Starting phenix.real_space_refine on Wed Nov 15 01:23:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykp_10829/11_2023/6ykp_10829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykp_10829/11_2023/6ykp_10829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykp_10829/11_2023/6ykp_10829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykp_10829/11_2023/6ykp_10829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykp_10829/11_2023/6ykp_10829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykp_10829/11_2023/6ykp_10829.pdb" } resolution = 2.98 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= 0.119 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 70 5.16 5 C 6592 2.51 5 N 1649 2.21 5 O 1879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 251": "NH1" <-> "NH2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10190 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "E" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "F" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 203 Classifications: {'peptide': 25} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 22} Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 210 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.48, per 1000 atoms: 0.54 Number of scatterers: 10190 At special positions: 0 Unit cell: (92.352, 97.344, 112.32, 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 70 16.00 O 1879 8.00 N 1649 7.00 C 6592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.505A pdb=" N ASP A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.663A pdb=" N ILE A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.901A pdb=" N TYR A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.718A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 91 removed outlier: 3.891A pdb=" N GLN A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.651A pdb=" N LEU A 96 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 98 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.558A pdb=" N ASP A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.528A pdb=" N GLU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 137 through 171 removed outlier: 3.507A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.722A pdb=" N LEU A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 184 through 199 removed outlier: 4.265A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.516A pdb=" N LYS A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.537A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'B' and resid 2 through 22 removed outlier: 3.523A pdb=" N MET B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 22 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.774A pdb=" N VAL B 30 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.832A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.720A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.571A pdb=" N ALA B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.713A pdb=" N GLU B 97 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.544A pdb=" N ASN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.782A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 171 removed outlier: 3.573A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.582A pdb=" N GLY B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.556A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 229 removed outlier: 3.553A pdb=" N ALA B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'C' and resid 2 through 22 removed outlier: 3.952A pdb=" N MET C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.562A pdb=" N HIS C 29 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 30 " --> pdb=" O PRO C 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 30' Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.508A pdb=" N LYS C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.587A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.513A pdb=" N ALA C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.589A pdb=" N GLU C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.502A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.614A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 170 removed outlier: 3.626A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TRP C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Proline residue: C 154 - end of helix removed outlier: 3.649A pdb=" N LEU C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.680A pdb=" N ALA C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.802A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.975A pdb=" N ASP C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.549A pdb=" N ASP D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.738A pdb=" N VAL D 30 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.702A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.658A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 removed outlier: 3.709A pdb=" N GLN D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 99 removed outlier: 3.604A pdb=" N LEU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 97 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.529A pdb=" N ASP D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.500A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 142 through 171 removed outlier: 4.104A pdb=" N TRP D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Proline residue: D 154 - end of helix removed outlier: 3.642A pdb=" N LEU D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 167 " --> pdb=" O PHE D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.514A pdb=" N MET D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 198 removed outlier: 3.873A pdb=" N VAL D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 211 Processing helix chain 'D' and resid 214 through 229 Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.652A pdb=" N ALA D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.591A pdb=" N LEU E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.687A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.730A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 91 removed outlier: 3.803A pdb=" N ALA E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 100 removed outlier: 3.714A pdb=" N GLU E 97 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER E 98 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.586A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 171 removed outlier: 3.998A pdb=" N TRP E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS E 153 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.784A pdb=" N ILE E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 167 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 Processing helix chain 'E' and resid 185 through 197 removed outlier: 3.748A pdb=" N THR E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 229 removed outlier: 3.932A pdb=" N ASP E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.634A pdb=" N ALA E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'F' and resid 23 through 39 removed outlier: 3.568A pdb=" N LEU F 27 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 40 removed outlier: 4.735A pdb=" N LEU G 26 " --> pdb=" O ASP G 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU G 27 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2282 1.33 - 1.45: 2111 1.45 - 1.57: 5853 1.57 - 1.69: 1 1.69 - 1.81: 125 Bond restraints: 10372 Sorted by residual: bond pdb=" CB PRO C 154 " pdb=" CG PRO C 154 " ideal model delta sigma weight residual 1.492 1.318 0.174 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CB THR D 5 " pdb=" CG2 THR D 5 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.76e+00 bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.364 0.128 5.00e-02 4.00e+02 6.57e+00 bond pdb=" CB PRO D 202 " pdb=" CG PRO D 202 " ideal model delta sigma weight residual 1.492 1.367 0.125 5.00e-02 4.00e+02 6.24e+00 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 93.91 - 103.30: 130 103.30 - 112.70: 5409 112.70 - 122.09: 7052 122.09 - 131.48: 1393 131.48 - 140.87: 30 Bond angle restraints: 14014 Sorted by residual: angle pdb=" C ASP F 22 " pdb=" N PHE F 23 " pdb=" CA PHE F 23 " ideal model delta sigma weight residual 121.70 140.87 -19.17 1.80e+00 3.09e-01 1.13e+02 angle pdb=" C VAL F 18 " pdb=" N PRO F 19 " pdb=" CA PRO F 19 " ideal model delta sigma weight residual 120.96 131.71 -10.75 1.41e+00 5.03e-01 5.81e+01 angle pdb=" CB LEU C 158 " pdb=" CG LEU C 158 " pdb=" CD2 LEU C 158 " ideal model delta sigma weight residual 110.70 93.91 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" CA LEU E 171 " pdb=" CB LEU E 171 " pdb=" CG LEU E 171 " ideal model delta sigma weight residual 116.30 134.27 -17.97 3.50e+00 8.16e-02 2.64e+01 angle pdb=" N TYR F 20 " pdb=" CA TYR F 20 " pdb=" C TYR F 20 " ideal model delta sigma weight residual 110.80 100.31 10.49 2.13e+00 2.20e-01 2.43e+01 ... (remaining 14009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 6070 23.66 - 47.32: 128 47.32 - 70.99: 16 70.99 - 94.65: 2 94.65 - 118.31: 2 Dihedral angle restraints: 6218 sinusoidal: 2425 harmonic: 3793 Sorted by residual: dihedral pdb=" CA ALA F 21 " pdb=" C ALA F 21 " pdb=" N ASP F 22 " pdb=" CA ASP F 22 " ideal model delta harmonic sigma weight residual 180.00 61.69 118.31 0 5.00e+00 4.00e-02 5.60e+02 dihedral pdb=" CA VAL F 18 " pdb=" C VAL F 18 " pdb=" N PRO F 19 " pdb=" CA PRO F 19 " ideal model delta harmonic sigma weight residual 180.00 74.94 105.06 0 5.00e+00 4.00e-02 4.42e+02 dihedral pdb=" CA ASP F 22 " pdb=" C ASP F 22 " pdb=" N PHE F 23 " pdb=" CA PHE F 23 " ideal model delta harmonic sigma weight residual 0.00 -30.48 30.48 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 6215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1420 0.099 - 0.197: 198 0.197 - 0.296: 19 0.296 - 0.395: 2 0.395 - 0.493: 1 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CA PHE F 23 " pdb=" N PHE F 23 " pdb=" C PHE F 23 " pdb=" CB PHE F 23 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CB VAL F 18 " pdb=" CA VAL F 18 " pdb=" CG1 VAL F 18 " pdb=" CG2 VAL F 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL G 18 " pdb=" CA VAL G 18 " pdb=" CG1 VAL G 18 " pdb=" CG2 VAL G 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1637 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 149 " 0.030 2.00e-02 2.50e+03 3.65e-02 2.34e+01 pdb=" CG PHE E 149 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE E 149 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE E 149 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE E 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 149 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE E 149 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 149 " 0.026 2.00e-02 2.50e+03 3.13e-02 1.71e+01 pdb=" CG PHE C 149 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE C 149 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE C 149 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 149 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 149 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 149 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 149 " -0.026 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE B 149 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 149 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 149 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 149 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 149 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 149 " -0.001 2.00e-02 2.50e+03 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3483 2.86 - 3.37: 9895 3.37 - 3.88: 16736 3.88 - 4.39: 21342 4.39 - 4.90: 34121 Nonbonded interactions: 85577 Sorted by model distance: nonbonded pdb=" OH TYR B 60 " pdb=" OH TYR B 145 " model vdw 2.350 2.440 nonbonded pdb=" OG1 THR E 189 " pdb=" OD1 ASP G 22 " model vdw 2.360 2.440 nonbonded pdb=" OH TYR E 60 " pdb=" OH TYR E 145 " model vdw 2.380 2.440 nonbonded pdb=" OH TYR C 60 " pdb=" OH TYR C 145 " model vdw 2.382 2.440 nonbonded pdb=" NH1 ARG B 77 " pdb=" OE1 GLN B 80 " model vdw 2.393 2.520 ... (remaining 85572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 15 through 39) } 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: 0.880 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: 4.200 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.014 0.174 10372 Z= 0.909 Angle : 1.228 19.173 14014 Z= 0.626 Chirality : 0.072 0.493 1640 Planarity : 0.009 0.084 1763 Dihedral : 10.753 118.312 3766 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 0.09 % Allowed : 1.02 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % 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: -6.56 (0.13), residues: 1312 helix: -4.62 (0.07), residues: 1051 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.161 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 1.5248 time to fit residues: 403.3286 Evaluate side-chains 164 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 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 131 GLN A 138 HIS B 52 HIS B 125 HIS B 138 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN E 125 HIS E 210 ASN E 243 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10372 Z= 0.195 Angle : 0.635 13.376 14014 Z= 0.324 Chirality : 0.043 0.265 1640 Planarity : 0.006 0.082 1763 Dihedral : 5.851 52.242 1371 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.98 % Favored : 97.87 % Rotamer: Outliers : 2.78 % Allowed : 11.29 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: -4.05 (0.19), residues: 1312 helix: -2.80 (0.12), residues: 1068 sheet: None (None), residues: 0 loop : -0.65 (0.37), residues: 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.202 Fit side-chains outliers start: 30 outliers final: 5 residues processed: 204 average time/residue: 1.3347 time to fit residues: 290.7390 Evaluate side-chains 159 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1208 time to fit residues: 1.9926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.0770 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 243 ASN B 110 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10372 Z= 0.159 Angle : 0.584 13.553 14014 Z= 0.287 Chirality : 0.041 0.258 1640 Planarity : 0.004 0.069 1763 Dihedral : 5.235 47.968 1371 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.96 % Allowed : 14.89 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: -2.32 (0.21), residues: 1312 helix: -1.54 (0.14), residues: 1066 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.170 Fit side-chains outliers start: 32 outliers final: 8 residues processed: 175 average time/residue: 1.3469 time to fit residues: 252.0978 Evaluate side-chains 155 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1207 time to fit residues: 2.1394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 138 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10372 Z= 0.223 Angle : 0.593 13.140 14014 Z= 0.292 Chirality : 0.043 0.265 1640 Planarity : 0.004 0.079 1763 Dihedral : 5.013 44.347 1371 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 3.42 % Allowed : 15.36 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: -1.42 (0.22), residues: 1312 helix: -0.91 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : -0.06 (0.41), residues: 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 1.035 Fit side-chains outliers start: 37 outliers final: 12 residues processed: 182 average time/residue: 1.2146 time to fit residues: 237.2525 Evaluate side-chains 165 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.7273 time to fit residues: 5.6992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.0040 chunk 51 optimal weight: 0.0010 chunk 106 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS C 254 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN E 254 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10372 Z= 0.143 Angle : 0.548 12.757 14014 Z= 0.268 Chirality : 0.041 0.288 1640 Planarity : 0.004 0.076 1763 Dihedral : 4.674 40.034 1371 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.87 % Rotamer: Outliers : 2.22 % Allowed : 17.67 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: -0.39 (0.23), residues: 1312 helix: -0.18 (0.16), residues: 1057 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.003 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 170 average time/residue: 1.3025 time to fit residues: 237.8069 Evaluate side-chains 157 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0909 time to fit residues: 1.7315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS C 254 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10372 Z= 0.169 Angle : 0.570 14.872 14014 Z= 0.275 Chirality : 0.042 0.294 1640 Planarity : 0.004 0.080 1763 Dihedral : 4.598 40.528 1371 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 1.76 % Allowed : 19.43 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: 0.17 (0.23), residues: 1312 helix: 0.18 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : 0.44 (0.36), residues: 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.176 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 162 average time/residue: 1.2898 time to fit residues: 224.5580 Evaluate side-chains 158 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1137 time to fit residues: 1.9137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN B 138 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10372 Z= 0.165 Angle : 0.567 13.152 14014 Z= 0.273 Chirality : 0.042 0.321 1640 Planarity : 0.004 0.079 1763 Dihedral : 4.523 39.924 1371 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.06 % Favored : 97.87 % Rotamer: Outliers : 1.48 % Allowed : 19.89 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: 0.35 (0.23), residues: 1312 helix: 0.36 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : 0.27 (0.39), residues: 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 2.191 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 169 average time/residue: 1.3148 time to fit residues: 237.8340 Evaluate side-chains 157 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1372 time to fit residues: 1.7529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10372 Z= 0.172 Angle : 0.578 13.063 14014 Z= 0.278 Chirality : 0.042 0.332 1640 Planarity : 0.004 0.080 1763 Dihedral : 4.525 40.023 1371 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.44 % Favored : 97.48 % Rotamer: Outliers : 1.76 % Allowed : 20.26 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: 0.52 (0.24), residues: 1312 helix: 0.48 (0.16), residues: 1057 sheet: None (None), residues: 0 loop : 0.34 (0.40), residues: 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.138 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 158 average time/residue: 1.2543 time to fit residues: 212.8788 Evaluate side-chains 155 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1419 time to fit residues: 1.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 104 optimal weight: 0.0970 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS C 52 HIS C 254 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10372 Z= 0.165 Angle : 0.585 12.083 14014 Z= 0.284 Chirality : 0.043 0.348 1640 Planarity : 0.005 0.081 1763 Dihedral : 4.489 39.171 1371 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 1.48 % Allowed : 20.54 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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 (0.24), residues: 1312 helix: 0.59 (0.16), residues: 1057 sheet: None (None), residues: 0 loop : 0.35 (0.40), residues: 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.119 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 164 average time/residue: 1.2182 time to fit residues: 214.8545 Evaluate side-chains 158 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.1068 time to fit residues: 2.8090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 243 ASN C 254 GLN D 254 GLN E 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10372 Z= 0.202 Angle : 0.605 12.099 14014 Z= 0.296 Chirality : 0.044 0.356 1640 Planarity : 0.005 0.085 1763 Dihedral : 4.558 39.972 1371 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 1.48 % Allowed : 20.91 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: 0.71 (0.23), residues: 1312 helix: 0.59 (0.16), residues: 1037 sheet: None (None), residues: 0 loop : 0.49 (0.38), residues: 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.152 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 163 average time/residue: 1.3378 time to fit residues: 233.4217 Evaluate side-chains 159 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1582 time to fit residues: 2.0533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS C 254 GLN D 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116112 restraints weight = 10987.237| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.10 r_work: 0.3195 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10372 Z= 0.169 Angle : 0.584 12.364 14014 Z= 0.285 Chirality : 0.043 0.359 1640 Planarity : 0.004 0.080 1763 Dihedral : 4.494 38.752 1371 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.13 % Favored : 97.79 % Rotamer: Outliers : 1.48 % Allowed : 21.09 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.38 % 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: 0.88 (0.24), residues: 1312 helix: 0.72 (0.17), residues: 1037 sheet: None (None), residues: 0 loop : 0.54 (0.38), residues: 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4270.73 seconds wall clock time: 76 minutes 25.52 seconds (4585.52 seconds total)