Starting phenix.real_space_refine on Wed Mar 4 12:55:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhh_22337/03_2026/7jhh_22337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhh_22337/03_2026/7jhh_22337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jhh_22337/03_2026/7jhh_22337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhh_22337/03_2026/7jhh_22337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jhh_22337/03_2026/7jhh_22337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhh_22337/03_2026/7jhh_22337.map" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 51 5.16 5 C 8559 2.51 5 N 2253 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13418 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3074 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 3.16, per 1000 atoms: 0.24 Number of scatterers: 13418 At special positions: 0 Unit cell: (103.929, 129.654, 163.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 6 15.00 O 2549 8.00 N 2253 7.00 C 8559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " 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 Links applied ALPHA1-4 " GLC C 1 " - " GLC C 2 " TRANS " VAL A 13 " - " PHE M 371 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 634.7 milliseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 27 sheets defined 30.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.947A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 114 through 135 removed outlier: 3.561A pdb=" N ARG A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 removed outlier: 4.164A pdb=" N ASN A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.702A pdb=" N ILE A 199 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.898A pdb=" N ILE A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.697A pdb=" N MET A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 549 removed outlier: 3.585A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.731A pdb=" N VAL B 215 " --> pdb=" O HIS B 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.670A pdb=" N SER G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 removed outlier: 3.589A pdb=" N ASP G 40 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 68 removed outlier: 3.632A pdb=" N ALA G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.974A pdb=" N GLU G 110 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.578A pdb=" N GLU G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.648A pdb=" N ARG G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.635A pdb=" N LEU G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'G' and resid 212 through 223 removed outlier: 3.741A pdb=" N ALA G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 removed outlier: 3.681A pdb=" N ALA G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 284 through 295 removed outlier: 3.575A pdb=" N GLU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 324 removed outlier: 3.708A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 324 " --> pdb=" O GLN G 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 32 removed outlier: 3.545A pdb=" N LEU M 20 " --> pdb=" O GLY M 16 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 52 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 66 through 73 removed outlier: 3.718A pdb=" N SER M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 88 Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 131 through 140 removed outlier: 3.693A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 143 No H-bonds generated for 'chain 'M' and resid 141 through 143' Processing helix chain 'M' and resid 153 through 163 removed outlier: 4.033A pdb=" N THR M 157 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.692A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 219 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 231 through 238 Processing helix chain 'M' and resid 272 through 284 Processing helix chain 'M' and resid 286 through 297 removed outlier: 3.876A pdb=" N GLU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL M 293 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 312 removed outlier: 3.867A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 326 Processing helix chain 'M' and resid 334 through 352 removed outlier: 4.096A pdb=" N ALA M 338 " --> pdb=" O PRO M 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR M 341 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA M 342 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 367 Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.626A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 128' Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.960A pdb=" N GLU L 188 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.926A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.583A pdb=" N LEU H 205 " --> pdb=" O SER H 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 100 removed outlier: 4.123A pdb=" N THR N 100 " --> pdb=" O PRO N 97 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.987A pdb=" N VAL A 34 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR A 23 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 32 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 83 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU A 96 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 81 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404 Processing sheet with id=AA4, first strand: chain 'B' and resid 250 through 255 removed outlier: 3.533A pdb=" N LYS B 270 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N LYS G 47 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL G 49 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N TRP G 75 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE G 51 " --> pdb=" O TRP G 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY G 84 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP G 76 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE G 82 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 153 through 156 removed outlier: 3.747A pdb=" N LEU G 153 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR G 165 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 207 through 208 removed outlier: 6.534A pdb=" N VAL G 207 " --> pdb=" O VAL G 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'G' and resid 278 through 280 removed outlier: 4.140A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.613A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.613A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'M' and resid 145 through 147 removed outlier: 8.165A pdb=" N SER M 145 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR M 225 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU M 147 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ASN M 227 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA M 223 " --> pdb=" O ASN M 118 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN M 227 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER M 114 " --> pdb=" O ASN M 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 170 through 171 removed outlier: 4.032A pdb=" N LYS M 170 " --> pdb=" O ASP M 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.175A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.175A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.522A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.522A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER L 68 " --> pdb=" O ASP L 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.207A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.581A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA L 194 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.596A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS H 25 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.512A pdb=" N ALA H 95 " --> pdb=" O VAL H 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.530A pdb=" N SER H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.524A pdb=" N LYS H 159 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.524A pdb=" N LYS H 159 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 185 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.864A pdb=" N TYR H 210 " --> pdb=" O VAL H 227 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 14 through 17 removed outlier: 3.585A pdb=" N CYS N 31 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 67 through 69 removed outlier: 6.644A pdb=" N TRP N 45 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL N 59 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET N 43 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS N 105 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN N 122 " --> pdb=" O CYS N 105 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE N 107 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TRP N 120 " --> pdb=" O ILE N 107 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1335 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: 1.96 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4249 1.34 - 1.46: 3141 1.46 - 1.58: 6258 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13738 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.60e+01 ... (remaining 13733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 18542 3.76 - 7.52: 104 7.52 - 11.28: 11 11.28 - 15.04: 0 15.04 - 18.80: 2 Bond angle restraints: 18659 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.07 18.80 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 121.31 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.69 8.11 1.00e+00 1.00e+00 6.57e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.59 5.10 1.00e+00 1.00e+00 2.60e+01 ... (remaining 18654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 8143 23.71 - 47.41: 127 47.41 - 71.12: 11 71.12 - 94.82: 6 94.82 - 118.53: 1 Dihedral angle restraints: 8288 sinusoidal: 3329 harmonic: 4959 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 19.66 73.34 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 58.53 -118.53 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA ASN A 69 " pdb=" C ASN A 69 " pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1850 0.079 - 0.159: 221 0.159 - 0.238: 13 0.238 - 0.318: 0 0.318 - 0.397: 2 Chirality restraints: 2086 Sorted by residual: chirality pdb=" C1 GLC C 2 " pdb=" O4 GLC C 1 " pdb=" C2 GLC C 2 " pdb=" O5 GLC C 2 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 1.88e+01 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 GLC C 1 " pdb=" C2 GLC C 1 " pdb=" O1 GLC C 1 " pdb=" O5 GLC C 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2083 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO L 9 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 430 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 431 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 144 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.028 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3867 2.82 - 3.34: 11216 3.34 - 3.86: 21641 3.86 - 4.38: 24291 4.38 - 4.90: 42444 Nonbonded interactions: 103459 Sorted by model distance: nonbonded pdb=" OE1 GLU M 111 " pdb=" O2 GLC C 1 " model vdw 2.300 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.310 3.040 nonbonded pdb=" OG1 THR G 89 " pdb=" O1B ADP G 402 " model vdw 2.347 3.040 nonbonded pdb=" OD2 ASP G 52 " pdb=" OG SER G 54 " model vdw 2.365 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.368 3.040 ... (remaining 103454 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.230 Find NCS groups from input model: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.004 0.082 13745 Z= 0.206 Angle : 0.790 18.796 18675 Z= 0.447 Chirality : 0.051 0.397 2086 Planarity : 0.007 0.061 2359 Dihedral : 9.124 118.528 5088 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.17), residues: 1682 helix: -2.88 (0.16), residues: 434 sheet: -1.80 (0.27), residues: 327 loop : -1.98 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 435 TYR 0.016 0.002 TYR H 102 PHE 0.029 0.002 PHE A 225 TRP 0.020 0.002 TRP H 119 HIS 0.006 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00352 (13738) covalent geometry : angle 0.78054 (18659) SS BOND : bond 0.00372 ( 5) SS BOND : angle 5.24720 ( 10) hydrogen bonds : bond 0.20653 ( 452) hydrogen bonds : angle 8.83066 ( 1335) link_ALPHA1-4 : bond 0.00850 ( 1) link_ALPHA1-4 : angle 1.33096 ( 3) link_TRANS : bond 0.00102 ( 1) link_TRANS : angle 0.48354 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7035 (t0) cc_final: 0.6476 (t0) REVERT: A 99 SER cc_start: 0.8405 (m) cc_final: 0.8102 (t) REVERT: A 222 PRO cc_start: 0.9282 (Cg_exo) cc_final: 0.8975 (Cg_endo) REVERT: B 192 GLU cc_start: 0.6717 (pt0) cc_final: 0.6342 (tt0) REVERT: B 193 MET cc_start: 0.7938 (mtt) cc_final: 0.7571 (mpp) REVERT: B 252 VAL cc_start: 0.8328 (t) cc_final: 0.7904 (t) REVERT: G 75 TRP cc_start: 0.7189 (t-100) cc_final: 0.6902 (t-100) REVERT: G 143 SER cc_start: 0.8540 (t) cc_final: 0.8225 (p) REVERT: G 169 HIS cc_start: 0.7884 (m-70) cc_final: 0.7384 (m170) REVERT: G 189 MET cc_start: 0.9024 (mmt) cc_final: 0.8782 (mmt) REVERT: G 319 LEU cc_start: 0.9056 (mt) cc_final: 0.8336 (tp) REVERT: M 67 PHE cc_start: 0.8835 (m-10) cc_final: 0.8089 (m-80) REVERT: M 94 TRP cc_start: 0.7809 (m100) cc_final: 0.7489 (m100) REVERT: M 113 LEU cc_start: 0.8276 (mt) cc_final: 0.7943 (mt) REVERT: M 365 GLN cc_start: 0.8580 (tp40) cc_final: 0.8214 (tp40) REVERT: L 83 ASP cc_start: 0.7388 (m-30) cc_final: 0.6407 (m-30) REVERT: L 97 ILE cc_start: 0.9072 (mt) cc_final: 0.8865 (mm) REVERT: L 203 SER cc_start: 0.7022 (t) cc_final: 0.5982 (p) REVERT: H 213 ASN cc_start: 0.8350 (m110) cc_final: 0.7654 (m-40) REVERT: N 45 TRP cc_start: 0.7203 (m100) cc_final: 0.6801 (m100) REVERT: N 82 ASP cc_start: 0.7148 (t70) cc_final: 0.6779 (t70) REVERT: N 92 MET cc_start: 0.8959 (mtm) cc_final: 0.8516 (mtm) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.1292 time to fit residues: 83.1549 Evaluate side-chains 238 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 146 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS G 223 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 HIS M 86 GLN M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 HIS H 180 HIS N 12 GLN N 86 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.087706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064941 restraints weight = 57634.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067134 restraints weight = 32385.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068462 restraints weight = 22516.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069431 restraints weight = 17928.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069985 restraints weight = 15462.852| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 13745 Z= 0.233 Angle : 0.752 13.715 18675 Z= 0.382 Chirality : 0.045 0.236 2086 Planarity : 0.006 0.052 2359 Dihedral : 6.117 73.461 1937 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.80 % Allowed : 11.89 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.19), residues: 1682 helix: -1.21 (0.22), residues: 449 sheet: -1.25 (0.27), residues: 347 loop : -1.27 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.021 0.002 TYR H 109 PHE 0.028 0.002 PHE M 279 TRP 0.015 0.002 TRP H 119 HIS 0.006 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00516 (13738) covalent geometry : angle 0.75072 (18659) SS BOND : bond 0.00627 ( 5) SS BOND : angle 1.96528 ( 10) hydrogen bonds : bond 0.03779 ( 452) hydrogen bonds : angle 6.25351 ( 1335) link_ALPHA1-4 : bond 0.00492 ( 1) link_ALPHA1-4 : angle 2.00059 ( 3) link_TRANS : bond 0.00494 ( 1) link_TRANS : angle 0.60132 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.7063 (t0) cc_final: 0.6786 (t0) REVERT: A 453 LEU cc_start: 0.8274 (tp) cc_final: 0.8070 (tp) REVERT: B 258 ARG cc_start: 0.8285 (tpt-90) cc_final: 0.7767 (tpt-90) REVERT: G 159 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7858 (tp30) REVERT: G 169 HIS cc_start: 0.8366 (m-70) cc_final: 0.7789 (m170) REVERT: G 259 ASP cc_start: 0.8485 (m-30) cc_final: 0.8183 (p0) REVERT: G 319 LEU cc_start: 0.9169 (mt) cc_final: 0.8879 (mp) REVERT: G 320 GLN cc_start: 0.8698 (tp40) cc_final: 0.8335 (mm110) REVERT: M 67 PHE cc_start: 0.8985 (m-10) cc_final: 0.8579 (m-80) REVERT: M 94 TRP cc_start: 0.8114 (m100) cc_final: 0.7524 (m100) REVERT: M 148 MET cc_start: 0.7683 (tpp) cc_final: 0.7427 (tpp) REVERT: M 224 MET cc_start: 0.8430 (mtm) cc_final: 0.8220 (ptp) REVERT: M 321 MET cc_start: 0.8877 (mmm) cc_final: 0.8476 (mmp) REVERT: M 344 ARG cc_start: 0.8937 (ttp-170) cc_final: 0.8705 (ttm170) REVERT: L 19 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7404 (ttp80) REVERT: L 34 VAL cc_start: 0.9348 (t) cc_final: 0.9123 (m) REVERT: L 64 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8394 (p) REVERT: L 97 ILE cc_start: 0.9309 (mt) cc_final: 0.9059 (mm) REVERT: L 138 ASN cc_start: 0.8574 (t0) cc_final: 0.8291 (t0) REVERT: H 93 ASP cc_start: 0.8050 (m-30) cc_final: 0.7838 (m-30) REVERT: N 41 TYR cc_start: 0.7038 (m-80) cc_final: 0.6727 (m-80) REVERT: N 43 MET cc_start: 0.6840 (mmp) cc_final: 0.6570 (mmp) REVERT: N 48 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7248 (tp-100) REVERT: N 92 MET cc_start: 0.9046 (mtm) cc_final: 0.7770 (mtt) outliers start: 41 outliers final: 24 residues processed: 276 average time/residue: 0.1192 time to fit residues: 47.4788 Evaluate side-chains 201 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain M residue 255 SER Chi-restraints excluded: chain M residue 337 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 95 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 18 optimal weight: 0.8980 chunk 133 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 91 optimal weight: 0.0970 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064796 restraints weight = 56777.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066936 restraints weight = 32067.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068350 restraints weight = 22245.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069216 restraints weight = 17598.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069842 restraints weight = 15150.513| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13745 Z= 0.145 Angle : 0.655 8.998 18675 Z= 0.329 Chirality : 0.044 0.187 2086 Planarity : 0.005 0.045 2359 Dihedral : 5.800 65.421 1937 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.60 % Allowed : 15.10 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1682 helix: -0.58 (0.24), residues: 439 sheet: -1.11 (0.27), residues: 359 loop : -0.98 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 459 TYR 0.026 0.001 TYR B 242 PHE 0.019 0.002 PHE M 279 TRP 0.021 0.002 TRP N 45 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00326 (13738) covalent geometry : angle 0.65377 (18659) SS BOND : bond 0.00447 ( 5) SS BOND : angle 1.31537 ( 10) hydrogen bonds : bond 0.03354 ( 452) hydrogen bonds : angle 5.83750 ( 1335) link_ALPHA1-4 : bond 0.00144 ( 1) link_ALPHA1-4 : angle 1.98877 ( 3) link_TRANS : bond 0.00098 ( 1) link_TRANS : angle 0.11599 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.8514 (m-30) cc_final: 0.8109 (m-30) REVERT: A 453 LEU cc_start: 0.8347 (tp) cc_final: 0.8128 (tp) REVERT: B 242 TYR cc_start: 0.6883 (m-80) cc_final: 0.6674 (m-80) REVERT: B 263 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.4967 (m-10) REVERT: G 33 MET cc_start: 0.8534 (mtm) cc_final: 0.8282 (ttp) REVERT: G 75 TRP cc_start: 0.7355 (t-100) cc_final: 0.6731 (t-100) REVERT: G 159 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7844 (tp30) REVERT: G 320 GLN cc_start: 0.8645 (tp40) cc_final: 0.8360 (tp40) REVERT: M 67 PHE cc_start: 0.8958 (m-10) cc_final: 0.8478 (m-80) REVERT: M 94 TRP cc_start: 0.7545 (m100) cc_final: 0.7099 (m100) REVERT: M 210 TYR cc_start: 0.6728 (t80) cc_final: 0.6260 (t80) REVERT: M 321 MET cc_start: 0.8867 (mmm) cc_final: 0.8611 (mmm) REVERT: L 19 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7457 (ttp80) REVERT: L 34 VAL cc_start: 0.9372 (t) cc_final: 0.9116 (p) REVERT: L 83 ASP cc_start: 0.7862 (m-30) cc_final: 0.7629 (m-30) REVERT: L 97 ILE cc_start: 0.9317 (mt) cc_final: 0.9071 (mm) REVERT: L 138 ASN cc_start: 0.8566 (t0) cc_final: 0.8259 (t0) REVERT: N 12 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5046 (pp30) REVERT: N 41 TYR cc_start: 0.7136 (m-80) cc_final: 0.6819 (m-80) outliers start: 38 outliers final: 21 residues processed: 241 average time/residue: 0.1062 time to fit residues: 38.6132 Evaluate side-chains 201 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 18 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.088102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066907 restraints weight = 56494.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068139 restraints weight = 33100.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068242 restraints weight = 25021.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068631 restraints weight = 24551.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068679 restraints weight = 22121.191| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13745 Z= 0.119 Angle : 0.635 8.254 18675 Z= 0.313 Chirality : 0.043 0.218 2086 Planarity : 0.004 0.050 2359 Dihedral : 5.531 51.282 1937 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.66 % Allowed : 16.26 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1682 helix: -0.29 (0.25), residues: 431 sheet: -0.91 (0.27), residues: 359 loop : -0.84 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 97 TYR 0.024 0.001 TYR G 98 PHE 0.021 0.001 PHE N 46 TRP 0.019 0.001 TRP A 269 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00275 (13738) covalent geometry : angle 0.63395 (18659) SS BOND : bond 0.00138 ( 5) SS BOND : angle 0.97891 ( 10) hydrogen bonds : bond 0.03141 ( 452) hydrogen bonds : angle 5.54076 ( 1335) link_ALPHA1-4 : bond 0.00217 ( 1) link_ALPHA1-4 : angle 1.98958 ( 3) link_TRANS : bond 0.00045 ( 1) link_TRANS : angle 0.12684 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8312 (m) REVERT: A 105 ASP cc_start: 0.8514 (m-30) cc_final: 0.8289 (m-30) REVERT: A 256 MET cc_start: 0.7404 (tpp) cc_final: 0.7187 (tpp) REVERT: A 453 LEU cc_start: 0.8371 (tp) cc_final: 0.8152 (tp) REVERT: B 237 MET cc_start: 0.7869 (ptp) cc_final: 0.7408 (ptp) REVERT: B 242 TYR cc_start: 0.7048 (m-80) cc_final: 0.6521 (m-80) REVERT: G 33 MET cc_start: 0.8596 (mtm) cc_final: 0.8359 (ttp) REVERT: G 159 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7900 (tp30) REVERT: M 42 LYS cc_start: 0.8924 (mmtm) cc_final: 0.8354 (mmmt) REVERT: M 57 PRO cc_start: 0.7173 (Cg_endo) cc_final: 0.6905 (Cg_exo) REVERT: M 67 PHE cc_start: 0.8890 (m-10) cc_final: 0.8446 (m-80) REVERT: M 94 TRP cc_start: 0.7509 (m100) cc_final: 0.7084 (m100) REVERT: M 148 MET cc_start: 0.7753 (tpp) cc_final: 0.7476 (tpp) REVERT: M 210 TYR cc_start: 0.6930 (t80) cc_final: 0.6428 (t80) REVERT: M 321 MET cc_start: 0.8828 (mmm) cc_final: 0.8515 (mmp) REVERT: L 34 VAL cc_start: 0.9339 (t) cc_final: 0.9101 (p) REVERT: L 97 ILE cc_start: 0.9357 (mt) cc_final: 0.9072 (mm) REVERT: L 138 ASN cc_start: 0.8340 (t0) cc_final: 0.8050 (t0) REVERT: N 41 TYR cc_start: 0.7074 (m-80) cc_final: 0.6806 (m-80) outliers start: 39 outliers final: 28 residues processed: 234 average time/residue: 0.0951 time to fit residues: 34.2217 Evaluate side-chains 202 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 78 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.087429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066433 restraints weight = 56809.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067474 restraints weight = 32975.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067601 restraints weight = 25480.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067945 restraints weight = 24286.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068046 restraints weight = 22374.964| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13745 Z= 0.127 Angle : 0.641 13.064 18675 Z= 0.314 Chirality : 0.042 0.166 2086 Planarity : 0.004 0.052 2359 Dihedral : 5.453 46.482 1937 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.21 % Allowed : 16.33 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1682 helix: -0.08 (0.25), residues: 440 sheet: -0.76 (0.27), residues: 354 loop : -0.75 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 19 TYR 0.023 0.001 TYR G 98 PHE 0.019 0.001 PHE N 46 TRP 0.034 0.002 TRP A 398 HIS 0.007 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00291 (13738) covalent geometry : angle 0.63989 (18659) SS BOND : bond 0.00132 ( 5) SS BOND : angle 1.21481 ( 10) hydrogen bonds : bond 0.03010 ( 452) hydrogen bonds : angle 5.34469 ( 1335) link_ALPHA1-4 : bond 0.00056 ( 1) link_ALPHA1-4 : angle 1.87685 ( 3) link_TRANS : bond 0.00112 ( 1) link_TRANS : angle 0.12266 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8313 (m) REVERT: A 105 ASP cc_start: 0.8731 (m-30) cc_final: 0.8461 (m-30) REVERT: A 453 LEU cc_start: 0.8293 (tp) cc_final: 0.7995 (tp) REVERT: B 193 MET cc_start: 0.6530 (ppp) cc_final: 0.6327 (ppp) REVERT: B 251 MET cc_start: 0.7403 (tpp) cc_final: 0.7106 (tpp) REVERT: G 159 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7875 (tp30) REVERT: G 320 GLN cc_start: 0.8540 (tp40) cc_final: 0.8309 (mm110) REVERT: M 67 PHE cc_start: 0.8820 (m-10) cc_final: 0.8407 (m-80) REVERT: M 94 TRP cc_start: 0.7504 (m100) cc_final: 0.7053 (m100) REVERT: M 204 MET cc_start: 0.5934 (tpt) cc_final: 0.5694 (tpt) REVERT: M 210 TYR cc_start: 0.6984 (t80) cc_final: 0.6476 (t80) REVERT: M 224 MET cc_start: 0.8202 (ptp) cc_final: 0.7888 (ptp) REVERT: M 321 MET cc_start: 0.8746 (mmm) cc_final: 0.8473 (mmp) REVERT: M 359 GLU cc_start: 0.8349 (pt0) cc_final: 0.7832 (pt0) REVERT: L 19 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7310 (ttp80) REVERT: L 34 VAL cc_start: 0.9391 (t) cc_final: 0.9157 (p) REVERT: L 97 ILE cc_start: 0.9337 (mt) cc_final: 0.9054 (mm) REVERT: L 138 ASN cc_start: 0.8285 (t0) cc_final: 0.8039 (t0) REVERT: N 12 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.5226 (pp30) REVERT: N 36 ARG cc_start: 0.4195 (ptm-80) cc_final: 0.3047 (ptm160) REVERT: N 41 TYR cc_start: 0.7164 (m-80) cc_final: 0.6763 (m-80) REVERT: N 53 GLU cc_start: 0.8219 (pm20) cc_final: 0.8005 (pm20) REVERT: N 55 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8218 (mp0) outliers start: 47 outliers final: 33 residues processed: 228 average time/residue: 0.1050 time to fit residues: 35.5812 Evaluate side-chains 210 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 26 optimal weight: 0.0030 chunk 119 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.065876 restraints weight = 56421.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067028 restraints weight = 33240.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.067296 restraints weight = 25037.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067807 restraints weight = 23901.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067793 restraints weight = 21551.314| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13745 Z= 0.123 Angle : 0.642 12.686 18675 Z= 0.312 Chirality : 0.042 0.255 2086 Planarity : 0.004 0.043 2359 Dihedral : 5.410 42.742 1937 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.07 % Allowed : 17.35 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1682 helix: 0.13 (0.25), residues: 446 sheet: -0.63 (0.27), residues: 356 loop : -0.70 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 28 TYR 0.019 0.001 TYR G 98 PHE 0.018 0.001 PHE N 46 TRP 0.045 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00283 (13738) covalent geometry : angle 0.64170 (18659) SS BOND : bond 0.00175 ( 5) SS BOND : angle 1.05844 ( 10) hydrogen bonds : bond 0.02975 ( 452) hydrogen bonds : angle 5.19110 ( 1335) link_ALPHA1-4 : bond 0.00040 ( 1) link_ALPHA1-4 : angle 1.91564 ( 3) link_TRANS : bond 0.00100 ( 1) link_TRANS : angle 0.10582 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8287 (m) REVERT: A 105 ASP cc_start: 0.8707 (m-30) cc_final: 0.8463 (m-30) REVERT: A 453 LEU cc_start: 0.8361 (tp) cc_final: 0.8138 (tp) REVERT: B 193 MET cc_start: 0.6477 (ppp) cc_final: 0.6250 (ppp) REVERT: B 251 MET cc_start: 0.7537 (tpp) cc_final: 0.7247 (tpp) REVERT: G 159 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7898 (tp30) REVERT: G 320 GLN cc_start: 0.8531 (tp40) cc_final: 0.8310 (mm110) REVERT: M 67 PHE cc_start: 0.8860 (m-10) cc_final: 0.8353 (m-80) REVERT: M 94 TRP cc_start: 0.7584 (m100) cc_final: 0.7016 (m100) REVERT: M 148 MET cc_start: 0.7973 (tpp) cc_final: 0.7537 (tpp) REVERT: M 210 TYR cc_start: 0.7039 (t80) cc_final: 0.6535 (t80) REVERT: M 321 MET cc_start: 0.8801 (mmm) cc_final: 0.8511 (mmp) REVERT: M 355 GLN cc_start: 0.8096 (mt0) cc_final: 0.7858 (mm-40) REVERT: L 19 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7176 (ttp80) REVERT: L 34 VAL cc_start: 0.9394 (t) cc_final: 0.9175 (p) REVERT: L 97 ILE cc_start: 0.9302 (mt) cc_final: 0.8991 (mm) REVERT: L 138 ASN cc_start: 0.8315 (t0) cc_final: 0.8015 (t0) REVERT: H 54 ILE cc_start: 0.9264 (tt) cc_final: 0.8977 (pt) REVERT: N 36 ARG cc_start: 0.4553 (ptm-80) cc_final: 0.3494 (ptm160) REVERT: N 41 TYR cc_start: 0.7400 (m-80) cc_final: 0.7066 (m-80) REVERT: N 46 PHE cc_start: 0.7854 (m-80) cc_final: 0.7643 (t80) REVERT: N 93 ASN cc_start: 0.8647 (m-40) cc_final: 0.7570 (p0) outliers start: 45 outliers final: 35 residues processed: 217 average time/residue: 0.0948 time to fit residues: 32.1808 Evaluate side-chains 201 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 16 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS N 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.087323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064913 restraints weight = 56424.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.067055 restraints weight = 32487.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068456 restraints weight = 22822.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069332 restraints weight = 18178.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069929 restraints weight = 15758.259| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13745 Z= 0.120 Angle : 0.652 10.593 18675 Z= 0.316 Chirality : 0.043 0.247 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.360 42.457 1937 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.14 % Allowed : 17.90 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1682 helix: 0.39 (0.26), residues: 443 sheet: -0.49 (0.27), residues: 363 loop : -0.61 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 208 TYR 0.028 0.001 TYR L 87 PHE 0.038 0.001 PHE H 71 TRP 0.061 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00279 (13738) covalent geometry : angle 0.65168 (18659) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.99077 ( 10) hydrogen bonds : bond 0.02897 ( 452) hydrogen bonds : angle 5.07830 ( 1335) link_ALPHA1-4 : bond 0.00234 ( 1) link_ALPHA1-4 : angle 1.85815 ( 3) link_TRANS : bond 0.00090 ( 1) link_TRANS : angle 0.09649 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 234 ASN cc_start: 0.7740 (t0) cc_final: 0.7463 (t0) REVERT: B 242 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6392 (t80) REVERT: B 251 MET cc_start: 0.7481 (tpp) cc_final: 0.7182 (tpp) REVERT: G 159 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7884 (tp30) REVERT: G 206 MET cc_start: 0.8361 (mmm) cc_final: 0.8144 (mmm) REVERT: M 67 PHE cc_start: 0.8840 (m-10) cc_final: 0.8398 (m-80) REVERT: M 94 TRP cc_start: 0.7621 (m100) cc_final: 0.6994 (m100) REVERT: M 148 MET cc_start: 0.7950 (tpp) cc_final: 0.7627 (tpp) REVERT: M 321 MET cc_start: 0.8799 (mmm) cc_final: 0.8522 (mmp) REVERT: L 19 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7175 (ttp80) REVERT: L 34 VAL cc_start: 0.9408 (t) cc_final: 0.9203 (p) REVERT: L 83 ASP cc_start: 0.7854 (t0) cc_final: 0.7611 (t0) REVERT: L 97 ILE cc_start: 0.9261 (mt) cc_final: 0.8926 (mm) REVERT: L 138 ASN cc_start: 0.8294 (t0) cc_final: 0.8080 (t0) REVERT: H 54 ILE cc_start: 0.9249 (tt) cc_final: 0.8980 (pt) REVERT: N 22 GLN cc_start: 0.7396 (pp30) cc_final: 0.6978 (tp-100) REVERT: N 36 ARG cc_start: 0.3956 (ptm-80) cc_final: 0.3306 (ptm160) REVERT: N 41 TYR cc_start: 0.7394 (m-80) cc_final: 0.7083 (m-80) REVERT: N 93 ASN cc_start: 0.8610 (m-40) cc_final: 0.7388 (p0) outliers start: 46 outliers final: 37 residues processed: 214 average time/residue: 0.0917 time to fit residues: 30.9799 Evaluate side-chains 209 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 108 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 0.0970 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 164 ASN G 148 ASN ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS M 323 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.083567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060956 restraints weight = 56778.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062905 restraints weight = 33696.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064181 restraints weight = 24089.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064958 restraints weight = 19467.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065488 restraints weight = 17097.165| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13745 Z= 0.226 Angle : 0.738 9.844 18675 Z= 0.366 Chirality : 0.044 0.218 2086 Planarity : 0.006 0.117 2359 Dihedral : 5.761 49.194 1937 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.48 % Allowed : 18.31 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1682 helix: 0.51 (0.25), residues: 433 sheet: -0.59 (0.26), residues: 370 loop : -0.67 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 90 TYR 0.025 0.002 TYR L 87 PHE 0.022 0.002 PHE N 46 TRP 0.041 0.002 TRP A 398 HIS 0.009 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00498 (13738) covalent geometry : angle 0.73710 (18659) SS BOND : bond 0.00533 ( 5) SS BOND : angle 0.99846 ( 10) hydrogen bonds : bond 0.03319 ( 452) hydrogen bonds : angle 5.38704 ( 1335) link_ALPHA1-4 : bond 0.00815 ( 1) link_ALPHA1-4 : angle 1.86010 ( 3) link_TRANS : bond 0.00463 ( 1) link_TRANS : angle 0.21977 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 159 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7904 (tp30) REVERT: G 267 GLN cc_start: 0.9028 (pm20) cc_final: 0.8519 (pm20) REVERT: M 67 PHE cc_start: 0.8878 (m-10) cc_final: 0.8507 (m-80) REVERT: M 94 TRP cc_start: 0.7974 (m100) cc_final: 0.7329 (m100) REVERT: M 148 MET cc_start: 0.8152 (tpp) cc_final: 0.7800 (tpp) REVERT: M 321 MET cc_start: 0.8785 (mmm) cc_final: 0.8564 (mmm) REVERT: L 97 ILE cc_start: 0.9298 (mt) cc_final: 0.8992 (mm) REVERT: L 171 ASP cc_start: 0.8451 (t0) cc_final: 0.8198 (t0) REVERT: N 12 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.4875 (tp40) REVERT: N 22 GLN cc_start: 0.7670 (pp30) cc_final: 0.7275 (tp-100) REVERT: N 36 ARG cc_start: 0.4232 (ptm-80) cc_final: 0.3598 (ptp-170) REVERT: N 52 LYS cc_start: 0.7636 (tttm) cc_final: 0.7402 (tmmt) REVERT: N 55 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8363 (mp0) REVERT: N 93 ASN cc_start: 0.8570 (m-40) cc_final: 0.7928 (p0) outliers start: 51 outliers final: 41 residues processed: 204 average time/residue: 0.0989 time to fit residues: 31.2787 Evaluate side-chains 197 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 180 HIS Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 136 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 HIS ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.085554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066488 restraints weight = 55926.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066890 restraints weight = 33579.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066986 restraints weight = 30319.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067274 restraints weight = 26788.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067581 restraints weight = 24560.524| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13745 Z= 0.131 Angle : 0.700 10.773 18675 Z= 0.341 Chirality : 0.044 0.218 2086 Planarity : 0.004 0.043 2359 Dihedral : 5.552 46.077 1937 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.32 % Allowed : 19.06 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1682 helix: 0.61 (0.26), residues: 435 sheet: -0.51 (0.27), residues: 358 loop : -0.60 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 19 TYR 0.024 0.001 TYR H 161 PHE 0.022 0.002 PHE H 71 TRP 0.035 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00304 (13738) covalent geometry : angle 0.69994 (18659) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.85171 ( 10) hydrogen bonds : bond 0.02929 ( 452) hydrogen bonds : angle 5.20347 ( 1335) link_ALPHA1-4 : bond 0.00049 ( 1) link_ALPHA1-4 : angle 1.64202 ( 3) link_TRANS : bond 0.00044 ( 1) link_TRANS : angle 0.06318 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7304 (m-40) cc_final: 0.7047 (m110) REVERT: A 256 MET cc_start: 0.8144 (mmm) cc_final: 0.7851 (mmm) REVERT: B 242 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6983 (t80) REVERT: B 251 MET cc_start: 0.7727 (tpp) cc_final: 0.7363 (tpp) REVERT: G 159 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7917 (tp30) REVERT: G 267 GLN cc_start: 0.9014 (pm20) cc_final: 0.8454 (pm20) REVERT: M 67 PHE cc_start: 0.8907 (m-10) cc_final: 0.8499 (m-80) REVERT: M 94 TRP cc_start: 0.7757 (m100) cc_final: 0.6960 (m100) REVERT: M 148 MET cc_start: 0.8106 (tpp) cc_final: 0.7758 (tpp) REVERT: M 321 MET cc_start: 0.8841 (mmm) cc_final: 0.8584 (mmp) REVERT: H 194 LEU cc_start: 0.9292 (tp) cc_final: 0.9028 (tt) REVERT: N 12 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.4860 (tp40) REVERT: N 22 GLN cc_start: 0.7603 (pp30) cc_final: 0.7227 (tp-100) REVERT: N 36 ARG cc_start: 0.4428 (ptm-80) cc_final: 0.3819 (ptm160) REVERT: N 46 PHE cc_start: 0.7309 (t80) cc_final: 0.7056 (t80) REVERT: N 93 ASN cc_start: 0.8556 (m-40) cc_final: 0.7781 (p0) outliers start: 34 outliers final: 29 residues processed: 210 average time/residue: 0.0946 time to fit residues: 31.2769 Evaluate side-chains 195 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 102 optimal weight: 0.0770 chunk 108 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.084714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061942 restraints weight = 56736.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063982 restraints weight = 32631.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065309 restraints weight = 23032.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.066142 restraints weight = 18475.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066680 restraints weight = 16082.762| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13745 Z= 0.163 Angle : 0.714 10.574 18675 Z= 0.349 Chirality : 0.044 0.247 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.532 43.969 1937 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.32 % Allowed : 19.74 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1682 helix: 0.49 (0.25), residues: 436 sheet: -0.41 (0.27), residues: 353 loop : -0.60 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 19 TYR 0.020 0.002 TYR L 87 PHE 0.018 0.002 PHE H 71 TRP 0.030 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd covalent geometry : bond 0.00373 (13738) covalent geometry : angle 0.71335 (18659) SS BOND : bond 0.00222 ( 5) SS BOND : angle 1.04189 ( 10) hydrogen bonds : bond 0.03085 ( 452) hydrogen bonds : angle 5.22604 ( 1335) link_ALPHA1-4 : bond 0.00210 ( 1) link_ALPHA1-4 : angle 1.71434 ( 3) link_TRANS : bond 0.00224 ( 1) link_TRANS : angle 0.11270 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7269 (m-40) cc_final: 0.7015 (m110) REVERT: B 242 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7363 (t80) REVERT: B 251 MET cc_start: 0.7676 (tpp) cc_final: 0.7299 (tpp) REVERT: G 267 GLN cc_start: 0.9020 (pm20) cc_final: 0.8446 (pm20) REVERT: M 67 PHE cc_start: 0.8894 (m-10) cc_final: 0.8478 (m-80) REVERT: M 94 TRP cc_start: 0.7870 (m100) cc_final: 0.7282 (m100) REVERT: M 148 MET cc_start: 0.8159 (tpp) cc_final: 0.7810 (tpp) REVERT: M 321 MET cc_start: 0.8781 (mmm) cc_final: 0.8496 (mmm) REVERT: H 194 LEU cc_start: 0.9319 (tp) cc_final: 0.9018 (tt) REVERT: N 22 GLN cc_start: 0.7535 (pp30) cc_final: 0.7212 (tp-100) REVERT: N 28 ARG cc_start: 0.7527 (tpp80) cc_final: 0.7310 (tpp80) REVERT: N 36 ARG cc_start: 0.4186 (ptm-80) cc_final: 0.3683 (ptm160) REVERT: N 53 GLU cc_start: 0.8075 (pm20) cc_final: 0.7640 (pm20) REVERT: N 55 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8265 (mm-30) REVERT: N 93 ASN cc_start: 0.8619 (m-40) cc_final: 0.7622 (p0) outliers start: 34 outliers final: 30 residues processed: 194 average time/residue: 0.0858 time to fit residues: 26.5358 Evaluate side-chains 191 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 143 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.085400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062723 restraints weight = 56930.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064759 restraints weight = 32697.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.066095 restraints weight = 23097.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.066924 restraints weight = 18509.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.067486 restraints weight = 16122.376| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13745 Z= 0.140 Angle : 0.710 10.565 18675 Z= 0.346 Chirality : 0.044 0.231 2086 Planarity : 0.004 0.043 2359 Dihedral : 5.516 42.425 1937 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.19 % Allowed : 20.15 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1682 helix: 0.45 (0.26), residues: 435 sheet: -0.41 (0.27), residues: 366 loop : -0.56 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 19 TYR 0.020 0.001 TYR H 109 PHE 0.024 0.002 PHE N 46 TRP 0.028 0.002 TRP A 398 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00325 (13738) covalent geometry : angle 0.70954 (18659) SS BOND : bond 0.00251 ( 5) SS BOND : angle 0.91734 ( 10) hydrogen bonds : bond 0.03073 ( 452) hydrogen bonds : angle 5.23173 ( 1335) link_ALPHA1-4 : bond 0.00107 ( 1) link_ALPHA1-4 : angle 1.62373 ( 3) link_TRANS : bond 0.00101 ( 1) link_TRANS : angle 0.05907 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.58 seconds wall clock time: 41 minutes 35.01 seconds (2495.01 seconds total)