 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 106 Chain: "d" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1907 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "e" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 787 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.39, per 1000 atoms: 0.62 Number of scatterers: 21689 At special positions: 0 Unit cell: (130.38, 137.8, 138.86, 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 133 16.00 O 4015 8.00 N 3712 7.00 C 13829 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=2.04 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: 5.01 Conformation dependent library (CDL) restraints added in 3.1 seconds 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5342 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 25 sheets defined 41.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 106 through 124 removed outlier: 3.626A pdb=" N TYR A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) 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 234 Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.556A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 102 removed outlier: 3.684A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 229 through 252 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 76 through 99 Processing helix chain 'C' and resid 103 through 119 Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 221 through 239 Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.529A pdb=" N GLU D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 103 removed outlier: 3.778A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 173 through 185 Processing helix chain 'D' and resid 190 through 206 Processing helix chain 'D' and resid 230 through 239 removed outlier: 3.724A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.686A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 98 Processing helix chain 'E' and resid 104 through 122 Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 164 through 175 removed outlier: 4.358A pdb=" N ALA E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.611A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.849A 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: 4.662A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU F 193 " --> pdb=" O ASP F 189 " (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 243 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 185 Processing helix chain 'G' and resid 190 through 206 Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid -26 through -12 removed outlier: 3.800A pdb=" N LYS H -13 " --> pdb=" O ALA H -17 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'I' and resid 56 through 79 Processing helix chain 'I' and resid 83 through 98 removed outlier: 3.938A pdb=" N LYS I 98 " --> pdb=" O LEU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 173 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.544A pdb=" N VAL J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 95 Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'J' and resid 152 through 170 Processing helix chain 'c' and resid 17 through 25 Processing helix chain 'c' and resid 26 through 30 removed outlier: 4.043A pdb=" N ARG c 29 " --> pdb=" O GLU c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 45 Processing helix chain 'c' and resid 61 through 66 Processing helix chain 'c' and resid 76 through 87 Processing helix chain 'c' and resid 142 through 154 removed outlier: 4.359A pdb=" N TYR c 147 " --> pdb=" O GLU c 143 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN c 148 " --> pdb=" O ASP c 144 " (cutoff:3.500A) Processing helix chain 'c' and resid 214 through 226 Processing helix chain 'c' and resid 243 through 249 Processing helix chain 'c' and resid 250 through 255 Processing helix chain 'c' and resid 265 through 279 removed outlier: 3.950A pdb=" N LYS c 275 " --> pdb=" O GLU c 271 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 40 Processing helix chain 'd' and resid 66 through 69 removed outlier: 3.573A pdb=" N THR d 69 " --> pdb=" O GLY d 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 66 through 69' Processing helix chain 'd' and resid 98 through 114 Processing helix chain 'd' and resid 130 through 137 removed outlier: 3.798A pdb=" N THR d 137 " --> pdb=" O GLN d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 159 Processing helix chain 'd' and resid 185 through 198 removed outlier: 3.631A pdb=" N THR d 189 " --> pdb=" O GLY d 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 213 through 229 removed outlier: 3.804A pdb=" N TRP d 227 " --> pdb=" O TYR d 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 54 removed outlier: 4.386A pdb=" N LEU e 50 " --> pdb=" O HIS e 46 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER e 51 " --> pdb=" O PRO e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 71 Processing helix chain 'e' and resid 73 through 89 removed outlier: 3.948A pdb=" N VAL e 89 " --> pdb=" O ALA e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 107 Processing helix chain 'e' and resid 113 through 118 removed outlier: 3.657A pdb=" N ILE e 117 " --> pdb=" O GLY e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.604A pdb=" N ILE A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 133 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.504A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.575A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 130 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 131 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 144 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AA9, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.557A pdb=" N CYS D 76 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 70 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.612A 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 64 removed outlier: 3.567A pdb=" N LEU E 132 " --> pdb=" O THR E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 163 through 166 removed outlier: 3.736A pdb=" N GLU F 213 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 67 through 68 removed outlier: 3.685A pdb=" N GLY F 139 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.385A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 69 through 71 removed outlier: 4.033A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 124 through 127 removed outlier: 3.696A pdb=" N GLY H 11 " --> pdb=" O TYR H 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 35 through 38 removed outlier: 5.330A pdb=" N PHE H 36 " --> pdb=" O CYS H 43 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS H 43 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 99 " --> pdb=" O CYS H 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 215 through 218 removed outlier: 3.601A pdb=" N LYS H 215 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 197 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR H 217 " --> pdb=" O ILE I 195 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE I 195 " --> pdb=" O THR H 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I 191 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP I 25 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA I 10 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 42 through 44 removed outlier: 3.712A pdb=" N PHE I 43 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE I 121 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR I 133 " --> pdb=" O ILE I 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 129 through 130 removed outlier: 3.929A pdb=" N VAL J 13 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE J 183 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG J 181 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 35 through 37 removed outlier: 3.643A pdb=" N MET J 118 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 56 through 57 removed outlier: 5.281A pdb=" N GLU c 95 " --> pdb=" O HIS c 125 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS c 125 " --> pdb=" O GLU c 95 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY c 97 " --> pdb=" O PHE c 123 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS c 121 " --> pdb=" O ALA c 99 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS c 70 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N CYS c 135 " --> pdb=" O LYS c 70 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE c 72 " --> pdb=" O CYS c 135 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS c 137 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA c 74 " --> pdb=" O CYS c 137 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS c 169 " --> pdb=" O ILE c 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 212 through 213 removed outlier: 3.510A pdb=" N SER d 72 " --> pdb=" O GLY d 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 3 through 4 removed outlier: 3.516A pdb=" N SER d 42 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL d 77 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR d 46 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ALA d 75 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU d 88 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU d 90 " --> pdb=" O PRO d 20 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU d 121 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET d 19 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N SER d 123 " --> pdb=" O MET d 19 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS d 206 " --> pdb=" O SER d 122 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3474 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: 7.65 Time building geometry restraints manager: 6.08 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: 7082 1.34 - 1.46: 3909 1.46 - 1.58: 10886 1.58 - 1.70: 1 1.70 - 1.81: 206 Bond restraints: 22084 Sorted by residual: bond pdb=" CB PRO e 44 " pdb=" CG PRO e 44 " ideal model delta sigma weight residual 1.492 1.676 -0.184 5.00e-02 4.00e+02 1.35e+01 bond pdb=" CG PRO e 44 " pdb=" CD PRO e 44 " ideal model delta sigma weight residual 1.503 1.390 0.113 3.40e-02 8.65e+02 1.10e+01 bond pdb=" N LEU e 43 " pdb=" CA LEU e 43 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.76e+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 6.13e+00 bond pdb=" N SER B 2 " pdb=" CA SER B 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 ... (remaining 22079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 29810 3.22 - 6.44: 114 6.44 - 9.66: 3 9.66 - 12.88: 1 12.88 - 16.11: 1 Bond angle restraints: 29929 Sorted by residual: angle pdb=" CA PRO e 44 " pdb=" N PRO e 44 " pdb=" CD PRO e 44 " ideal model delta sigma weight residual 112.00 95.89 16.11 1.40e+00 5.10e-01 1.32e+02 angle pdb=" N PRO e 44 " pdb=" CD PRO e 44 " pdb=" CG PRO e 44 " ideal model delta sigma weight residual 103.20 96.09 7.11 1.50e+00 4.44e-01 2.25e+01 angle pdb=" C TYR H -10 " pdb=" CA TYR H -10 " pdb=" CB TYR H -10 " ideal model delta sigma weight residual 115.79 110.55 5.24 1.19e+00 7.06e-01 1.94e+01 angle pdb=" N ILE C 181 " pdb=" CA ILE C 181 " pdb=" C ILE C 181 " ideal model delta sigma weight residual 112.43 108.92 3.51 9.20e-01 1.18e+00 1.46e+01 angle pdb=" N SER c 128 " pdb=" CA SER c 128 " pdb=" C SER c 128 " ideal model delta sigma weight residual 113.41 109.06 4.35 1.22e+00 6.72e-01 1.27e+01 ... (remaining 29924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11825 17.97 - 35.94: 1154 35.94 - 53.91: 245 53.91 - 71.88: 51 71.88 - 89.84: 23 Dihedral angle restraints: 13298 sinusoidal: 5009 harmonic: 8289 Sorted by residual: dihedral pdb=" CA CYS G 154 " pdb=" C CYS G 154 " pdb=" N ASP G 155 " pdb=" CA ASP G 155 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE G 210 " pdb=" C PHE G 210 " pdb=" N LYS G 211 " pdb=" CA LYS G 211 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET I 158 " pdb=" C MET I 158 " pdb=" N ASP I 159 " pdb=" CA ASP I 159 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 13295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2381 0.032 - 0.063: 688 0.063 - 0.095: 245 0.095 - 0.126: 151 0.126 - 0.157: 7 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA ILE J 183 " pdb=" N ILE J 183 " pdb=" C ILE J 183 " pdb=" CB ILE J 183 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA VAL D 50 " pdb=" N VAL D 50 " pdb=" C VAL D 50 " pdb=" CB VAL D 50 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE D 74 " pdb=" N ILE D 74 " pdb=" C ILE D 74 " pdb=" CB ILE D 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3469 not shown) Planarity restraints: 3821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU e 43 " -0.067 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO e 44 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO e 44 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO e 44 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA c 12 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO c 13 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO c 13 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO c 13 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA d 9 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO d 10 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO d 10 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO d 10 " -0.030 5.00e-02 4.00e+02 ... (remaining 3818 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 212 2.60 - 3.18: 19407 3.18 - 3.75: 36119 3.75 - 4.33: 50410 4.33 - 4.90: 82782 Nonbonded interactions: 188930 Sorted by model distance: nonbonded pdb=" OG1 THR C 8 " pdb=" OD1 ASN C 122 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN A 202 " pdb=" OG1 THR A 204 " model vdw 2.026 3.040 nonbonded pdb=" OD1 ASP J 184 " pdb=" N LYS J 185 " model vdw 2.063 3.120 nonbonded pdb=" OD1 ASP B 71 " pdb=" OG1 THR B 223 " model vdw 2.113 3.040 nonbonded pdb=" OE2 GLU C 170 " pdb=" NZ LYS C 174 " model vdw 2.134 3.120 ... (remaining 188925 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: 4.780 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 50.000 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.184 22085 Z= 0.148 Angle : 0.614 16.106 29931 Z= 0.363 Chirality : 0.039 0.157 3472 Planarity : 0.004 0.091 3821 Dihedral : 15.368 89.845 7953 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.09 % Allowed : 18.30 % Favored : 81.61 % 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: -0.40 (0.16), residues: 2808 helix: 1.79 (0.16), residues: 1124 sheet: -1.97 (0.20), residues: 592 loop : -1.41 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 154 HIS 0.006 0.001 HIS D 155 PHE 0.013 0.001 PHE J 36 TYR 0.014 0.001 TYR H 90 ARG 0.003 0.000 ARG J 93 Details of bonding type rmsd hydrogen bonds : bond 0.17272 ( 1201) hydrogen bonds : angle 7.76707 ( 3474) SS BOND : bond 0.00583 ( 1) SS BOND : angle 6.37740 ( 2) covalent geometry : bond 0.00310 (22084) covalent geometry : angle 0.61206 (29929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8489 (mmt) cc_final: 0.8216 (mtt) REVERT: A 233 ILE cc_start: 0.8725 (mm) cc_final: 0.8509 (mm) REVERT: B 116 ASP cc_start: 0.8503 (m-30) cc_final: 0.8296 (m-30) REVERT: B 174 MET cc_start: 0.8273 (ttm) cc_final: 0.7840 (ttm) REVERT: C 23 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8379 (mm-40) REVERT: C 71 MET cc_start: 0.8685 (ptm) cc_final: 0.8377 (ptm) REVERT: D 66 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8287 (mmmm) REVERT: D 114 GLN cc_start: 0.8611 (tt0) cc_final: 0.8140 (tm-30) REVERT: F 68 PHE cc_start: 0.7729 (m-80) cc_final: 0.7512 (m-80) REVERT: F 203 ASP cc_start: 0.7630 (t0) cc_final: 0.7364 (t0) REVERT: G 3 ARG cc_start: 0.8234 (mpp80) cc_final: 0.7029 (mmm160) REVERT: G 131 MET cc_start: 0.8541 (mpp) cc_final: 0.8255 (mtm) REVERT: H 135 MET cc_start: 0.8451 (tpp) cc_final: 0.8115 (tpp) REVERT: I 90 MET cc_start: 0.8902 (mtp) cc_final: 0.8649 (mtm) REVERT: I 106 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8577 (mt-10) REVERT: I 131 MET cc_start: 0.8807 (tmm) cc_final: 0.8579 (tmm) REVERT: I 146 MET cc_start: 0.6507 (mmt) cc_final: 0.6173 (mmt) REVERT: I 192 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8408 (ptmm) REVERT: I 198 ARG cc_start: 0.8237 (mtm180) cc_final: 0.8013 (mtm-85) REVERT: c 78 ASN cc_start: 0.8342 (m110) cc_final: 0.8067 (m-40) REVERT: d 32 MET cc_start: 0.9048 (mmm) cc_final: 0.8493 (mmm) REVERT: d 179 ILE cc_start: 0.8091 (mm) cc_final: 0.7385 (pp) REVERT: d 210 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6988 (tt0) REVERT: e 49 GLU cc_start: 0.8653 (tp30) cc_final: 0.8373 (tp30) REVERT: e 56 GLN cc_start: 0.7912 (tp-100) cc_final: 0.6968 (tm-30) REVERT: e 106 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.7941 (mtt-85) REVERT: e 108 ASN cc_start: 0.8485 (p0) cc_final: 0.8256 (p0) REVERT: e 137 LYS cc_start: 0.9299 (tttm) cc_final: 0.9026 (ttmt) outliers start: 2 outliers final: 2 residues processed: 493 average time/residue: 1.3585 time to fit residues: 769.7981 Evaluate side-chains 388 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain G residue 209 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 252 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 102 GLN B 88 ASN B 155 ASN C 154 HIS C 159 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 178 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN H 62 ASN J 63 ASN J 65 GLN J 87 ASN J 99 HIS c 78 ASN c 145 GLN c 268 GLN d 133 GLN e 99 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073512 restraints weight = 57219.326| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.05 r_work: 0.3027 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 22085 Z= 0.147 Angle : 0.607 7.606 29931 Z= 0.316 Chirality : 0.043 0.177 3472 Planarity : 0.005 0.058 3821 Dihedral : 4.617 38.674 3079 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 2.68 % Allowed : 18.97 % Favored : 78.35 % 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 (0.16), residues: 2808 helix: 1.86 (0.15), residues: 1139 sheet: -1.54 (0.20), residues: 610 loop : -1.20 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 189 HIS 0.010 0.001 HIS D 155 PHE 0.020 0.001 PHE G 210 TYR 0.019 0.001 TYR H 90 ARG 0.007 0.001 ARG J 93 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 1201) hydrogen bonds : angle 5.53670 ( 3474) SS BOND : bond 0.00413 ( 1) SS BOND : angle 2.60139 ( 2) covalent geometry : bond 0.00335 (22084) covalent geometry : angle 0.60648 (29929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 442 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: A 57 TYR cc_start: 0.8038 (m-80) cc_final: 0.7697 (m-80) REVERT: A 150 ASP cc_start: 0.8837 (m-30) cc_final: 0.8554 (m-30) REVERT: A 212 ILE cc_start: 0.9406 (pt) cc_final: 0.9202 (pp) REVERT: A 233 ILE cc_start: 0.8858 (mm) cc_final: 0.8549 (mm) REVERT: B 41 ASP cc_start: 0.8531 (m-30) cc_final: 0.8245 (m-30) REVERT: C 16 LEU cc_start: 0.8725 (mp) cc_final: 0.8469 (mt) REVERT: C 20 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: C 23 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8716 (mm-40) REVERT: C 39 ASP cc_start: 0.8808 (m-30) cc_final: 0.8474 (m-30) REVERT: D 7 GLU cc_start: 0.7745 (tp30) cc_final: 0.7371 (tp30) REVERT: D 91 LYS cc_start: 0.8991 (tptp) cc_final: 0.8742 (tptp) REVERT: D 104 ASN cc_start: 0.8000 (m-40) cc_final: 0.7639 (m110) REVERT: D 114 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: D 191 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6532 (mt) REVERT: E 72 ILE cc_start: 0.9473 (pt) cc_final: 0.9169 (pp) REVERT: E 125 ARG cc_start: 0.8125 (mmt180) cc_final: 0.7561 (mtp85) REVERT: F 68 PHE cc_start: 0.8314 (m-80) cc_final: 0.8063 (m-80) REVERT: G 3 ARG cc_start: 0.8092 (mpp80) cc_final: 0.6931 (mmp-170) REVERT: G 83 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8702 (mtt) REVERT: H -22 ASN cc_start: 0.8906 (t0) cc_final: 0.7209 (t0) REVERT: H -18 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8455 (mp0) REVERT: H 215 LYS cc_start: 0.9088 (pptt) cc_final: 0.8799 (pptt) REVERT: I 75 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8794 (mt-10) REVERT: I 78 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8600 (mt-10) REVERT: I 80 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8157 (ptt-90) REVERT: I 90 MET cc_start: 0.9355 (mtp) cc_final: 0.9134 (mtm) REVERT: I 146 MET cc_start: 0.6998 (mmt) cc_final: 0.6725 (ttm) REVERT: I 189 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8363 (pp) REVERT: J 37 LYS cc_start: 0.8645 (ptmm) cc_final: 0.8382 (ptmm) REVERT: J 53 THR cc_start: 0.8899 (p) cc_final: 0.8665 (p) REVERT: J 74 GLU cc_start: 0.8442 (pm20) cc_final: 0.7918 (mt-10) REVERT: c 88 MET cc_start: 0.8647 (mmm) cc_final: 0.8437 (mmm) REVERT: d 55 MET cc_start: 0.8687 (ptm) cc_final: 0.8464 (ppp) REVERT: d 229 GLN cc_start: 0.9375 (mt0) cc_final: 0.8906 (mp10) REVERT: e 49 GLU cc_start: 0.9035 (tp30) cc_final: 0.8762 (tp30) REVERT: e 56 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7678 (tm-30) REVERT: e 58 ASN cc_start: 0.9172 (m-40) cc_final: 0.8883 (m-40) REVERT: e 60 ASP cc_start: 0.8840 (m-30) cc_final: 0.8092 (m-30) REVERT: e 106 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8567 (mtt-85) REVERT: e 110 GLU cc_start: 0.8041 (pp20) cc_final: 0.7632 (pt0) REVERT: e 137 LYS cc_start: 0.9273 (tttm) cc_final: 0.9004 (ttmt) outliers start: 60 outliers final: 21 residues processed: 477 average time/residue: 1.3205 time to fit residues: 722.7136 Evaluate side-chains 409 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 381 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 144 ASP Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 266 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 251 optimal weight: 0.0020 chunk 205 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 233 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 112 GLN C 154 HIS D 23 GLN D 178 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 65 GLN d 29 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072289 restraints weight = 57228.357| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.04 r_work: 0.3008 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22085 Z= 0.127 Angle : 0.569 8.155 29931 Z= 0.295 Chirality : 0.042 0.254 3472 Planarity : 0.004 0.055 3821 Dihedral : 4.412 40.444 3077 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 2.99 % Allowed : 20.18 % Favored : 76.83 % 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 (0.16), residues: 2808 helix: 2.00 (0.15), residues: 1141 sheet: -1.24 (0.21), residues: 590 loop : -1.11 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 93 HIS 0.009 0.001 HIS D 155 PHE 0.017 0.001 PHE J 36 TYR 0.021 0.001 TYR H 90 ARG 0.009 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 1201) hydrogen bonds : angle 5.13412 ( 3474) SS BOND : bond 0.01066 ( 1) SS BOND : angle 3.46092 ( 2) covalent geometry : bond 0.00289 (22084) covalent geometry : angle 0.56817 (29929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 424 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: A 79 MET cc_start: 0.8574 (mmt) cc_final: 0.8240 (mtt) REVERT: A 103 GLU cc_start: 0.8778 (tp30) cc_final: 0.8400 (tt0) REVERT: A 150 ASP cc_start: 0.8755 (m-30) cc_final: 0.8537 (m-30) REVERT: A 212 ILE cc_start: 0.9433 (pt) cc_final: 0.9187 (pp) REVERT: A 233 ILE cc_start: 0.8884 (mm) cc_final: 0.8612 (mm) REVERT: B 174 MET cc_start: 0.8796 (ttm) cc_final: 0.8411 (ttp) REVERT: C 16 LEU cc_start: 0.8758 (mp) cc_final: 0.8465 (mm) REVERT: C 20 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: C 39 ASP cc_start: 0.8761 (m-30) cc_final: 0.8453 (m-30) REVERT: D 7 GLU cc_start: 0.7779 (tp30) cc_final: 0.7374 (tp30) REVERT: D 91 LYS cc_start: 0.9008 (tptp) cc_final: 0.8756 (tptp) REVERT: D 114 GLN cc_start: 0.8813 (tt0) cc_final: 0.8045 (tm-30) REVERT: D 170 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8432 (pt) REVERT: D 178 GLN cc_start: 0.7929 (tp40) cc_final: 0.7726 (tp-100) REVERT: E 47 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (m) REVERT: E 72 ILE cc_start: 0.9426 (pt) cc_final: 0.9164 (pp) REVERT: E 125 ARG cc_start: 0.8064 (mmt180) cc_final: 0.7571 (mtp85) REVERT: F 151 MET cc_start: 0.8505 (tmm) cc_final: 0.8166 (tmm) REVERT: F 203 ASP cc_start: 0.7829 (t0) cc_final: 0.7474 (t0) REVERT: G 3 ARG cc_start: 0.8106 (mpp80) cc_final: 0.6890 (mmm160) REVERT: G 58 ASP cc_start: 0.7265 (p0) cc_final: 0.6824 (p0) REVERT: G 83 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8800 (mtt) REVERT: G 209 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: H -22 ASN cc_start: 0.8837 (t0) cc_final: 0.7175 (t0) REVERT: H -18 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8401 (mp0) REVERT: H -16 ASP cc_start: 0.8801 (t0) cc_final: 0.8547 (t0) REVERT: H -13 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8386 (ptmm) REVERT: H -3 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8580 (mtpm) REVERT: H 12 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9170 (mm) REVERT: H 215 LYS cc_start: 0.8890 (pptt) cc_final: 0.8689 (pptt) REVERT: I 75 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8811 (mt-10) REVERT: I 90 MET cc_start: 0.9347 (mtp) cc_final: 0.9134 (mtm) REVERT: I 146 MET cc_start: 0.7101 (mmt) cc_final: 0.6750 (ttm) REVERT: I 189 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8330 (pp) REVERT: I 198 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7873 (mtm-85) REVERT: J 37 LYS cc_start: 0.8729 (ptmm) cc_final: 0.8202 (tttm) REVERT: c 78 ASN cc_start: 0.8817 (m-40) cc_final: 0.8456 (m-40) REVERT: d 32 MET cc_start: 0.9155 (mmm) cc_final: 0.8697 (mmm) REVERT: d 229 GLN cc_start: 0.9355 (mt0) cc_final: 0.8970 (mp10) REVERT: e 49 GLU cc_start: 0.9090 (tp30) cc_final: 0.8728 (tp30) REVERT: e 58 ASN cc_start: 0.9229 (m-40) cc_final: 0.8942 (m110) REVERT: e 63 ASN cc_start: 0.9006 (m-40) cc_final: 0.8783 (m110) REVERT: e 66 THR cc_start: 0.9190 (m) cc_final: 0.8881 (t) REVERT: e 110 GLU cc_start: 0.8178 (pp20) cc_final: 0.7837 (pt0) REVERT: e 137 LYS cc_start: 0.9401 (tttm) cc_final: 0.9132 (ttmt) outliers start: 67 outliers final: 19 residues processed: 466 average time/residue: 1.3709 time to fit residues: 736.4359 Evaluate side-chains 407 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 380 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 186 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 97 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 221 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 86 ASN E 175 HIS ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 65 GLN e 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067791 restraints weight = 58671.462| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.02 r_work: 0.2911 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22085 Z= 0.171 Angle : 0.598 8.883 29931 Z= 0.310 Chirality : 0.042 0.191 3472 Planarity : 0.004 0.057 3821 Dihedral : 4.366 22.633 3075 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 3.84 % Allowed : 20.22 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2808 helix: 2.11 (0.15), residues: 1129 sheet: -1.02 (0.20), residues: 608 loop : -1.01 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 93 HIS 0.007 0.001 HIS D 99 PHE 0.015 0.001 PHE I 100 TYR 0.028 0.001 TYR H 90 ARG 0.009 0.001 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 1201) hydrogen bonds : angle 4.95163 ( 3474) SS BOND : bond 0.01235 ( 1) SS BOND : angle 4.96683 ( 2) covalent geometry : bond 0.00388 (22084) covalent geometry : angle 0.59622 (29929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 439 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: A 79 MET cc_start: 0.8781 (mmt) cc_final: 0.8487 (mtt) REVERT: A 103 GLU cc_start: 0.8844 (tp30) cc_final: 0.8433 (tt0) REVERT: A 212 ILE cc_start: 0.9472 (pt) cc_final: 0.9228 (pp) REVERT: A 233 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8732 (mm) REVERT: C 16 LEU cc_start: 0.8865 (mp) cc_final: 0.8576 (mm) REVERT: C 20 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: D 7 GLU cc_start: 0.8060 (tp30) cc_final: 0.7605 (tp30) REVERT: D 178 GLN cc_start: 0.8095 (tp40) cc_final: 0.7828 (tp-100) REVERT: D 182 GLN cc_start: 0.8918 (pp30) cc_final: 0.8677 (pp30) REVERT: D 191 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7119 (tp) REVERT: E 68 ASN cc_start: 0.9063 (t0) cc_final: 0.8818 (t0) REVERT: E 72 ILE cc_start: 0.9434 (pt) cc_final: 0.9151 (pp) REVERT: E 125 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7598 (mtp85) REVERT: F 71 ASP cc_start: 0.8299 (t0) cc_final: 0.8025 (t0) REVERT: F 94 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (mp0) REVERT: F 151 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8407 (tmm) REVERT: F 203 ASP cc_start: 0.7884 (t0) cc_final: 0.7490 (t0) REVERT: G 138 MET cc_start: 0.9217 (ttm) cc_final: 0.8963 (ttp) REVERT: G 209 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: H -24 ARG cc_start: 0.8928 (ttm170) cc_final: 0.8683 (ptp-110) REVERT: H -22 ASN cc_start: 0.8887 (t0) cc_final: 0.7288 (t0) REVERT: H -18 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8355 (mp0) REVERT: H -3 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8637 (mtpm) REVERT: H 12 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9314 (mm) REVERT: H 90 TYR cc_start: 0.8145 (m-80) cc_final: 0.7905 (m-10) REVERT: H 215 LYS cc_start: 0.9023 (pptt) cc_final: 0.8507 (pptt) REVERT: I 80 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8342 (ptt-90) REVERT: I 90 MET cc_start: 0.9349 (mtp) cc_final: 0.9115 (mtm) REVERT: I 125 ASP cc_start: 0.8427 (m-30) cc_final: 0.8185 (m-30) REVERT: I 131 MET cc_start: 0.8699 (tmm) cc_final: 0.8451 (tpp) REVERT: I 146 MET cc_start: 0.7395 (mmt) cc_final: 0.6959 (ttm) REVERT: I 189 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8478 (pp) REVERT: I 198 ARG cc_start: 0.8312 (mtm180) cc_final: 0.8104 (mtm-85) REVERT: J 37 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8507 (tttm) REVERT: J 65 GLN cc_start: 0.9189 (tp40) cc_final: 0.8922 (tm-30) REVERT: J 74 GLU cc_start: 0.8623 (pm20) cc_final: 0.8308 (mt-10) REVERT: J 90 ASP cc_start: 0.9405 (t0) cc_final: 0.9054 (t0) REVERT: J 93 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8096 (mtm-85) REVERT: c 8 GLU cc_start: 0.8762 (tp30) cc_final: 0.8509 (tp30) REVERT: c 36 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8107 (tm-30) REVERT: c 40 GLN cc_start: 0.8663 (mm110) cc_final: 0.8316 (mm110) REVERT: c 94 GLU cc_start: 0.8554 (tt0) cc_final: 0.8151 (pt0) REVERT: c 95 GLU cc_start: 0.8248 (tt0) cc_final: 0.8016 (tt0) REVERT: c 143 GLU cc_start: 0.8938 (pm20) cc_final: 0.8474 (pt0) REVERT: c 146 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: c 148 GLN cc_start: 0.8755 (mt0) cc_final: 0.8469 (mt0) REVERT: d 229 GLN cc_start: 0.9404 (mt0) cc_final: 0.8987 (mp10) REVERT: e 49 GLU cc_start: 0.9184 (tp30) cc_final: 0.8981 (tp30) REVERT: e 56 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7154 (tm-30) REVERT: e 60 ASP cc_start: 0.9050 (m-30) cc_final: 0.8606 (m-30) REVERT: e 66 THR cc_start: 0.9261 (m) cc_final: 0.8963 (t) REVERT: e 106 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8545 (mtt-85) REVERT: e 137 LYS cc_start: 0.9464 (tttm) cc_final: 0.9258 (tttt) outliers start: 86 outliers final: 26 residues processed: 487 average time/residue: 1.3185 time to fit residues: 736.4204 Evaluate side-chains 422 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 385 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 122 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 265 optimal weight: 0.0570 chunk 203 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 84 ASN D 182 GLN E 16 GLN E 86 ASN F 23 GLN G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN I 93 ASN J 61 GLN J 63 ASN J 65 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 268 GLN e 63 ASN e 88 GLN e 123 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068763 restraints weight = 58189.247| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.03 r_work: 0.2931 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22085 Z= 0.127 Angle : 0.581 9.860 29931 Z= 0.297 Chirality : 0.042 0.282 3472 Planarity : 0.004 0.054 3821 Dihedral : 4.294 22.644 3075 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 4.15 % Allowed : 21.79 % 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: 0.53 (0.16), residues: 2808 helix: 2.24 (0.15), residues: 1124 sheet: -0.86 (0.20), residues: 608 loop : -0.94 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 93 HIS 0.006 0.001 HIS C 154 PHE 0.013 0.001 PHE J 36 TYR 0.025 0.001 TYR C 153 ARG 0.007 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1201) hydrogen bonds : angle 4.85839 ( 3474) SS BOND : bond 0.01114 ( 1) SS BOND : angle 5.84993 ( 2) covalent geometry : bond 0.00291 (22084) covalent geometry : angle 0.57915 (29929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 427 time to evaluate : 2.295 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 20 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 23 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: A 79 MET cc_start: 0.8698 (mmt) cc_final: 0.8488 (mtt) REVERT: A 103 GLU cc_start: 0.8859 (tp30) cc_final: 0.8399 (tt0) REVERT: A 212 ILE cc_start: 0.9477 (pt) cc_final: 0.9240 (pp) REVERT: A 233 ILE cc_start: 0.8991 (mm) cc_final: 0.8711 (mm) REVERT: B 174 MET cc_start: 0.9058 (ttm) cc_final: 0.8854 (ttp) REVERT: B 178 ASP cc_start: 0.8660 (m-30) cc_final: 0.8424 (m-30) REVERT: C 16 LEU cc_start: 0.8781 (mp) cc_final: 0.8485 (mm) REVERT: C 20 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: C 39 ASP cc_start: 0.8730 (m-30) cc_final: 0.8435 (m-30) REVERT: C 178 ASP cc_start: 0.8336 (p0) cc_final: 0.7842 (t0) REVERT: D 7 GLU cc_start: 0.8059 (tp30) cc_final: 0.7626 (tp30) REVERT: D 107 MET cc_start: 0.8543 (tpt) cc_final: 0.8317 (mmt) REVERT: D 178 GLN cc_start: 0.8094 (tp40) cc_final: 0.7809 (tp-100) REVERT: D 191 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7146 (tp) REVERT: E 27 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8710 (mm-30) REVERT: E 72 ILE cc_start: 0.9425 (pt) cc_final: 0.9137 (pp) REVERT: E 125 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7597 (mtp85) REVERT: F 71 ASP cc_start: 0.8381 (t0) cc_final: 0.8148 (t0) REVERT: G 3 ARG cc_start: 0.8373 (mpp80) cc_final: 0.7035 (mmm160) REVERT: G 209 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: H -22 ASN cc_start: 0.8913 (t0) cc_final: 0.7178 (t0) REVERT: H -18 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8366 (mp0) REVERT: H -3 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8877 (mtmm) REVERT: H 12 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.9312 (mm) REVERT: H 146 MET cc_start: 0.6701 (mmp) cc_final: 0.6352 (tpp) REVERT: H 215 LYS cc_start: 0.9040 (pptt) cc_final: 0.8576 (pptt) REVERT: I 80 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8387 (ptt-90) REVERT: I 83 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: I 90 MET cc_start: 0.9324 (mtp) cc_final: 0.9065 (mtm) REVERT: I 131 MET cc_start: 0.8752 (tmm) cc_final: 0.8550 (tpp) REVERT: I 189 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8465 (pp) REVERT: I 198 ARG cc_start: 0.8332 (mtm180) cc_final: 0.8104 (mtm-85) REVERT: J 37 LYS cc_start: 0.8980 (ptmm) cc_final: 0.8547 (tttm) REVERT: J 65 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8842 (tm-30) REVERT: J 74 GLU cc_start: 0.8652 (pm20) cc_final: 0.8400 (mt-10) REVERT: J 86 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8067 (ttm170) REVERT: J 90 ASP cc_start: 0.9434 (t0) cc_final: 0.8968 (t0) REVERT: J 93 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8240 (mtm-85) REVERT: c 8 GLU cc_start: 0.8604 (tp30) cc_final: 0.8347 (tp30) REVERT: c 36 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8098 (tm-30) REVERT: c 40 GLN cc_start: 0.8680 (mm110) cc_final: 0.8394 (mm110) REVERT: c 143 GLU cc_start: 0.8905 (pm20) cc_final: 0.8481 (pt0) REVERT: c 146 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: c 148 GLN cc_start: 0.8766 (mt0) cc_final: 0.8405 (mt0) REVERT: d 229 GLN cc_start: 0.9375 (mt0) cc_final: 0.9009 (mp10) REVERT: e 49 GLU cc_start: 0.9179 (tp30) cc_final: 0.8940 (tp30) REVERT: e 66 THR cc_start: 0.9253 (m) cc_final: 0.8988 (t) REVERT: e 129 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8591 (tm-30) outliers start: 93 outliers final: 31 residues processed: 476 average time/residue: 1.5675 time to fit residues: 852.9500 Evaluate side-chains 432 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 390 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 68 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 251 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 276 optimal weight: 0.0980 chunk 115 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 187 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 220 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN D 214 ASN E 86 ASN G 33 ASN G 53 GLN J 61 GLN J 65 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN e 63 ASN e 87 GLN e 90 GLN e 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.069330 restraints weight = 57984.801| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.01 r_work: 0.2939 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22085 Z= 0.119 Angle : 0.579 10.521 29931 Z= 0.295 Chirality : 0.041 0.159 3472 Planarity : 0.004 0.053 3821 Dihedral : 4.226 23.149 3075 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 3.79 % Allowed : 23.30 % Favored : 72.90 % 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: 0.60 (0.16), residues: 2808 helix: 2.25 (0.15), residues: 1124 sheet: -0.78 (0.20), residues: 610 loop : -0.85 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 189 HIS 0.005 0.001 HIS C 154 PHE 0.014 0.001 PHE I 39 TYR 0.029 0.001 TYR C 153 ARG 0.008 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1201) hydrogen bonds : angle 4.77505 ( 3474) SS BOND : bond 0.00535 ( 1) SS BOND : angle 2.83271 ( 2) covalent geometry : bond 0.00270 (22084) covalent geometry : angle 0.57831 (29929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 425 time to evaluate : 4.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8495 (t) REVERT: A 103 GLU cc_start: 0.8835 (tp30) cc_final: 0.8424 (tt0) REVERT: A 212 ILE cc_start: 0.9454 (pt) cc_final: 0.9203 (pp) REVERT: A 233 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8673 (mm) REVERT: B 174 MET cc_start: 0.8992 (ttm) cc_final: 0.8668 (ttm) REVERT: B 178 ASP cc_start: 0.8700 (m-30) cc_final: 0.8462 (m-30) REVERT: C 16 LEU cc_start: 0.8722 (mp) cc_final: 0.8431 (mm) REVERT: C 20 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: C 39 ASP cc_start: 0.8699 (m-30) cc_final: 0.8410 (m-30) REVERT: C 178 ASP cc_start: 0.8347 (p0) cc_final: 0.7890 (t0) REVERT: D 7 GLU cc_start: 0.8088 (tp30) cc_final: 0.7625 (tp30) REVERT: D 10 ARG cc_start: 0.8573 (mmt180) cc_final: 0.8273 (mmt90) REVERT: D 178 GLN cc_start: 0.8088 (tp40) cc_final: 0.7768 (tp-100) REVERT: D 182 GLN cc_start: 0.8839 (pp30) cc_final: 0.8585 (pp30) REVERT: E 72 ILE cc_start: 0.9398 (pt) cc_final: 0.9085 (pp) REVERT: E 125 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7547 (mtp85) REVERT: F 151 MET cc_start: 0.8546 (tmt) cc_final: 0.8155 (tmt) REVERT: F 203 ASP cc_start: 0.7875 (t0) cc_final: 0.7494 (t0) REVERT: G 3 ARG cc_start: 0.8431 (mpp80) cc_final: 0.7069 (mmm160) REVERT: G 123 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9161 (tm-30) REVERT: G 209 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: H -39 SER cc_start: 0.5772 (OUTLIER) cc_final: 0.5076 (p) REVERT: H -22 ASN cc_start: 0.8872 (t0) cc_final: 0.7192 (t0) REVERT: H -18 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8251 (mp0) REVERT: H -3 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8944 (mtmm) REVERT: H 12 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9326 (mm) REVERT: H 146 MET cc_start: 0.6594 (mmp) cc_final: 0.6298 (tpp) REVERT: H 215 LYS cc_start: 0.8933 (pptt) cc_final: 0.8470 (pptt) REVERT: I 78 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8445 (tt0) REVERT: I 80 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7829 (ptt-90) REVERT: I 90 MET cc_start: 0.9353 (mtp) cc_final: 0.9112 (mtm) REVERT: I 131 MET cc_start: 0.8679 (tmm) cc_final: 0.8478 (tpp) REVERT: I 146 MET cc_start: 0.7308 (mmt) cc_final: 0.7067 (ttm) REVERT: I 198 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8210 (mtm-85) REVERT: J 37 LYS cc_start: 0.8992 (ptmm) cc_final: 0.8625 (tttm) REVERT: J 65 GLN cc_start: 0.9153 (tp40) cc_final: 0.8866 (tm-30) REVERT: J 74 GLU cc_start: 0.8624 (pm20) cc_final: 0.8332 (mt-10) REVERT: J 86 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8058 (ttm170) REVERT: J 142 ILE cc_start: 0.8717 (mp) cc_final: 0.8203 (tt) REVERT: c 8 GLU cc_start: 0.8506 (tp30) cc_final: 0.8205 (tp30) REVERT: c 36 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8098 (tm-30) REVERT: c 40 GLN cc_start: 0.8753 (mm110) cc_final: 0.8453 (mm110) REVERT: c 143 GLU cc_start: 0.8904 (pm20) cc_final: 0.8675 (pt0) REVERT: c 148 GLN cc_start: 0.8692 (mt0) cc_final: 0.8393 (mt0) REVERT: c 170 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8152 (mmt-90) REVERT: d 32 MET cc_start: 0.9212 (mmm) cc_final: 0.8881 (mmm) REVERT: d 229 GLN cc_start: 0.9344 (mt0) cc_final: 0.8973 (mp10) REVERT: e 49 GLU cc_start: 0.9151 (tp30) cc_final: 0.8894 (tp30) REVERT: e 56 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7105 (tm-30) REVERT: e 60 ASP cc_start: 0.9093 (m-30) cc_final: 0.8548 (m-30) REVERT: e 66 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8955 (t) REVERT: e 106 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8604 (mtt-85) REVERT: e 129 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8601 (tm-30) outliers start: 85 outliers final: 32 residues processed: 471 average time/residue: 1.5557 time to fit residues: 837.6350 Evaluate side-chains 427 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 386 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 6.9990 chunk 251 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 220 ASN D 97 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN J 61 GLN e 63 ASN e 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066974 restraints weight = 58561.737| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.03 r_work: 0.2894 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22085 Z= 0.160 Angle : 0.611 11.366 29931 Z= 0.313 Chirality : 0.042 0.230 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.296 26.605 3075 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 3.48 % Allowed : 24.29 % Favored : 72.23 % 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: 0.64 (0.16), residues: 2808 helix: 2.24 (0.15), residues: 1124 sheet: -0.75 (0.20), residues: 622 loop : -0.78 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.006 0.001 HIS C 154 PHE 0.020 0.001 PHE J 36 TYR 0.031 0.002 TYR C 153 ARG 0.008 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1201) hydrogen bonds : angle 4.82038 ( 3474) SS BOND : bond 0.00989 ( 1) SS BOND : angle 6.43534 ( 2) covalent geometry : bond 0.00375 (22084) covalent geometry : angle 0.60901 (29929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8787 (tp30) cc_final: 0.8386 (tt0) REVERT: A 212 ILE cc_start: 0.9470 (pt) cc_final: 0.9227 (pp) REVERT: A 233 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8704 (mm) REVERT: C 120 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: C 178 ASP cc_start: 0.8414 (p0) cc_final: 0.7933 (t0) REVERT: D 7 GLU cc_start: 0.8111 (tp30) cc_final: 0.7661 (tp30) REVERT: D 10 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8323 (mmt90) REVERT: D 107 MET cc_start: 0.8491 (tpt) cc_final: 0.8139 (mmt) REVERT: D 178 GLN cc_start: 0.8221 (tp40) cc_final: 0.7912 (tp-100) REVERT: D 182 GLN cc_start: 0.8872 (pp30) cc_final: 0.8575 (pp30) REVERT: E 27 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8767 (mm-30) REVERT: E 72 ILE cc_start: 0.9389 (pt) cc_final: 0.9115 (pp) REVERT: E 125 ARG cc_start: 0.8044 (mmt180) cc_final: 0.7498 (mtp85) REVERT: F 203 ASP cc_start: 0.7941 (t0) cc_final: 0.7550 (t0) REVERT: G 3 ARG cc_start: 0.8452 (mpp80) cc_final: 0.7147 (mmm160) REVERT: G 209 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8539 (m-30) REVERT: H -39 SER cc_start: 0.5821 (OUTLIER) cc_final: 0.5113 (p) REVERT: H -22 ASN cc_start: 0.8923 (t0) cc_final: 0.7206 (t0) REVERT: H -18 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8284 (mp0) REVERT: H -3 LYS cc_start: 0.9333 (mtpt) cc_final: 0.9041 (mtmm) REVERT: H 146 MET cc_start: 0.6734 (mmp) cc_final: 0.6382 (tpp) REVERT: H 215 LYS cc_start: 0.8955 (pptt) cc_final: 0.8493 (pptt) REVERT: I 75 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8807 (mm-30) REVERT: I 78 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8696 (mt-10) REVERT: I 80 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8082 (ptt-90) REVERT: I 146 MET cc_start: 0.7261 (mmt) cc_final: 0.7006 (ttp) REVERT: I 198 ARG cc_start: 0.8475 (mtm180) cc_final: 0.8176 (mtm-85) REVERT: J 37 LYS cc_start: 0.9081 (ptmm) cc_final: 0.8756 (tttm) REVERT: J 65 GLN cc_start: 0.9165 (tp40) cc_final: 0.8939 (tm-30) REVERT: J 86 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8163 (ttm170) REVERT: J 142 ILE cc_start: 0.8696 (mp) cc_final: 0.8250 (tt) REVERT: c 8 GLU cc_start: 0.8655 (tp30) cc_final: 0.8332 (tp30) REVERT: c 36 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8170 (tm-30) REVERT: c 52 ARG cc_start: 0.6918 (tpp80) cc_final: 0.6580 (tpp80) REVERT: c 143 GLU cc_start: 0.8910 (pm20) cc_final: 0.8684 (pt0) REVERT: c 146 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7675 (mm110) REVERT: c 170 ARG cc_start: 0.8395 (mmt-90) cc_final: 0.8175 (mmt-90) REVERT: d 229 GLN cc_start: 0.9359 (mt0) cc_final: 0.8953 (mp10) REVERT: e 49 GLU cc_start: 0.9167 (tp30) cc_final: 0.8954 (tp30) REVERT: e 56 GLN cc_start: 0.8246 (mm-40) cc_final: 0.6790 (tm-30) REVERT: e 66 THR cc_start: 0.9309 (m) cc_final: 0.9035 (t) REVERT: e 106 ARG cc_start: 0.8917 (ttm-80) cc_final: 0.8614 (mtt-85) REVERT: e 129 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8592 (tm-30) outliers start: 78 outliers final: 35 residues processed: 447 average time/residue: 1.3083 time to fit residues: 671.2226 Evaluate side-chains 423 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 381 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 238 ASP Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 250 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 102 GLN B 220 ASN D 97 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN c 40 GLN c 148 GLN c 195 GLN e 63 ASN e 87 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.065883 restraints weight = 58568.822| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.00 r_work: 0.2877 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22085 Z= 0.173 Angle : 0.628 12.212 29931 Z= 0.323 Chirality : 0.043 0.181 3472 Planarity : 0.004 0.057 3821 Dihedral : 4.391 25.807 3075 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 2.99 % Allowed : 24.87 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2808 helix: 2.19 (0.15), residues: 1125 sheet: -0.70 (0.20), residues: 621 loop : -0.71 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 189 HIS 0.007 0.001 HIS C 154 PHE 0.021 0.001 PHE c 71 TYR 0.033 0.002 TYR C 153 ARG 0.015 0.001 ARG J 93 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 1201) hydrogen bonds : angle 4.83676 ( 3474) SS BOND : bond 0.00860 ( 1) SS BOND : angle 4.82988 ( 2) covalent geometry : bond 0.00402 (22084) covalent geometry : angle 0.62705 (29929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 396 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8829 (tp30) cc_final: 0.8398 (tt0) REVERT: A 212 ILE cc_start: 0.9454 (pt) cc_final: 0.9212 (pp) REVERT: A 233 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8734 (mm) REVERT: C 8 THR cc_start: 0.9110 (m) cc_final: 0.8847 (p) REVERT: C 20 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8630 (mp0) REVERT: C 39 ASP cc_start: 0.8758 (m-30) cc_final: 0.8487 (m-30) REVERT: C 175 ASN cc_start: 0.9183 (m-40) cc_final: 0.8951 (m-40) REVERT: C 178 ASP cc_start: 0.8393 (p0) cc_final: 0.7965 (OUTLIER) REVERT: D 7 GLU cc_start: 0.8125 (tp30) cc_final: 0.7757 (tp30) REVERT: D 10 ARG cc_start: 0.8594 (mmt180) cc_final: 0.8356 (mmt90) REVERT: D 53 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8734 (mpp80) REVERT: D 178 GLN cc_start: 0.8279 (tp40) cc_final: 0.7964 (tp-100) REVERT: E 27 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8794 (mm-30) REVERT: E 72 ILE cc_start: 0.9402 (pt) cc_final: 0.9116 (pp) REVERT: E 125 ARG cc_start: 0.8032 (mmt180) cc_final: 0.7462 (mtp85) REVERT: F 153 ASP cc_start: 0.8697 (m-30) cc_final: 0.8430 (m-30) REVERT: F 203 ASP cc_start: 0.7969 (t0) cc_final: 0.7571 (t0) REVERT: G 3 ARG cc_start: 0.8436 (mpp80) cc_final: 0.7155 (mmm160) REVERT: G 209 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: H -39 SER cc_start: 0.5887 (OUTLIER) cc_final: 0.5232 (p) REVERT: H -22 ASN cc_start: 0.8925 (t0) cc_final: 0.7332 (t0) REVERT: H -18 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8267 (mp0) REVERT: H -3 LYS cc_start: 0.9345 (mtpt) cc_final: 0.9071 (mtmm) REVERT: H 146 MET cc_start: 0.6825 (mmp) cc_final: 0.6455 (tpp) REVERT: H 147 GLU cc_start: 0.7273 (pm20) cc_final: 0.6862 (pm20) REVERT: H 149 GLU cc_start: 0.8778 (pm20) cc_final: 0.8528 (pm20) REVERT: I 80 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8299 (ptt-90) REVERT: I 81 GLN cc_start: 0.9166 (mt0) cc_final: 0.8710 (mp10) REVERT: I 146 MET cc_start: 0.7349 (mmt) cc_final: 0.6834 (mmt) REVERT: I 189 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8482 (pp) REVERT: I 198 ARG cc_start: 0.8475 (mtm180) cc_final: 0.8252 (mtm-85) REVERT: J 37 LYS cc_start: 0.9024 (ptmm) cc_final: 0.8637 (tttm) REVERT: J 38 MET cc_start: 0.8775 (tpp) cc_final: 0.8423 (mmm) REVERT: J 61 GLN cc_start: 0.9350 (tt0) cc_final: 0.9018 (tt0) REVERT: J 65 GLN cc_start: 0.9152 (tp40) cc_final: 0.8877 (tm-30) REVERT: J 142 ILE cc_start: 0.8698 (mp) cc_final: 0.8257 (tt) REVERT: c 8 GLU cc_start: 0.8643 (tp30) cc_final: 0.8286 (tp30) REVERT: c 40 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8339 (mt0) REVERT: c 146 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7718 (mm110) REVERT: d 229 GLN cc_start: 0.9381 (mt0) cc_final: 0.8983 (mp10) REVERT: e 49 GLU cc_start: 0.9179 (tp30) cc_final: 0.8928 (tp30) REVERT: e 56 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7216 (tm-30) REVERT: e 66 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9051 (t) REVERT: e 106 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8542 (mtt-85) REVERT: e 129 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8603 (tm-30) outliers start: 67 outliers final: 32 residues processed: 432 average time/residue: 1.3553 time to fit residues: 666.0291 Evaluate side-chains 415 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 376 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 4.9990 chunk 265 optimal weight: 0.0970 chunk 161 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 220 ASN D 97 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN J 63 ASN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066144 restraints weight = 58345.041| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.04 r_work: 0.2875 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22085 Z= 0.142 Angle : 0.632 11.416 29931 Z= 0.322 Chirality : 0.042 0.280 3472 Planarity : 0.004 0.057 3821 Dihedral : 4.355 23.525 3075 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 2.46 % Allowed : 25.58 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2808 helix: 2.20 (0.15), residues: 1125 sheet: -0.68 (0.20), residues: 623 loop : -0.68 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 100 HIS 0.009 0.001 HIS C 154 PHE 0.025 0.001 PHE c 71 TYR 0.035 0.001 TYR A 83 ARG 0.013 0.000 ARG J 93 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1201) hydrogen bonds : angle 4.79213 ( 3474) SS BOND : bond 0.00807 ( 1) SS BOND : angle 3.69240 ( 2) covalent geometry : bond 0.00330 (22084) covalent geometry : angle 0.63137 (29929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 399 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8839 (tp30) cc_final: 0.8395 (tt0) REVERT: A 212 ILE cc_start: 0.9442 (pt) cc_final: 0.9182 (pp) REVERT: A 233 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8731 (mm) REVERT: B 41 ASP cc_start: 0.8878 (m-30) cc_final: 0.8561 (p0) REVERT: C 8 THR cc_start: 0.9112 (m) cc_final: 0.8856 (p) REVERT: C 20 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: C 39 ASP cc_start: 0.8805 (m-30) cc_final: 0.8507 (m-30) REVERT: C 175 ASN cc_start: 0.9171 (m-40) cc_final: 0.8928 (m-40) REVERT: C 178 ASP cc_start: 0.8429 (p0) cc_final: 0.8008 (OUTLIER) REVERT: D 7 GLU cc_start: 0.8121 (tp30) cc_final: 0.7771 (tp30) REVERT: D 10 ARG cc_start: 0.8567 (mmt180) cc_final: 0.8359 (mmt90) REVERT: D 53 ARG cc_start: 0.9113 (mmm-85) cc_final: 0.8820 (mpp80) REVERT: D 182 GLN cc_start: 0.8856 (pp30) cc_final: 0.8568 (pp30) REVERT: E 8 ASN cc_start: 0.9229 (p0) cc_final: 0.8809 (m-40) REVERT: E 27 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8754 (mm-30) REVERT: E 72 ILE cc_start: 0.9403 (pt) cc_final: 0.9098 (pp) REVERT: E 125 ARG cc_start: 0.7983 (mmt180) cc_final: 0.7369 (mtp85) REVERT: F 151 MET cc_start: 0.8702 (tmt) cc_final: 0.8331 (tmt) REVERT: F 153 ASP cc_start: 0.8727 (m-30) cc_final: 0.8385 (m-30) REVERT: F 203 ASP cc_start: 0.7935 (t0) cc_final: 0.7547 (t0) REVERT: G 3 ARG cc_start: 0.8431 (mpp80) cc_final: 0.7113 (mmm160) REVERT: G 209 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: H -39 SER cc_start: 0.5894 (OUTLIER) cc_final: 0.5254 (p) REVERT: H -27 ASP cc_start: 0.8962 (p0) cc_final: 0.8664 (p0) REVERT: H -22 ASN cc_start: 0.8887 (t0) cc_final: 0.7209 (t0) REVERT: H -18 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8251 (mp0) REVERT: H -3 LYS cc_start: 0.9368 (mtpt) cc_final: 0.9085 (mtmm) REVERT: H 85 GLN cc_start: 0.9199 (mt0) cc_final: 0.8915 (mm-40) REVERT: H 147 GLU cc_start: 0.7207 (pm20) cc_final: 0.6977 (pm20) REVERT: H 149 GLU cc_start: 0.8772 (pm20) cc_final: 0.8539 (pm20) REVERT: H 215 LYS cc_start: 0.8814 (pttp) cc_final: 0.8438 (pptt) REVERT: I 80 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8462 (ptt-90) REVERT: I 81 GLN cc_start: 0.9177 (mt0) cc_final: 0.8435 (mp10) REVERT: I 146 MET cc_start: 0.7471 (mmt) cc_final: 0.6881 (mmt) REVERT: I 189 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8430 (pp) REVERT: J 37 LYS cc_start: 0.8959 (ptmm) cc_final: 0.8466 (tttm) REVERT: J 65 GLN cc_start: 0.9136 (tp40) cc_final: 0.8908 (tm-30) REVERT: J 74 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8282 (mt-10) REVERT: J 93 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8461 (mtm-85) REVERT: J 142 ILE cc_start: 0.8676 (mp) cc_final: 0.8236 (tt) REVERT: c 40 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8342 (mt0) REVERT: c 146 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7577 (mm110) REVERT: c 240 MET cc_start: 0.8634 (mtp) cc_final: 0.8179 (mmm) REVERT: d 229 GLN cc_start: 0.9373 (mt0) cc_final: 0.8955 (mp10) REVERT: e 49 GLU cc_start: 0.9184 (tp30) cc_final: 0.8938 (tp30) REVERT: e 56 GLN cc_start: 0.8043 (mm-40) cc_final: 0.6973 (tm-30) REVERT: e 66 THR cc_start: 0.9267 (m) cc_final: 0.8974 (t) REVERT: e 106 ARG cc_start: 0.8922 (ttm-80) cc_final: 0.8501 (mtt-85) REVERT: e 129 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8540 (tm-30) REVERT: e 136 TYR cc_start: 0.9470 (t80) cc_final: 0.9146 (t80) outliers start: 55 outliers final: 33 residues processed: 429 average time/residue: 1.3411 time to fit residues: 655.9287 Evaluate side-chains 409 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 370 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -24 ARG Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 142 CYS Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 85 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 148 GLN B 220 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN I 40 GLN J 61 GLN c 195 GLN e 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.079153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.065634 restraints weight = 58691.372| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.04 r_work: 0.2867 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22085 Z= 0.161 Angle : 0.656 14.254 29931 Z= 0.334 Chirality : 0.043 0.287 3472 Planarity : 0.004 0.057 3821 Dihedral : 4.404 28.536 3075 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 26.88 % Favored : 71.12 % 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: 0.65 (0.16), residues: 2808 helix: 2.12 (0.15), residues: 1137 sheet: -0.69 (0.20), residues: 627 loop : -0.69 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 100 HIS 0.009 0.001 HIS C 154 PHE 0.030 0.001 PHE c 71 TYR 0.041 0.002 TYR A 83 ARG 0.012 0.001 ARG J 93 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1201) hydrogen bonds : angle 4.80703 ( 3474) SS BOND : bond 0.00744 ( 1) SS BOND : angle 7.53118 ( 2) covalent geometry : bond 0.00377 (22084) covalent geometry : angle 0.65269 (29929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5616 Ramachandran restraints generated. 2808 Oldfield, 0 Emsley, 2808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 386 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8845 (tp30) cc_final: 0.8420 (tt0) REVERT: A 212 ILE cc_start: 0.9442 (pt) cc_final: 0.9186 (pp) REVERT: A 233 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8748 (mm) REVERT: B 41 ASP cc_start: 0.8853 (m-30) cc_final: 0.8552 (p0) REVERT: C 8 THR cc_start: 0.9120 (m) cc_final: 0.8858 (p) REVERT: C 20 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: C 39 ASP cc_start: 0.8817 (m-30) cc_final: 0.8519 (m-30) REVERT: C 120 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7995 (mm-40) REVERT: C 175 ASN cc_start: 0.9174 (m-40) cc_final: 0.8939 (m-40) REVERT: C 178 ASP cc_start: 0.8439 (p0) cc_final: 0.8077 (t0) REVERT: D 7 GLU cc_start: 0.8150 (tp30) cc_final: 0.7704 (tp30) REVERT: D 10 ARG cc_start: 0.8575 (mmt180) cc_final: 0.8348 (mmt90) REVERT: D 53 ARG cc_start: 0.9112 (mmm-85) cc_final: 0.8840 (mpp80) REVERT: D 114 GLN cc_start: 0.8892 (tt0) cc_final: 0.8126 (tm-30) REVERT: D 182 GLN cc_start: 0.8849 (pp30) cc_final: 0.8573 (pp30) REVERT: E 8 ASN cc_start: 0.9240 (p0) cc_final: 0.8828 (m110) REVERT: E 27 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8781 (mm-30) REVERT: E 72 ILE cc_start: 0.9406 (pt) cc_final: 0.9097 (pp) REVERT: E 125 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7389 (mtp85) REVERT: F 153 ASP cc_start: 0.8749 (m-30) cc_final: 0.8469 (m-30) REVERT: F 203 ASP cc_start: 0.7987 (t0) cc_final: 0.7575 (t0) REVERT: G 3 ARG cc_start: 0.8402 (mpp80) cc_final: 0.7081 (mmm160) REVERT: G 112 ASP cc_start: 0.9017 (p0) cc_final: 0.8671 (p0) REVERT: G 209 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8694 (m-30) REVERT: H -39 SER cc_start: 0.5949 (OUTLIER) cc_final: 0.5283 (p) REVERT: H -27 ASP cc_start: 0.8972 (p0) cc_final: 0.8666 (p0) REVERT: H -22 ASN cc_start: 0.8872 (t0) cc_final: 0.7466 (m-40) REVERT: H -18 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8348 (mp0) REVERT: H -3 LYS cc_start: 0.9363 (mtpt) cc_final: 0.9071 (mtmt) REVERT: H 85 GLN cc_start: 0.9197 (mt0) cc_final: 0.8895 (mm-40) REVERT: H 147 GLU cc_start: 0.7297 (pm20) cc_final: 0.7011 (pm20) REVERT: H 149 GLU cc_start: 0.8790 (pm20) cc_final: 0.8554 (pm20) REVERT: H 215 LYS cc_start: 0.8404 (pttp) cc_final: 0.8119 (pptt) REVERT: I 80 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8426 (ptt-90) REVERT: I 81 GLN cc_start: 0.9192 (mt0) cc_final: 0.8548 (mp10) REVERT: I 104 TYR cc_start: 0.8148 (m-80) cc_final: 0.7671 (m-80) REVERT: I 113 ASP cc_start: 0.8602 (t0) cc_final: 0.8344 (p0) REVERT: I 189 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8426 (pp) REVERT: I 191 GLU cc_start: 0.8922 (tp30) cc_final: 0.8679 (tp30) REVERT: J 37 LYS cc_start: 0.8942 (ptmm) cc_final: 0.8266 (tttm) REVERT: J 65 GLN cc_start: 0.9168 (tp40) cc_final: 0.8882 (tm-30) REVERT: J 74 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8402 (mt-10) REVERT: J 93 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8401 (mtm-85) REVERT: c 40 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8310 (mt0) REVERT: c 146 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7535 (mm110) REVERT: c 240 MET cc_start: 0.8636 (mtp) cc_final: 0.8157 (mmm) REVERT: d 229 GLN cc_start: 0.9381 (mt0) cc_final: 0.8958 (mp10) REVERT: e 49 GLU cc_start: 0.9184 (tp30) cc_final: 0.8948 (tp30) REVERT: e 56 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7064 (tm-30) REVERT: e 60 ASP cc_start: 0.9036 (m-30) cc_final: 0.8414 (m-30) REVERT: e 66 THR cc_start: 0.9256 (m) cc_final: 0.8998 (t) REVERT: e 106 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8510 (mtt-85) REVERT: e 129 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8417 (tm-30) REVERT: e 136 TYR cc_start: 0.9465 (t80) cc_final: 0.9202 (t80) outliers start: 45 outliers final: 31 residues processed: 413 average time/residue: 1.3169 time to fit residues: 625.1547 Evaluate side-chains 411 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 123 TYR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain c residue 49 LEU Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 146 GLN Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 169 ASN B 220 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 ASN c 268 GLN e 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066217 restraints weight = 58262.694| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.04 r_work: 0.2880 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22085 Z= 0.143 Angle : 0.646 13.230 29931 Z= 0.331 Chirality : 0.042 0.261 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.410 34.033 3075 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 2.05 % Allowed : 27.01 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2808 helix: 2.09 (0.15), residues: 1136 sheet: -0.62 (0.20), residues: 628 loop : -0.66 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 105 HIS 0.009 0.001 HIS C 154 PHE 0.028 0.001 PHE c 71 TYR 0.040 0.001 TYR A 83 ARG 0.013 0.000 ARG J 181 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 1201) hydrogen bonds : angle 4.81507 ( 3474) SS BOND : bond 0.02051 ( 1) SS BOND : angle 6.63778 ( 2) covalent geometry : bond 0.00332 (22084) covalent geometry : angle 0.64324 (29929) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14892.58 seconds wall clock time: 259 minutes 44.52 seconds (15584.52 seconds total)