Starting phenix.real_space_refine on Thu Feb 13 11:55:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xbd_33103/02_2025/7xbd_33103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xbd_33103/02_2025/7xbd_33103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xbd_33103/02_2025/7xbd_33103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xbd_33103/02_2025/7xbd_33103.map" model { file = "/net/cci-nas-00/data/ceres_data/7xbd_33103/02_2025/7xbd_33103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xbd_33103/02_2025/7xbd_33103.cif" } resolution = 3.11 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= -0.001 sd= 0.048 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 56 5.16 5 C 5699 2.51 5 N 1569 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8981 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain breaks: 2 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Time building chain proxies: 5.17, per 1000 atoms: 0.58 Number of scatterers: 8981 At special positions: 0 Unit cell: (90.45, 128.417, 130.65, 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 56 16.00 O 1657 8.00 N 1569 7.00 C 5699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 996.8 milliseconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 35.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 26 through 52 removed outlier: 3.856A pdb=" N LEU A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 removed outlier: 3.578A pdb=" N PHE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Proline residue: A 80 - end of helix removed outlier: 3.856A pdb=" N ALA A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 96 through 113 removed outlier: 4.830A pdb=" N HIS A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE A 106 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.851A pdb=" N LEU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 158 removed outlier: 4.176A pdb=" N ALA A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.265A pdb=" N ALA A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.625A pdb=" N LEU A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 249 removed outlier: 3.532A pdb=" N VAL A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 241 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.762A pdb=" N HIS A 253 " --> pdb=" O TRP A 249 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 257 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N CYS A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 removed outlier: 3.956A pdb=" N ALA A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'B' and resid 7 through 31 removed outlier: 3.662A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.618A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.955A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 3.696A pdb=" N ALA B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.308A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.606A pdb=" N TYR B 170 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.571A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.703A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.669A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 13 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.785A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.637A pdb=" N LYS D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 4.096A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.664A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.746A pdb=" N ASP E 223 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 220 through 224' Processing helix chain 'F' and resid 3 through 11 removed outlier: 3.643A pdb=" N LEU F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.161A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE B 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 36 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 76 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.710A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 4.056A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.841A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.597A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.489A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.446A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.329A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 315 through 320 removed outlier: 3.708A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 319 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.950A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 17 through 21 removed outlier: 3.528A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AB7, first strand: chain 'E' and resid 158 through 160 removed outlier: 3.513A pdb=" N CYS E 159 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 174 through 179 removed outlier: 3.607A pdb=" N TYR E 228 " --> pdb=" O PHE E 177 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 876 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: 2.36 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2938 1.35 - 1.47: 2269 1.47 - 1.59: 3886 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 9172 Sorted by residual: bond pdb=" CB TRP E 47 " pdb=" CG TRP E 47 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.30e+00 bond pdb=" CB ASP C 303 " pdb=" CG ASP C 303 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.66e-01 bond pdb=" CB GLN B 89 " pdb=" CG GLN B 89 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.62e-01 bond pdb=" SD MET E 230 " pdb=" CE MET E 230 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 8.01e-01 bond pdb=" CA ILE B 140 " pdb=" CB ILE B 140 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 7.27e-01 ... (remaining 9167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 12138 1.41 - 2.83: 236 2.83 - 4.24: 49 4.24 - 5.65: 13 5.65 - 7.07: 4 Bond angle restraints: 12440 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 109.34 4.37 9.50e-01 1.11e+00 2.12e+01 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 113.42 108.79 4.63 1.17e+00 7.31e-01 1.56e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.80e+00 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 115.81 -6.00 2.21e+00 2.05e-01 7.38e+00 angle pdb=" CA VAL B 219 " pdb=" C VAL B 219 " pdb=" N ASP B 220 " ideal model delta sigma weight residual 118.90 116.51 2.39 9.40e-01 1.13e+00 6.46e+00 ... (remaining 12435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4803 17.20 - 34.40: 515 34.40 - 51.61: 106 51.61 - 68.81: 5 68.81 - 86.01: 7 Dihedral angle restraints: 5436 sinusoidal: 2102 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 166.92 -73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CA SER C 279 " pdb=" C SER C 279 " pdb=" N LYS C 280 " pdb=" CA LYS C 280 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CB CYS A 98 " pdb=" SG CYS A 98 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual -86.00 -54.96 -31.04 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 5433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 868 0.031 - 0.062: 368 0.062 - 0.094: 103 0.094 - 0.125: 61 0.125 - 0.156: 9 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA TYR E 190 " pdb=" N TYR E 190 " pdb=" C TYR E 190 " pdb=" CB TYR E 190 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1406 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 59 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO D 60 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO E 236 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 12 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO F 13 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 13 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 13 " 0.024 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 658 2.74 - 3.28: 8403 3.28 - 3.82: 13687 3.82 - 4.36: 16419 4.36 - 4.90: 29414 Nonbonded interactions: 68581 Sorted by model distance: nonbonded pdb=" OD2 ASP A 122 " pdb=" OH TYR B 243 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.208 3.040 nonbonded pdb=" OG SER E 158 " pdb=" O PHE E 212 " model vdw 2.212 3.040 nonbonded pdb=" O PHE A 81 " pdb=" OG1 THR A 84 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 112 " pdb=" O LYS B 145 " model vdw 2.231 3.040 ... (remaining 68576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9172 Z= 0.173 Angle : 0.531 7.065 12440 Z= 0.281 Chirality : 0.041 0.156 1409 Planarity : 0.004 0.077 1582 Dihedral : 14.055 86.009 3276 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.25), residues: 1135 helix: -1.09 (0.27), residues: 354 sheet: -0.54 (0.35), residues: 251 loop : -1.51 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 82 HIS 0.002 0.001 HIS C 62 PHE 0.017 0.001 PHE E 29 TYR 0.018 0.001 TYR C 145 ARG 0.004 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.818 Fit side-chains REVERT: D 21 MET cc_start: 0.4760 (mmt) cc_final: 0.3973 (mtm) REVERT: E 213 THR cc_start: 0.7700 (t) cc_final: 0.7340 (m) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2432 time to fit residues: 33.6503 Evaluate side-chains 84 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0010 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.208784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167254 restraints weight = 9854.337| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.37 r_work: 0.3686 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9172 Z= 0.170 Angle : 0.550 6.482 12440 Z= 0.288 Chirality : 0.042 0.156 1409 Planarity : 0.005 0.064 1582 Dihedral : 4.276 26.206 1262 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.04 % Allowed : 5.81 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1135 helix: 0.10 (0.29), residues: 349 sheet: -0.61 (0.33), residues: 266 loop : -1.54 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS A 176 PHE 0.009 0.001 PHE C 235 TYR 0.015 0.001 TYR C 145 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.7162 (ttt) cc_final: 0.6845 (ttt) REVERT: A 250 MET cc_start: 0.6510 (tpt) cc_final: 0.6167 (tpt) REVERT: B 32 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6361 (mmp-170) REVERT: C 171 ILE cc_start: 0.7214 (mm) cc_final: 0.6825 (mm) REVERT: C 251 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6505 (ptt180) REVERT: E 213 THR cc_start: 0.7755 (t) cc_final: 0.7462 (m) outliers start: 10 outliers final: 6 residues processed: 111 average time/residue: 0.2595 time to fit residues: 38.3093 Evaluate side-chains 102 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 290 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.208102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166654 restraints weight = 10000.093| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.58 r_work: 0.3676 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9172 Z= 0.178 Angle : 0.522 6.436 12440 Z= 0.273 Chirality : 0.042 0.156 1409 Planarity : 0.004 0.059 1582 Dihedral : 4.173 27.343 1262 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.35 % Allowed : 9.54 % Favored : 89.11 % 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: -1.01 (0.25), residues: 1135 helix: 0.40 (0.28), residues: 357 sheet: -0.50 (0.33), residues: 269 loop : -1.51 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.003 0.001 HIS A 102 PHE 0.015 0.001 PHE E 239 TYR 0.017 0.001 TYR C 145 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.947 Fit side-chains REVERT: A 43 ASN cc_start: 0.4884 (m110) cc_final: 0.4527 (m110) REVERT: A 237 MET cc_start: 0.7169 (mmm) cc_final: 0.6894 (mmt) REVERT: A 250 MET cc_start: 0.6589 (tpt) cc_final: 0.6247 (tpt) REVERT: B 32 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6381 (mmp-170) REVERT: C 251 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6508 (ptt180) REVERT: C 339 TRP cc_start: 0.7703 (m100) cc_final: 0.7458 (m100) REVERT: E 213 THR cc_start: 0.7772 (t) cc_final: 0.7458 (m) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.2660 time to fit residues: 38.0874 Evaluate side-chains 106 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS E 39 GLN E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162907 restraints weight = 9892.919| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.37 r_work: 0.3642 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9172 Z= 0.231 Angle : 0.562 6.625 12440 Z= 0.293 Chirality : 0.043 0.164 1409 Planarity : 0.004 0.061 1582 Dihedral : 4.374 27.177 1262 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.28 % Allowed : 10.89 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1135 helix: 0.41 (0.29), residues: 353 sheet: -0.61 (0.33), residues: 273 loop : -1.44 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 82 HIS 0.003 0.001 HIS A 102 PHE 0.013 0.002 PHE C 235 TYR 0.016 0.002 TYR C 145 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.965 Fit side-chains REVERT: A 43 ASN cc_start: 0.5083 (m110) cc_final: 0.4662 (m110) REVERT: A 237 MET cc_start: 0.7044 (mmm) cc_final: 0.6843 (mmt) REVERT: A 250 MET cc_start: 0.6631 (tpt) cc_final: 0.6280 (tpt) REVERT: C 251 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6332 (ptt180) REVERT: E 213 THR cc_start: 0.7714 (t) cc_final: 0.7395 (m) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.2677 time to fit residues: 41.1145 Evaluate side-chains 113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.208097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166071 restraints weight = 9859.380| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.51 r_work: 0.3670 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9172 Z= 0.152 Angle : 0.492 6.260 12440 Z= 0.258 Chirality : 0.041 0.149 1409 Planarity : 0.004 0.058 1582 Dihedral : 4.100 26.463 1262 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.07 % Allowed : 13.90 % Favored : 84.02 % 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: -0.82 (0.25), residues: 1135 helix: 0.71 (0.29), residues: 350 sheet: -0.55 (0.33), residues: 274 loop : -1.40 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.004 0.001 HIS C 225 PHE 0.013 0.001 PHE E 239 TYR 0.017 0.001 TYR C 145 ARG 0.002 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.977 Fit side-chains REVERT: A 43 ASN cc_start: 0.4871 (m110) cc_final: 0.4491 (m110) REVERT: B 243 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.5880 (m-80) REVERT: C 251 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6167 (ptt180) outliers start: 20 outliers final: 13 residues processed: 117 average time/residue: 0.2523 time to fit residues: 39.6032 Evaluate side-chains 116 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 69 optimal weight: 0.0010 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.208015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166022 restraints weight = 9887.236| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.56 r_work: 0.3667 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9172 Z= 0.167 Angle : 0.516 6.131 12440 Z= 0.268 Chirality : 0.041 0.166 1409 Planarity : 0.004 0.058 1582 Dihedral : 4.077 27.085 1262 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.07 % Allowed : 15.15 % Favored : 82.78 % 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: -0.79 (0.25), residues: 1135 helix: 0.75 (0.29), residues: 350 sheet: -0.54 (0.33), residues: 274 loop : -1.38 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.003 0.001 HIS C 225 PHE 0.011 0.001 PHE E 239 TYR 0.019 0.001 TYR C 145 ARG 0.002 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.961 Fit side-chains REVERT: A 43 ASN cc_start: 0.4916 (m110) cc_final: 0.4532 (m110) REVERT: A 250 MET cc_start: 0.6633 (tpt) cc_final: 0.6313 (tpt) REVERT: B 243 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.5533 (m-80) REVERT: C 251 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6128 (ptt180) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.2467 time to fit residues: 39.6402 Evaluate side-chains 119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.200940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158338 restraints weight = 9981.014| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.49 r_work: 0.3579 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9172 Z= 0.376 Angle : 0.670 7.551 12440 Z= 0.347 Chirality : 0.046 0.172 1409 Planarity : 0.005 0.066 1582 Dihedral : 4.774 27.708 1262 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.28 % Allowed : 15.77 % Favored : 81.95 % 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: -1.16 (0.25), residues: 1135 helix: 0.36 (0.28), residues: 352 sheet: -0.73 (0.32), residues: 276 loop : -1.55 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 339 HIS 0.010 0.001 HIS C 225 PHE 0.017 0.002 PHE A 192 TYR 0.015 0.002 TYR C 145 ARG 0.008 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.998 Fit side-chains REVERT: B 210 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6880 (mm) REVERT: B 243 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: C 251 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6700 (ptt180) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.2536 time to fit residues: 40.8077 Evaluate side-chains 119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.207051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164664 restraints weight = 10053.968| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.42 r_work: 0.3656 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9172 Z= 0.163 Angle : 0.529 7.364 12440 Z= 0.275 Chirality : 0.042 0.149 1409 Planarity : 0.004 0.057 1582 Dihedral : 4.277 26.398 1262 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.97 % Allowed : 16.49 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1135 helix: 0.70 (0.29), residues: 348 sheet: -0.60 (0.32), residues: 273 loop : -1.46 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 339 HIS 0.007 0.001 HIS C 225 PHE 0.016 0.001 PHE C 235 TYR 0.019 0.001 TYR C 145 ARG 0.002 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.949 Fit side-chains REVERT: A 43 ASN cc_start: 0.5182 (m110) cc_final: 0.4707 (m110) REVERT: A 250 MET cc_start: 0.6810 (tpt) cc_final: 0.6333 (tpt) REVERT: B 243 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.5613 (m-80) REVERT: C 189 SER cc_start: 0.8479 (t) cc_final: 0.8278 (t) REVERT: C 251 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6551 (ptt180) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 0.2508 time to fit residues: 37.4541 Evaluate side-chains 117 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.9559 > 50: distance: 12 - 26: 3.002 distance: 36 - 51: 22.241 distance: 48 - 51: 24.453 distance: 51 - 52: 23.326 distance: 52 - 53: 29.010 distance: 52 - 55: 16.597 distance: 53 - 54: 7.910 distance: 53 - 56: 9.715 distance: 56 - 57: 15.024 distance: 57 - 58: 7.956 distance: 57 - 60: 6.580 distance: 58 - 59: 18.418 distance: 58 - 64: 22.556 distance: 59 - 89: 11.198 distance: 60 - 61: 16.212 distance: 61 - 62: 15.514 distance: 61 - 63: 33.209 distance: 64 - 65: 10.707 distance: 65 - 66: 16.631 distance: 65 - 68: 32.030 distance: 66 - 67: 13.889 distance: 66 - 75: 22.884 distance: 68 - 69: 3.554 distance: 69 - 70: 24.219 distance: 69 - 71: 10.598 distance: 70 - 72: 23.629 distance: 71 - 73: 9.001 distance: 72 - 74: 13.743 distance: 73 - 74: 5.654 distance: 75 - 76: 11.873 distance: 76 - 77: 23.098 distance: 76 - 79: 8.774 distance: 77 - 78: 27.196 distance: 77 - 81: 22.952 distance: 79 - 80: 12.419 distance: 81 - 82: 9.498 distance: 82 - 83: 15.745 distance: 82 - 85: 4.009 distance: 83 - 84: 12.539 distance: 83 - 89: 16.121 distance: 85 - 86: 24.949 distance: 86 - 87: 24.731 distance: 86 - 88: 38.473 distance: 89 - 90: 12.988 distance: 90 - 91: 22.159 distance: 90 - 93: 25.102 distance: 91 - 92: 4.103 distance: 91 - 95: 18.494 distance: 93 - 94: 36.397 distance: 95 - 96: 16.309 distance: 96 - 97: 27.080 distance: 96 - 99: 18.613 distance: 97 - 98: 33.658 distance: 97 - 109: 41.795 distance: 99 - 100: 12.476 distance: 100 - 101: 15.583 distance: 100 - 102: 17.684 distance: 101 - 103: 16.317 distance: 102 - 104: 23.554 distance: 102 - 105: 19.719 distance: 103 - 104: 11.557 distance: 104 - 106: 36.345 distance: 105 - 107: 32.409 distance: 106 - 108: 31.716 distance: 107 - 108: 33.793 distance: 109 - 110: 27.514 distance: 110 - 111: 16.738 distance: 110 - 113: 17.628 distance: 111 - 112: 11.282 distance: 111 - 117: 7.219 distance: 112 - 144: 25.704 distance: 113 - 114: 14.670 distance: 114 - 115: 29.956 distance: 115 - 116: 23.688 distance: 117 - 123: 13.973 distance: 118 - 119: 11.241 distance: 118 - 121: 20.083 distance: 119 - 120: 18.014 distance: 119 - 124: 5.986 distance: 120 - 149: 25.174 distance: 121 - 122: 24.583 distance: 122 - 123: 24.268 distance: 124 - 125: 6.915 distance: 125 - 126: 5.277 distance: 125 - 128: 10.661 distance: 126 - 127: 5.798 distance: 126 - 134: 6.235 distance: 128 - 129: 4.079 distance: 129 - 130: 20.747 distance: 129 - 131: 19.286 distance: 130 - 132: 11.099 distance: 131 - 133: 12.781 distance: 132 - 133: 24.292