Starting phenix.real_space_refine on Wed Nov 20 13:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm5_41379/11_2024/8tm5_41379.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm5_41379/11_2024/8tm5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm5_41379/11_2024/8tm5_41379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm5_41379/11_2024/8tm5_41379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm5_41379/11_2024/8tm5_41379.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm5_41379/11_2024/8tm5_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-5513/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: 12.80, per 1000 atoms: 0.59 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: 5.57 Conformation dependent library (CDL) restraints added in 2.7 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: 2.60 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: 6.28 Time building geometry restraints manager: 6.40 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 46.400 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.010 ------------------------------------------------------------------------------- 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 22084 Z= 0.218 Angle : 0.612 16.106 29929 Z= 0.362 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 *********************** 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 : 2.729 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: 1.2631 time to fit residues: 714.7064 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 : 2.261 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 22084 Z= 0.222 Angle : 0.606 7.606 29929 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 *********************** 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 : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 57 TYR cc_start: 0.7686 (m-80) cc_final: 0.7465 (m-80) REVERT: A 150 ASP cc_start: 0.8458 (m-30) cc_final: 0.8215 (m-30) REVERT: A 233 ILE cc_start: 0.8798 (mm) cc_final: 0.8556 (mm) REVERT: B 41 ASP cc_start: 0.8193 (m-30) cc_final: 0.7941 (m-30) REVERT: C 16 LEU cc_start: 0.8715 (mp) cc_final: 0.8390 (mt) REVERT: C 20 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: C 23 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8492 (mm-40) REVERT: C 39 ASP cc_start: 0.8433 (m-30) cc_final: 0.8209 (m-30) REVERT: D 91 LYS cc_start: 0.8792 (tptp) cc_final: 0.8555 (tptp) REVERT: D 104 ASN cc_start: 0.7662 (m-40) cc_final: 0.7333 (m110) REVERT: D 114 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: D 191 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6595 (mt) REVERT: E 72 ILE cc_start: 0.9379 (pt) cc_final: 0.9147 (pp) REVERT: E 125 ARG cc_start: 0.7343 (mmt180) cc_final: 0.7021 (mtp85) REVERT: F 68 PHE cc_start: 0.8119 (m-80) cc_final: 0.7893 (m-80) REVERT: G 3 ARG cc_start: 0.8071 (mpp80) cc_final: 0.7077 (mmp-170) REVERT: G 83 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7704 (mtt) REVERT: H -22 ASN cc_start: 0.8862 (t0) cc_final: 0.6767 (t0) REVERT: H 215 LYS cc_start: 0.8993 (pptt) cc_final: 0.8753 (pptt) REVERT: I 75 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8380 (mt-10) REVERT: I 78 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8427 (mt-10) REVERT: I 80 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8215 (ptt-90) REVERT: I 90 MET cc_start: 0.8961 (mtp) cc_final: 0.8690 (mtm) REVERT: I 106 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8370 (mt-10) REVERT: I 189 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8524 (pp) REVERT: J 53 THR cc_start: 0.8948 (p) cc_final: 0.8719 (p) REVERT: e 49 GLU cc_start: 0.8785 (tp30) cc_final: 0.8489 (tp30) REVERT: e 56 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7894 (tm-30) REVERT: e 58 ASN cc_start: 0.9185 (m-40) cc_final: 0.8897 (m-40) REVERT: e 60 ASP cc_start: 0.8620 (m-30) cc_final: 0.7746 (m-30) REVERT: e 106 ARG cc_start: 0.8726 (ttm-80) cc_final: 0.8422 (mtt-85) REVERT: e 110 GLU cc_start: 0.7601 (pp20) cc_final: 0.7246 (pt0) REVERT: e 137 LYS cc_start: 0.9360 (tttm) cc_final: 0.9073 (ttmt) outliers start: 60 outliers final: 21 residues processed: 477 average time/residue: 1.2777 time to fit residues: 696.7939 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 : 2.744 ------------------------------------------------------------------------------- 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 140 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 D 23 GLN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H -22 ASN H 66 HIS J 61 GLN J 65 GLN J 189 HIS d 29 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22084 Z= 0.288 Angle : 0.618 8.404 29929 Z= 0.324 Chirality : 0.043 0.169 3472 Planarity : 0.005 0.055 3821 Dihedral : 4.563 38.044 3077 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 3.53 % Allowed : 20.00 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2808 helix: 1.92 (0.15), residues: 1137 sheet: -1.16 (0.20), residues: 615 loop : -1.06 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 93 HIS 0.008 0.001 HIS D 155 PHE 0.019 0.002 PHE G 210 TYR 0.030 0.002 TYR H 90 ARG 0.009 0.001 ARG D 168 *********************** 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 494 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 415 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: A 79 MET cc_start: 0.8549 (mmt) cc_final: 0.8239 (mtt) REVERT: A 103 GLU cc_start: 0.8409 (tp30) cc_final: 0.8188 (tt0) REVERT: A 233 ILE cc_start: 0.8847 (mm) cc_final: 0.8645 (mm) REVERT: B 174 MET cc_start: 0.8491 (ttm) cc_final: 0.7921 (ttp) REVERT: D 114 GLN cc_start: 0.8740 (tt0) cc_final: 0.8136 (tm-30) REVERT: D 178 GLN cc_start: 0.8221 (tp40) cc_final: 0.7946 (tp-100) REVERT: E 72 ILE cc_start: 0.9343 (pt) cc_final: 0.9125 (pp) REVERT: F 151 MET cc_start: 0.8454 (tmm) cc_final: 0.8055 (tmm) REVERT: F 203 ASP cc_start: 0.7746 (t0) cc_final: 0.7462 (t0) REVERT: G 3 ARG cc_start: 0.8179 (mpp80) cc_final: 0.7120 (mmm160) REVERT: G 58 ASP cc_start: 0.7029 (p0) cc_final: 0.6612 (p0) REVERT: H -22 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: H 141 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8543 (mmmm) REVERT: I 90 MET cc_start: 0.9010 (mtp) cc_final: 0.8730 (mtm) REVERT: I 106 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8268 (mt-10) REVERT: I 189 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8575 (pp) REVERT: c 143 GLU cc_start: 0.8468 (pm20) cc_final: 0.8226 (pm20) REVERT: d 32 MET cc_start: 0.9084 (mmm) cc_final: 0.8692 (mmm) REVERT: e 49 GLU cc_start: 0.8848 (tp30) cc_final: 0.8477 (tp30) REVERT: e 60 ASP cc_start: 0.8674 (m-30) cc_final: 0.8257 (m-30) REVERT: e 66 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9040 (t) REVERT: e 106 ARG cc_start: 0.8841 (ttm-80) cc_final: 0.8329 (mtt-85) REVERT: e 137 LYS cc_start: 0.9483 (tttm) cc_final: 0.9237 (ttmt) outliers start: 79 outliers final: 22 residues processed: 461 average time/residue: 1.2491 time to fit residues: 661.1553 Evaluate side-chains 388 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 109 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 H residue -22 ASN 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 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 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 94 GLU Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 169 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 268 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 B 84 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 ASN J 61 GLN J 63 ASN J 65 GLN ** e 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN e 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22084 Z= 0.279 Angle : 0.601 8.938 29929 Z= 0.313 Chirality : 0.043 0.202 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.460 23.203 3075 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 3.71 % Allowed : 21.25 % Favored : 75.04 % 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: 0.33 (0.16), residues: 2808 helix: 2.06 (0.15), residues: 1130 sheet: -1.01 (0.20), residues: 627 loop : -0.99 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 189 HIS 0.005 0.001 HIS C 154 PHE 0.013 0.001 PHE J 36 TYR 0.027 0.001 TYR H 90 ARG 0.005 0.000 ARG J 93 *********************** 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 499 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 416 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8694 (mm) REVERT: C 8 THR cc_start: 0.8971 (m) cc_final: 0.8708 (p) REVERT: C 20 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: C 39 ASP cc_start: 0.8412 (m-30) cc_final: 0.8200 (m-30) REVERT: C 120 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7790 (mm-40) REVERT: C 178 ASP cc_start: 0.7916 (p0) cc_final: 0.7473 (t0) REVERT: D 178 GLN cc_start: 0.8258 (tp40) cc_final: 0.8047 (tp-100) REVERT: D 182 GLN cc_start: 0.8671 (pp30) cc_final: 0.8452 (pp30) REVERT: E 27 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8329 (mm-30) REVERT: E 72 ILE cc_start: 0.9329 (pt) cc_final: 0.9115 (pp) REVERT: F 151 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8286 (tmt) REVERT: G 3 ARG cc_start: 0.8316 (mpp80) cc_final: 0.7132 (mmm160) REVERT: H -22 ASN cc_start: 0.8715 (t0) cc_final: 0.8326 (t0) REVERT: H 146 MET cc_start: 0.7068 (mmp) cc_final: 0.6836 (mmp) REVERT: H 215 LYS cc_start: 0.8776 (pptt) cc_final: 0.8543 (pptt) REVERT: I 80 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8280 (ptt-90) REVERT: I 90 MET cc_start: 0.8969 (mtp) cc_final: 0.8732 (mtm) REVERT: I 106 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8280 (mt-10) REVERT: I 146 MET cc_start: 0.8265 (ttm) cc_final: 0.8032 (ttm) REVERT: I 189 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8630 (pp) REVERT: I 198 ARG cc_start: 0.8351 (mtm180) cc_final: 0.8095 (mtm-85) REVERT: J 37 LYS cc_start: 0.8856 (tttm) cc_final: 0.8610 (tptt) REVERT: J 69 MET cc_start: 0.8250 (ttp) cc_final: 0.8025 (ttp) REVERT: J 90 ASP cc_start: 0.9073 (t0) cc_final: 0.8651 (t0) REVERT: J 93 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.8043 (mtm-85) REVERT: c 8 GLU cc_start: 0.8429 (tp30) cc_final: 0.8151 (tp30) REVERT: c 36 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7618 (tm-30) REVERT: c 40 GLN cc_start: 0.8554 (mm110) cc_final: 0.8145 (mm110) REVERT: e 49 GLU cc_start: 0.8975 (tp30) cc_final: 0.8742 (tp30) REVERT: e 66 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9080 (t) REVERT: e 106 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8540 (mtt-85) REVERT: e 137 LYS cc_start: 0.9509 (tttm) cc_final: 0.9267 (tttt) outliers start: 83 outliers final: 28 residues processed: 459 average time/residue: 1.3757 time to fit residues: 716.1157 Evaluate side-chains 410 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 233 ILE 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 120 GLN Chi-restraints excluded: chain D residue 20 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 66 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 118 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -20 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 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 93 ILE Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 241 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 E 16 GLN G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN J 61 GLN J 65 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 GLN c 268 GLN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22084 Z= 0.213 Angle : 0.578 9.732 29929 Z= 0.299 Chirality : 0.041 0.181 3472 Planarity : 0.004 0.054 3821 Dihedral : 4.360 23.461 3075 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 3.66 % Allowed : 22.19 % Favored : 74.15 % 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: 0.50 (0.16), residues: 2808 helix: 2.20 (0.15), residues: 1123 sheet: -0.85 (0.20), residues: 601 loop : -0.95 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 189 HIS 0.006 0.001 HIS C 154 PHE 0.013 0.001 PHE J 56 TYR 0.025 0.001 TYR C 153 ARG 0.008 0.000 ARG I 99 *********************** 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 498 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 416 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8696 (mm) REVERT: B 178 ASP cc_start: 0.8338 (m-30) cc_final: 0.7649 (m-30) REVERT: C 20 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: C 120 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: C 178 ASP cc_start: 0.7877 (p0) cc_final: 0.7625 (t0) REVERT: C 219 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9053 (mm) REVERT: D 107 MET cc_start: 0.8251 (tpt) cc_final: 0.7988 (mmt) REVERT: D 178 GLN cc_start: 0.8244 (tp40) cc_final: 0.7999 (tp-100) REVERT: E 27 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8334 (mm-30) REVERT: E 72 ILE cc_start: 0.9324 (pt) cc_final: 0.9115 (pp) REVERT: E 91 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: F 151 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: F 203 ASP cc_start: 0.7767 (t0) cc_final: 0.7480 (t0) REVERT: G 3 ARG cc_start: 0.8314 (mpp80) cc_final: 0.7126 (mmm160) REVERT: H -22 ASN cc_start: 0.8776 (t0) cc_final: 0.8056 (m-40) REVERT: I 80 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8344 (ptt-90) REVERT: I 90 MET cc_start: 0.8947 (mtp) cc_final: 0.8684 (mtm) REVERT: I 106 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8254 (mt-10) REVERT: I 189 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8638 (pp) REVERT: J 37 LYS cc_start: 0.8913 (tttm) cc_final: 0.8701 (tptt) REVERT: J 90 ASP cc_start: 0.9050 (t0) cc_final: 0.8563 (t0) REVERT: J 93 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8204 (mtm-85) REVERT: J 142 ILE cc_start: 0.9030 (mp) cc_final: 0.8515 (tt) REVERT: c 8 GLU cc_start: 0.8288 (tp30) cc_final: 0.7998 (tp30) REVERT: c 36 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7741 (tm-30) REVERT: c 40 GLN cc_start: 0.8533 (mm110) cc_final: 0.8118 (mm110) REVERT: e 66 THR cc_start: 0.9365 (m) cc_final: 0.9084 (t) REVERT: e 137 LYS cc_start: 0.9494 (tttm) cc_final: 0.9241 (tttt) outliers start: 82 outliers final: 32 residues processed: 459 average time/residue: 1.3892 time to fit residues: 727.6987 Evaluate side-chains 419 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 379 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 20 GLU 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 C residue 219 ILE Chi-restraints excluded: chain D residue 20 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain E residue 91 GLU 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 118 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain H residue -39 SER 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 138 VAL 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 77 ASN Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 201 MET Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 97 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS F 23 GLN G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 148 GLN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22084 Z= 0.224 Angle : 0.590 10.332 29929 Z= 0.305 Chirality : 0.041 0.154 3472 Planarity : 0.004 0.054 3821 Dihedral : 4.353 25.322 3075 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 3.39 % Allowed : 23.26 % Favored : 73.35 % 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: 0.58 (0.16), residues: 2808 helix: 2.22 (0.15), residues: 1123 sheet: -0.78 (0.20), residues: 608 loop : -0.86 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 189 HIS 0.006 0.001 HIS I 188 PHE 0.014 0.001 PHE c 71 TYR 0.027 0.001 TYR C 153 ARG 0.008 0.000 ARG D 168 *********************** 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 475 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 399 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8686 (mm) REVERT: B 174 MET cc_start: 0.8721 (ttm) cc_final: 0.8473 (ttm) REVERT: B 178 ASP cc_start: 0.8430 (m-30) cc_final: 0.8215 (m-30) REVERT: C 8 THR cc_start: 0.9056 (m) cc_final: 0.8788 (p) REVERT: C 20 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: C 120 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7888 (mm-40) REVERT: C 178 ASP cc_start: 0.7985 (p0) cc_final: 0.7749 (OUTLIER) REVERT: D 10 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7907 (mmt90) REVERT: D 178 GLN cc_start: 0.8322 (tp40) cc_final: 0.8094 (tp-100) REVERT: D 182 GLN cc_start: 0.8573 (pp30) cc_final: 0.8267 (pp30) REVERT: E 27 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 72 ILE cc_start: 0.9306 (pt) cc_final: 0.9086 (pp) REVERT: E 91 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: F 29 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8802 (ttpt) REVERT: F 71 ASP cc_start: 0.8459 (t0) cc_final: 0.8207 (t0) REVERT: F 151 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: G 3 ARG cc_start: 0.8330 (mpp80) cc_final: 0.7158 (mmm160) REVERT: H -27 ASP cc_start: 0.8726 (p0) cc_final: 0.8524 (p0) REVERT: H -22 ASN cc_start: 0.8870 (t0) cc_final: 0.8301 (m-40) REVERT: H -18 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: I 12 MET cc_start: 0.8078 (ptp) cc_final: 0.7860 (ttm) REVERT: I 80 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8262 (ptt-90) REVERT: I 90 MET cc_start: 0.8926 (mtp) cc_final: 0.8655 (mtm) REVERT: I 189 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8576 (pp) REVERT: J 37 LYS cc_start: 0.8959 (tttm) cc_final: 0.8686 (tptt) REVERT: J 74 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7214 (mt-10) REVERT: J 86 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8015 (ttm170) REVERT: J 142 ILE cc_start: 0.8930 (mp) cc_final: 0.8490 (tt) REVERT: e 66 THR cc_start: 0.9385 (m) cc_final: 0.9104 (t) REVERT: e 137 LYS cc_start: 0.9506 (tttm) cc_final: 0.9252 (ttmt) outliers start: 76 outliers final: 35 residues processed: 438 average time/residue: 1.3231 time to fit residues: 662.5919 Evaluate side-chains 416 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 20 GLU 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 20 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain E residue 91 GLU 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 29 LYS Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain H residue -39 SER Chi-restraints excluded: chain H residue -18 GLU 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 138 VAL Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 17 SER 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 253 ILE Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 131 ASP Chi-restraints excluded: chain d residue 201 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 226 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 267 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN D 97 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 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** G 75 ASN H 85 GLN J 61 GLN J 65 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 78 ASN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 GLN e 63 ASN e 87 GLN e 88 GLN e 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22084 Z= 0.278 Angle : 0.624 11.389 29929 Z= 0.322 Chirality : 0.042 0.184 3472 Planarity : 0.004 0.057 3821 Dihedral : 4.426 24.437 3075 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 3.53 % Allowed : 23.93 % Favored : 72.54 % 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: 0.61 (0.16), residues: 2808 helix: 2.17 (0.15), residues: 1124 sheet: -0.73 (0.20), residues: 616 loop : -0.78 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 189 HIS 0.007 0.001 HIS C 154 PHE 0.018 0.001 PHE c 71 TYR 0.033 0.002 TYR C 153 ARG 0.008 0.000 ARG D 168 *********************** 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 469 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 41 ASP cc_start: 0.8462 (m-30) cc_final: 0.8127 (p0) REVERT: C 8 THR cc_start: 0.9085 (m) cc_final: 0.8808 (p) REVERT: C 20 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: C 120 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7571 (mm-40) REVERT: D 133 MET cc_start: 0.8252 (mmm) cc_final: 0.7030 (mmm) REVERT: D 182 GLN cc_start: 0.8591 (pp30) cc_final: 0.8237 (pp30) REVERT: E 27 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8389 (mm-30) REVERT: E 72 ILE cc_start: 0.9297 (pt) cc_final: 0.9063 (pp) REVERT: E 91 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: F 29 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8837 (ttpt) REVERT: F 151 MET cc_start: 0.8605 (tmm) cc_final: 0.8226 (tmm) REVERT: G 3 ARG cc_start: 0.8362 (mpp80) cc_final: 0.7210 (mmm160) REVERT: H -39 SER cc_start: 0.6003 (OUTLIER) cc_final: 0.5296 (p) REVERT: H -24 ARG cc_start: 0.8704 (ptp-110) cc_final: 0.8492 (ptm160) REVERT: H -22 ASN cc_start: 0.8866 (t0) cc_final: 0.8401 (m-40) REVERT: I 75 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8418 (mm-30) REVERT: I 80 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8251 (ptt-90) REVERT: I 90 MET cc_start: 0.9023 (mtp) cc_final: 0.8767 (mtm) REVERT: I 189 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8635 (pp) REVERT: J 12 TYR cc_start: 0.8135 (p90) cc_final: 0.7757 (p90) REVERT: J 17 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8578 (t) REVERT: J 65 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7776 (tm130) REVERT: J 74 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7362 (mt-10) REVERT: J 86 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8013 (ttm170) REVERT: c 40 GLN cc_start: 0.7940 (mm110) cc_final: 0.7645 (mm110) REVERT: d 43 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8778 (ttmt) REVERT: e 66 THR cc_start: 0.9388 (m) cc_final: 0.9104 (t) REVERT: e 137 LYS cc_start: 0.9517 (tttm) cc_final: 0.9305 (tttt) outliers start: 79 outliers final: 33 residues processed: 433 average time/residue: 1.1445 time to fit residues: 570.2344 Evaluate side-chains 398 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain C residue 20 GLU 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 C residue 178 ASP Chi-restraints excluded: chain D residue 20 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 15 ILE 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 138 VAL 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 17 SER Chi-restraints excluded: chain J residue 65 GLN 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 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 43 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 H 91 GLN J 61 GLN J 63 ASN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22084 Z= 0.208 Angle : 0.622 12.334 29929 Z= 0.321 Chirality : 0.042 0.198 3472 Planarity : 0.004 0.057 3821 Dihedral : 4.402 27.521 3075 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Rotamer: Outliers : 3.26 % Allowed : 24.69 % Favored : 72.05 % 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: 2.18 (0.15), residues: 1123 sheet: -0.71 (0.20), residues: 626 loop : -0.74 (0.19), residues: 1059 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 0.020 0.001 PHE c 71 TYR 0.031 0.001 TYR C 153 ARG 0.009 0.000 ARG D 168 *********************** 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 469 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 396 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8719 (mm) REVERT: B 61 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7973 (t80) REVERT: C 8 THR cc_start: 0.9125 (m) cc_final: 0.8841 (p) REVERT: C 20 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: C 120 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7515 (mm-40) REVERT: C 215 GLN cc_start: 0.8891 (mp10) cc_final: 0.8654 (mp10) REVERT: D 10 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8443 (mmm-85) REVERT: D 133 MET cc_start: 0.8249 (mmm) cc_final: 0.7074 (mmm) REVERT: D 182 GLN cc_start: 0.8647 (pp30) cc_final: 0.8272 (pp30) REVERT: E 27 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 72 ILE cc_start: 0.9318 (pt) cc_final: 0.9089 (pp) REVERT: E 91 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: F 29 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8804 (ttpt) REVERT: F 151 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8074 (tmm) REVERT: F 153 ASP cc_start: 0.8165 (m-30) cc_final: 0.7459 (m-30) REVERT: G 3 ARG cc_start: 0.8367 (mpp80) cc_final: 0.7180 (mmm160) REVERT: H -22 ASN cc_start: 0.8868 (t0) cc_final: 0.8378 (m-40) REVERT: H 149 GLU cc_start: 0.7967 (pm20) cc_final: 0.7622 (pm20) REVERT: I 12 MET cc_start: 0.8136 (ptp) cc_final: 0.7929 (ttm) REVERT: I 80 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8478 (ptt180) REVERT: I 90 MET cc_start: 0.9013 (mtp) cc_final: 0.8759 (mtm) REVERT: J 12 TYR cc_start: 0.8166 (p90) cc_final: 0.7710 (p90) REVERT: J 37 LYS cc_start: 0.9005 (tttp) cc_final: 0.8760 (tptt) REVERT: J 74 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7324 (mt-10) REVERT: J 86 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7993 (ttm170) REVERT: c 40 GLN cc_start: 0.7931 (mm110) cc_final: 0.7644 (mm110) REVERT: d 43 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8791 (ttmt) REVERT: e 66 THR cc_start: 0.9380 (m) cc_final: 0.9114 (t) REVERT: e 137 LYS cc_start: 0.9519 (tttm) cc_final: 0.9306 (tttt) outliers start: 73 outliers final: 32 residues processed: 438 average time/residue: 1.2120 time to fit residues: 605.9155 Evaluate side-chains 413 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 20 GLU 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 20 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 15 ILE 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 132 VAL Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 43 LYS 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 54 ASN 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 243 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 225 optimal weight: 0.0060 chunk 236 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.7916 ------------------------------------------------------------------------------- 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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 65 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 GLN e 63 ASN e 87 GLN e 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22084 Z= 0.205 Angle : 0.632 11.353 29929 Z= 0.325 Chirality : 0.042 0.264 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.371 25.922 3075 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 2.86 % Allowed : 25.67 % Favored : 71.47 % 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: 2.14 (0.15), residues: 1123 sheet: -0.66 (0.20), residues: 636 loop : -0.71 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 100 HIS 0.009 0.001 HIS C 154 PHE 0.022 0.001 PHE c 71 TYR 0.031 0.001 TYR C 153 ARG 0.009 0.000 ARG D 168 *********************** 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 455 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 391 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8736 (mm) REVERT: B 61 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7982 (t80) REVERT: C 8 THR cc_start: 0.9142 (m) cc_final: 0.8852 (p) REVERT: C 20 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: C 120 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: C 215 GLN cc_start: 0.8855 (mp10) cc_final: 0.8614 (mp10) REVERT: D 133 MET cc_start: 0.8244 (mmm) cc_final: 0.7073 (mmm) REVERT: D 182 GLN cc_start: 0.8674 (pp30) cc_final: 0.8273 (pp30) REVERT: E 27 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8298 (mm-30) REVERT: E 72 ILE cc_start: 0.9322 (pt) cc_final: 0.9082 (pp) REVERT: E 91 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: F 29 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8780 (ttpt) REVERT: F 151 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8095 (tmm) REVERT: F 153 ASP cc_start: 0.8105 (m-30) cc_final: 0.7384 (m-30) REVERT: H 146 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7262 (tpp) REVERT: I 12 MET cc_start: 0.8114 (ptp) cc_final: 0.7890 (ttm) REVERT: I 80 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8396 (ptt-90) REVERT: I 90 MET cc_start: 0.9045 (mtp) cc_final: 0.8800 (mtm) REVERT: I 189 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8662 (pp) REVERT: J 12 TYR cc_start: 0.8211 (p90) cc_final: 0.7647 (p90) REVERT: J 37 LYS cc_start: 0.8968 (tttp) cc_final: 0.8691 (tptt) REVERT: J 86 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8021 (ttm170) REVERT: J 93 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8265 (mtm-85) REVERT: c 40 GLN cc_start: 0.7954 (mm110) cc_final: 0.7641 (mm110) REVERT: d 43 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8799 (ttmt) REVERT: e 66 THR cc_start: 0.9384 (m) cc_final: 0.9108 (t) outliers start: 64 outliers final: 35 residues processed: 428 average time/residue: 1.2594 time to fit residues: 620.7325 Evaluate side-chains 416 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 369 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 20 GLU 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 36 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain H residue -20 VAL Chi-restraints excluded: chain H residue -5 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 146 MET 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 86 ARG Chi-restraints excluded: chain J residue 94 SER 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 132 VAL Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 41 MET Chi-restraints excluded: chain d residue 43 LYS 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 163 optimal weight: 0.0470 chunk 264 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 276 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 170 optimal weight: 0.0980 chunk 135 optimal weight: 2.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN J 61 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 148 GLN e 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22084 Z= 0.204 Angle : 0.645 14.253 29929 Z= 0.332 Chirality : 0.042 0.238 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.372 24.780 3075 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 2.46 % Allowed : 26.43 % 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: 2.11 (0.15), residues: 1128 sheet: -0.59 (0.20), residues: 631 loop : -0.72 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 189 HIS 0.009 0.001 HIS C 154 PHE 0.027 0.001 PHE c 71 TYR 0.033 0.001 TYR C 153 ARG 0.010 0.000 ARG D 168 ********************** 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 438 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 383 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8720 (mm) REVERT: B 61 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7975 (t80) REVERT: C 8 THR cc_start: 0.9147 (m) cc_final: 0.8858 (p) REVERT: C 20 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: C 120 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7494 (mm-40) REVERT: C 215 GLN cc_start: 0.8831 (mp10) cc_final: 0.8591 (mp10) REVERT: D 114 GLN cc_start: 0.8671 (tt0) cc_final: 0.8137 (tm-30) REVERT: D 133 MET cc_start: 0.8239 (mmm) cc_final: 0.7065 (mmm) REVERT: D 182 GLN cc_start: 0.8672 (pp30) cc_final: 0.8264 (pp30) REVERT: E 27 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8343 (mp0) REVERT: E 72 ILE cc_start: 0.9308 (pt) cc_final: 0.9091 (pp) REVERT: E 91 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: F 29 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8774 (ttpt) REVERT: F 151 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8261 (tmt) REVERT: F 153 ASP cc_start: 0.8080 (m-30) cc_final: 0.7616 (m-30) REVERT: G 3 ARG cc_start: 0.8308 (mpp80) cc_final: 0.7057 (mmm160) REVERT: G 123 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8978 (tm-30) REVERT: H -39 SER cc_start: 0.6147 (OUTLIER) cc_final: 0.5459 (p) REVERT: I 12 MET cc_start: 0.8142 (ptp) cc_final: 0.7869 (ttm) REVERT: I 81 GLN cc_start: 0.8646 (mt0) cc_final: 0.8184 (mp10) REVERT: I 90 MET cc_start: 0.9044 (mtp) cc_final: 0.8795 (mtm) REVERT: I 189 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8667 (pp) REVERT: J 12 TYR cc_start: 0.8273 (p90) cc_final: 0.7742 (p90) REVERT: J 37 LYS cc_start: 0.8945 (tttp) cc_final: 0.8679 (tptt) REVERT: J 86 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8075 (ttm170) REVERT: J 93 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8271 (mtm-85) REVERT: c 40 GLN cc_start: 0.7955 (mm110) cc_final: 0.7632 (mm110) REVERT: d 43 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8848 (ttmt) REVERT: e 56 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7616 (tm-30) REVERT: e 66 THR cc_start: 0.9373 (m) cc_final: 0.9111 (t) outliers start: 55 outliers final: 35 residues processed: 416 average time/residue: 1.3309 time to fit residues: 635.9027 Evaluate side-chains 418 residues out of total 2444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 372 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 20 GLU 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 36 THR Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 187 CYS Chi-restraints excluded: chain G residue 15 ILE 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 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 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 132 VAL Chi-restraints excluded: chain c residue 253 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain d residue 35 ILE Chi-restraints excluded: chain d residue 43 LYS 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 175 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 220 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN J 61 GLN J 65 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 GLN e 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066495 restraints weight = 58497.773| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.06 r_work: 0.2884 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22084 Z= 0.206 Angle : 0.650 13.138 29929 Z= 0.333 Chirality : 0.042 0.267 3472 Planarity : 0.004 0.056 3821 Dihedral : 4.382 25.167 3075 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 2.63 % Allowed : 26.43 % Favored : 70.94 % 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: 0.66 (0.16), residues: 2808 helix: 2.10 (0.15), residues: 1127 sheet: -0.59 (0.20), residues: 636 loop : -0.68 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 100 HIS 0.009 0.001 HIS C 154 PHE 0.030 0.001 PHE c 71 TYR 0.033 0.001 TYR C 153 ARG 0.010 0.000 ARG D 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9371.23 seconds wall clock time: 344 minutes 29.32 seconds (20669.32 seconds total)