Starting phenix.real_space_refine on Sat Dec 9 00:24:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqy_34203/12_2023/8gqy_34203.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqy_34203/12_2023/8gqy_34203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqy_34203/12_2023/8gqy_34203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqy_34203/12_2023/8gqy_34203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqy_34203/12_2023/8gqy_34203.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gqy_34203/12_2023/8gqy_34203.pdb" } resolution = 3.4 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= 0.004 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 60 5.16 5 C 6230 2.51 5 N 1505 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 171": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9515 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "D" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "E" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1903 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Time building chain proxies: 5.74, per 1000 atoms: 0.60 Number of scatterers: 9515 At special positions: 0 Unit cell: (88.2, 88.2, 101.7, 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 60 16.00 O 1720 8.00 N 1505 7.00 C 6230 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: 3.21 Conformation dependent library (CDL) restraints added in 2.0 seconds 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.768A pdb=" N ALA A 12 " --> pdb=" O GLY A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.891A pdb=" N ASP A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 128 through 134 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.786A pdb=" N VAL A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 173 removed outlier: 3.739A pdb=" N LEU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 200 removed outlier: 3.563A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 4.204A pdb=" N LYS A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 231 removed outlier: 3.550A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.775A pdb=" N LYS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 24 removed outlier: 4.032A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.807A pdb=" N ALA B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.991A pdb=" N VAL B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 3.591A pdb=" N ILE B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 removed outlier: 3.597A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.581A pdb=" N LEU B 95 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLY B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.700A pdb=" N GLN B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.892A pdb=" N ASP B 111 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 119 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.452A pdb=" N ALA B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 3.991A pdb=" N GLU B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.600A pdb=" N GLN B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 179 through 200 removed outlier: 3.542A pdb=" N VAL B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.726A pdb=" N VAL B 204 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 231 removed outlier: 3.524A pdb=" N GLU B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.558A pdb=" N LYS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.758A pdb=" N ILE B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 4.125A pdb=" N GLY C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.623A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.516A pdb=" N ILE C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 removed outlier: 3.635A pdb=" N LEU C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.604A pdb=" N ILE C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.502A pdb=" N SER C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.718A pdb=" N GLU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 3.978A pdb=" N GLN C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.566A pdb=" N GLY C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 119 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 135 removed outlier: 3.525A pdb=" N LYS C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.746A pdb=" N THR C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 146 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRP C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 171 removed outlier: 3.703A pdb=" N GLN C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 179 through 200 removed outlier: 3.614A pdb=" N ALA C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 196 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 231 removed outlier: 3.790A pdb=" N VAL C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.501A pdb=" N VAL C 238 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.620A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 17 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 34 through 45 removed outlier: 3.775A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 removed outlier: 3.553A pdb=" N ARG D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 72 through 91 removed outlier: 3.757A pdb=" N ILE D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 78 " --> pdb=" O ASN D 74 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 4.272A pdb=" N GLU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY D 97 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.653A pdb=" N GLY D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 135 removed outlier: 3.944A pdb=" N ALA D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 154 removed outlier: 3.878A pdb=" N GLU D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.561A pdb=" N GLY D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN D 172 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 179 through 200 removed outlier: 3.949A pdb=" N THR D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 208 through 231 removed outlier: 3.532A pdb=" N MET D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 245 removed outlier: 3.511A pdb=" N VAL D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 244 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 removed outlier: 3.830A pdb=" N ALA E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 34 through 43 removed outlier: 4.137A pdb=" N VAL E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.835A pdb=" N ARG E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 91 removed outlier: 3.944A pdb=" N ILE E 80 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.540A pdb=" N LEU E 95 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU E 96 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY E 97 " --> pdb=" O ALA E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 98 through 106 removed outlier: 3.651A pdb=" N GLN E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP E 106 " --> pdb=" O TYR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 118 removed outlier: 3.635A pdb=" N ARG E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 154 removed outlier: 3.685A pdb=" N ALA E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS E 139 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 142 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TRP E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.524A pdb=" N LEU E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 200 removed outlier: 3.783A pdb=" N THR E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 208 removed outlier: 3.630A pdb=" N VAL E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 228 removed outlier: 3.654A pdb=" N TYR E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 247 removed outlier: 3.736A pdb=" N GLU E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1446 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: 2.34 Time building geometry restraints manager: 3.55 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: 3007 1.34 - 1.46: 1035 1.46 - 1.57: 5493 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 9655 Sorted by residual: bond pdb=" C VAL C 32 " pdb=" N PRO C 33 " ideal model delta sigma weight residual 1.334 1.348 -0.014 8.40e-03 1.42e+04 2.79e+00 bond pdb=" C GLY C 119 " pdb=" N ILE C 120 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.29e-02 6.01e+03 1.47e+00 bond pdb=" CG1 ILE D 221 " pdb=" CD1 ILE D 221 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE E 221 " pdb=" CD1 ILE E 221 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.01e+00 bond pdb=" CB ASP D 137 " pdb=" CG ASP D 137 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.77e-01 ... (remaining 9650 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 290 106.71 - 113.53: 5640 113.53 - 120.36: 3805 120.36 - 127.18: 3267 127.18 - 134.00: 73 Bond angle restraints: 13075 Sorted by residual: angle pdb=" C ASN A 31 " pdb=" N VAL A 32 " pdb=" CA VAL A 32 " ideal model delta sigma weight residual 120.24 123.93 -3.69 6.30e-01 2.52e+00 3.43e+01 angle pdb=" N VAL B 3 " pdb=" CA VAL B 3 " pdb=" C VAL B 3 " ideal model delta sigma weight residual 111.91 108.15 3.76 8.90e-01 1.26e+00 1.78e+01 angle pdb=" N ILE C 7 " pdb=" CA ILE C 7 " pdb=" C ILE C 7 " ideal model delta sigma weight residual 112.90 108.95 3.95 9.60e-01 1.09e+00 1.69e+01 angle pdb=" C VAL A 32 " pdb=" CA VAL A 32 " pdb=" CB VAL A 32 " ideal model delta sigma weight residual 114.35 110.75 3.60 1.06e+00 8.90e-01 1.15e+01 angle pdb=" N VAL A 3 " pdb=" CA VAL A 3 " pdb=" C VAL A 3 " ideal model delta sigma weight residual 111.91 109.17 2.74 8.90e-01 1.26e+00 9.46e+00 ... (remaining 13070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.50: 5309 14.50 - 29.00: 412 29.00 - 43.49: 126 43.49 - 57.99: 38 57.99 - 72.49: 5 Dihedral angle restraints: 5890 sinusoidal: 2300 harmonic: 3590 Sorted by residual: dihedral pdb=" CA GLN E 135 " pdb=" C GLN E 135 " pdb=" N LEU E 136 " pdb=" CA LEU E 136 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLN A 135 " pdb=" C GLN A 135 " pdb=" N LEU A 136 " pdb=" CA LEU A 136 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 682 0.025 - 0.051: 591 0.051 - 0.076: 265 0.076 - 0.101: 56 0.101 - 0.126: 16 Chirality restraints: 1610 Sorted by residual: chirality pdb=" CB VAL C 3 " pdb=" CA VAL C 3 " pdb=" CG1 VAL C 3 " pdb=" CG2 VAL C 3 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CB VAL B 3 " pdb=" CA VAL B 3 " pdb=" CG1 VAL B 3 " pdb=" CG2 VAL B 3 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.11 2.00e-01 2.50e+01 3.11e-01 ... (remaining 1607 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 202 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO C 203 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 203 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 203 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 202 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO E 203 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 203 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 203 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 202 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO B 203 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.021 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 123 2.67 - 3.23: 9442 3.23 - 3.79: 13488 3.79 - 4.34: 21454 4.34 - 4.90: 33480 Nonbonded interactions: 77987 Sorted by model distance: nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 192 " model vdw 2.117 2.440 nonbonded pdb=" O PHE B 29 " pdb=" OH TYR B 192 " model vdw 2.120 2.440 nonbonded pdb=" O PHE A 29 " pdb=" OH TYR A 192 " model vdw 2.142 2.440 nonbonded pdb=" O PHE C 29 " pdb=" OH TYR C 192 " model vdw 2.143 2.440 nonbonded pdb=" O PHE E 29 " pdb=" OH TYR E 192 " model vdw 2.216 2.440 ... (remaining 77982 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' } 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: 0.010 Normalize map: mean=0, sd=1: 11.680 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: 0.000 Extract box with map and model: 6.090 Check model and map are aligned: 0.000 Set scattering table: 0.280 Process input model: 27.440 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.005 0.046 9655 Z= 0.324 Angle : 0.657 5.736 13075 Z= 0.389 Chirality : 0.040 0.126 1610 Planarity : 0.004 0.043 1630 Dihedral : 12.578 72.490 3580 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.67 % Allowed : 9.25 % Favored : 85.07 % 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: -7.14 (0.13), residues: 1255 helix: -4.90 (0.06), residues: 985 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 147 HIS 0.001 0.000 HIS B 0 PHE 0.008 0.001 PHE A 55 TYR 0.007 0.001 TYR D 222 ARG 0.002 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 1.121 Fit side-chains outliers start: 57 outliers final: 20 residues processed: 246 average time/residue: 0.1872 time to fit residues: 66.2812 Evaluate side-chains 173 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1027 time to fit residues: 5.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN C 168 GLN C 198 ASN C 240 GLN D 198 ASN E 104 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9655 Z= 0.213 Angle : 0.652 10.498 13075 Z= 0.335 Chirality : 0.039 0.166 1610 Planarity : 0.006 0.033 1630 Dihedral : 5.307 18.704 1300 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.99 % Allowed : 16.22 % Favored : 81.79 % 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: -5.48 (0.16), residues: 1255 helix: -3.57 (0.11), residues: 1010 sheet: None (None), residues: 0 loop : -2.48 (0.28), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.009 0.001 PHE D 66 TYR 0.006 0.001 TYR B 102 ARG 0.002 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.045 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 172 average time/residue: 0.1727 time to fit residues: 44.3256 Evaluate side-chains 155 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0895 time to fit residues: 2.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9655 Z= 0.186 Angle : 0.547 7.005 13075 Z= 0.281 Chirality : 0.039 0.118 1610 Planarity : 0.004 0.032 1630 Dihedral : 4.925 17.579 1300 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.49 % Allowed : 17.01 % Favored : 80.50 % 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: -4.04 (0.19), residues: 1255 helix: -2.49 (0.14), residues: 1000 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.007 0.001 PHE A 200 TYR 0.012 0.001 TYR A 222 ARG 0.003 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.989 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 157 average time/residue: 0.1701 time to fit residues: 41.6333 Evaluate side-chains 144 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0878 time to fit residues: 3.7585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN E 74 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9655 Z= 0.174 Angle : 0.529 9.555 13075 Z= 0.265 Chirality : 0.039 0.177 1610 Planarity : 0.004 0.033 1630 Dihedral : 4.737 17.650 1300 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.59 % Allowed : 18.11 % Favored : 80.30 % 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: -3.19 (0.21), residues: 1255 helix: -1.89 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -2.13 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 147 HIS 0.001 0.000 HIS B 0 PHE 0.007 0.001 PHE A 200 TYR 0.008 0.001 TYR D 222 ARG 0.002 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.994 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 150 average time/residue: 0.1832 time to fit residues: 41.5177 Evaluate side-chains 140 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1979 time to fit residues: 2.8808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9655 Z= 0.172 Angle : 0.508 7.836 13075 Z= 0.258 Chirality : 0.038 0.112 1610 Planarity : 0.004 0.034 1630 Dihedral : 4.611 16.953 1300 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.49 % Allowed : 19.40 % Favored : 79.10 % 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: -2.64 (0.22), residues: 1255 helix: -1.51 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -1.89 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.007 0.001 PHE E 157 TYR 0.006 0.001 TYR D 222 ARG 0.002 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.010 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 144 average time/residue: 0.1799 time to fit residues: 39.0501 Evaluate side-chains 135 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0885 time to fit residues: 2.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9655 Z= 0.181 Angle : 0.507 7.048 13075 Z= 0.257 Chirality : 0.039 0.112 1610 Planarity : 0.004 0.033 1630 Dihedral : 4.547 16.364 1300 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.49 % Allowed : 20.10 % Favored : 78.41 % 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: -2.20 (0.22), residues: 1255 helix: -1.20 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -1.72 (0.31), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 147 HIS 0.002 0.000 HIS A 0 PHE 0.008 0.001 PHE E 157 TYR 0.007 0.001 TYR D 222 ARG 0.001 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.008 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 137 average time/residue: 0.1680 time to fit residues: 34.9893 Evaluate side-chains 132 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0861 time to fit residues: 2.5510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 198 ASN D 135 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9655 Z= 0.252 Angle : 0.552 10.719 13075 Z= 0.276 Chirality : 0.040 0.115 1610 Planarity : 0.004 0.032 1630 Dihedral : 4.666 16.180 1300 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.19 % Allowed : 21.09 % Favored : 77.71 % 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: -2.00 (0.22), residues: 1255 helix: -1.08 (0.16), residues: 980 sheet: None (None), residues: 0 loop : -1.56 (0.31), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 147 HIS 0.001 0.000 HIS B 0 PHE 0.012 0.001 PHE E 157 TYR 0.007 0.001 TYR D 222 ARG 0.002 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.081 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 142 average time/residue: 0.1877 time to fit residues: 39.5994 Evaluate side-chains 133 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1007 time to fit residues: 2.4597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9655 Z= 0.190 Angle : 0.512 9.563 13075 Z= 0.258 Chirality : 0.039 0.112 1610 Planarity : 0.004 0.036 1630 Dihedral : 4.538 15.986 1300 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.29 % Allowed : 21.29 % Favored : 77.41 % 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: -1.63 (0.23), residues: 1255 helix: -0.79 (0.16), residues: 985 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.007 0.001 PHE E 157 TYR 0.006 0.001 TYR D 222 ARG 0.001 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.176 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 146 average time/residue: 0.1841 time to fit residues: 39.8993 Evaluate side-chains 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0869 time to fit residues: 2.1197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9655 Z= 0.175 Angle : 0.531 12.152 13075 Z= 0.261 Chirality : 0.039 0.119 1610 Planarity : 0.004 0.035 1630 Dihedral : 4.444 15.879 1300 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.50 % Allowed : 22.49 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1255 helix: -0.54 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.008 0.001 PHE E 157 TYR 0.006 0.001 TYR D 222 ARG 0.002 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.151 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 132 average time/residue: 0.2064 time to fit residues: 40.7771 Evaluate side-chains 134 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1052 time to fit residues: 2.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 124 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 78 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 overall best weight: 0.2290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9655 Z= 0.128 Angle : 0.486 9.727 13075 Z= 0.244 Chirality : 0.038 0.110 1610 Planarity : 0.004 0.037 1630 Dihedral : 4.231 16.203 1300 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.30 % Allowed : 22.09 % Favored : 77.61 % 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: -0.76 (0.24), residues: 1255 helix: -0.17 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 147 HIS 0.001 0.000 HIS E 0 PHE 0.006 0.001 PHE E 157 TYR 0.005 0.001 TYR D 192 ARG 0.002 0.000 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2510 Ramachandran restraints generated. 1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.136 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 130 average time/residue: 0.1864 time to fit residues: 36.4223 Evaluate side-chains 124 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0880 time to fit residues: 1.6023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116738 restraints weight = 10705.586| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.33 r_work: 0.3023 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9655 Z= 0.159 Angle : 0.495 8.810 13075 Z= 0.247 Chirality : 0.039 0.133 1610 Planarity : 0.003 0.035 1630 Dihedral : 4.230 16.283 1300 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.60 % Allowed : 22.79 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1255 helix: -0.02 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -1.25 (0.32), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 147 HIS 0.001 0.000 HIS E 0 PHE 0.010 0.001 PHE E 157 TYR 0.006 0.001 TYR D 222 ARG 0.001 0.000 ARG E 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2015.02 seconds wall clock time: 38 minutes 3.70 seconds (2283.70 seconds total)