Starting phenix.real_space_refine on Sat Sep 12 04:41:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhh_22337/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhh_22337/09_2026/7jhh_22337.cif" } 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-2.2.1-6174/lib/python3.11/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 chiralities: 1 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 2.84, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 481.4 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: 0.41 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: 1.91 Time building geometry restraints manager: 1.38 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: 18545 3.76 - 7.52: 101 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: 8089 23.71 - 47.41: 123 47.41 - 71.12: 11 71.12 - 94.82: 6 94.82 - 118.53: 1 Dihedral angle restraints: 8230 sinusoidal: 3271 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 8227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.942: 2085 0.942 - 1.883: 0 1.883 - 2.825: 0 2.825 - 3.767: 0 3.767 - 4.708: 1 Chirality restraints: 2086 Sorted by residual: 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 2.33 -2.38 4.71 2.00e-01 2.50e+01 5.54e+02 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 ... (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: 0.960 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13745 Z= 0.205 Angle : 0.785 18.796 18675 Z= 0.446 Chirality : 0.115 4.708 2086 Planarity : 0.007 0.061 2359 Dihedral : 9.066 118.528 5030 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/Z covalent geometry : bond 0.00349 / 0.20 (13738) covalent geometry : angle 0.77538 / 0.44 (18659) SS BOND : bond 0.00372 / 0.22 ( 5) SS BOND : angle 5.24720 / 2.99 ( 10) hydrogen bonds : bond 0.20653 / 13.73 ( 452) hydrogen bonds : angle 8.83066 / 5.99 ( 1335) link_ALPHA1-4 : bond 0.00850 / 0.45 ( 1) link_ALPHA1-4 : angle 1.33096 / 0.70 ( 3) link_TRANS : bond 0.00102 / 0.05 ( 1) link_TRANS : angle 0.48354 / 0.27 ( 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 : 0.482 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: 0.1226 time to fit residues: 79.4250 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 : 0.516 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 3.9990 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: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.088373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067793 restraints weight = 57119.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070976 restraints weight = 38074.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.070712 restraints weight = 25303.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070628 restraints weight = 22603.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070927 restraints weight = 21520.733| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13745 Z= 0.214 Angle : 0.720 11.689 18675 Z= 0.366 Chirality : 0.045 0.296 2086 Planarity : 0.006 0.056 2359 Dihedral : 5.576 78.826 1879 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.73 % Allowed : 11.89 % Favored : 85.38 % 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: -2.01 (0.19), residues: 1682 helix: -1.29 (0.21), residues: 449 sheet: -1.11 (0.28), residues: 329 loop : -1.39 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 143 TYR 0.017 0.002 TYR H 109 PHE 0.025 0.002 PHE M 279 TRP 0.017 0.002 TRP M 10 HIS 0.006 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (13738) covalent geometry : angle 0.71751 / 0.36 (18659) SS BOND : bond 0.00548 / 0.27 ( 5) SS BOND : angle 2.01693 / 1.22 ( 10) hydrogen bonds : bond 0.04096 / 2.71 ( 452) hydrogen bonds : angle 6.34252 / 4.33 ( 1335) link_ALPHA1-4 : bond 0.01136 / 0.60 ( 1) link_ALPHA1-4 : angle 3.46924 / 1.85 ( 3) link_TRANS : bond 0.00411 / 0.22 ( 1) link_TRANS : angle 0.43163 / 0.20 ( 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 285 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.521 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 50 ASN cc_start: 0.6870 (t0) cc_final: 0.6561 (t0) REVERT: A 153 MET cc_start: 0.7626 (mmm) cc_final: 0.7356 (mmm) REVERT: B 252 VAL cc_start: 0.8120 (t) cc_final: 0.7172 (t) REVERT: B 258 ARG cc_start: 0.8185 (tpt-90) cc_final: 0.7968 (tpt-90) REVERT: G 159 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7853 (tp30) REVERT: G 169 HIS cc_start: 0.8218 (m-70) cc_final: 0.7759 (m170) REVERT: G 259 ASP cc_start: 0.8435 (m-30) cc_final: 0.8140 (p0) REVERT: G 319 LEU cc_start: 0.9187 (mt) cc_final: 0.8579 (tp) REVERT: M 67 PHE cc_start: 0.8850 (m-10) cc_final: 0.8551 (m-80) REVERT: M 94 TRP cc_start: 0.7841 (m100) cc_final: 0.7195 (m100) REVERT: M 148 MET cc_start: 0.7422 (tpp) cc_final: 0.7186 (tpp) REVERT: M 321 MET cc_start: 0.8827 (mmm) cc_final: 0.8449 (mmp) REVERT: L 19 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7290 (ttp80) REVERT: L 34 VAL cc_start: 0.9339 (t) cc_final: 0.9105 (m) REVERT: L 64 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8314 (p) REVERT: L 97 ILE cc_start: 0.9297 (mt) cc_final: 0.9038 (mm) REVERT: L 138 ASN cc_start: 0.8359 (t0) cc_final: 0.8076 (t0) REVERT: H 71 PHE cc_start: 0.7141 (m-10) cc_final: 0.6818 (m-10) REVERT: N 41 TYR cc_start: 0.6950 (m-80) cc_final: 0.6512 (m-80) REVERT: N 48 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7094 (tp-100) REVERT: N 52 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7320 (tmmt) REVERT: N 92 MET cc_start: 0.8992 (mtm) cc_final: 0.8150 (mtt) REVERT: N 93 ASN cc_start: 0.8745 (m-40) cc_final: 0.8542 (m-40) outliers start: 40 outliers final: 24 residues processed: 275 average time/residue: 0.1107 time to fit residues: 44.3531 Evaluate side-chains 203 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 61 PHE 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: 2.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 128 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 HIS A 135 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.087927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065183 restraints weight = 57108.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.067355 restraints weight = 32211.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068770 restraints weight = 22412.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069679 restraints weight = 17783.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.070243 restraints weight = 15357.260| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4531 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= 0.144 Angle : 0.658 8.578 18675 Z= 0.329 Chirality : 0.044 0.188 2086 Planarity : 0.005 0.047 2359 Dihedral : 5.299 64.349 1879 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.80 % Allowed : 14.41 % Favored : 82.79 % 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: -1.41 (0.20), residues: 1682 helix: -0.61 (0.24), residues: 434 sheet: -1.06 (0.27), residues: 359 loop : -0.97 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 134 TYR 0.031 0.001 TYR B 242 PHE 0.019 0.002 PHE M 279 TRP 0.019 0.002 TRP N 45 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (13738) covalent geometry : angle 0.65757 / 0.33 (18659) SS BOND : bond 0.00379 / 0.20 ( 5) SS BOND : angle 1.32192 / 0.78 ( 10) hydrogen bonds : bond 0.03373 / 2.23 ( 452) hydrogen bonds : angle 5.85358 / 4.01 ( 1335) link_ALPHA1-4 : bond 0.00535 / 0.28 ( 1) link_ALPHA1-4 : angle 1.92663 / 0.97 ( 3) link_TRANS : bond 0.00100 / 0.05 ( 1) link_TRANS : angle 0.10138 / 0.06 ( 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 267 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.554 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: A 256 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7876 (mmm) REVERT: A 535 ILE cc_start: 0.9412 (mm) cc_final: 0.8988 (tp) REVERT: A 536 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8328 (tt0) REVERT: B 242 TYR cc_start: 0.6791 (m-80) cc_final: 0.6583 (m-80) REVERT: B 263 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5231 (m-10) REVERT: B 267 LEU cc_start: 0.9145 (mp) cc_final: 0.8788 (tt) REVERT: G 75 TRP cc_start: 0.7401 (t-100) cc_final: 0.7080 (t-100) REVERT: G 105 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: G 159 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7843 (tp30) REVERT: G 320 GLN cc_start: 0.8661 (tp40) cc_final: 0.8287 (mm110) REVERT: M 42 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8327 (mmmt) REVERT: M 67 PHE cc_start: 0.8951 (m-10) cc_final: 0.8559 (m-80) REVERT: M 94 TRP cc_start: 0.7543 (m100) cc_final: 0.7115 (m100) REVERT: M 210 TYR cc_start: 0.6826 (t80) cc_final: 0.6398 (t80) REVERT: M 321 MET cc_start: 0.8878 (mmm) cc_final: 0.8627 (mmm) REVERT: L 19 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7419 (ttp80) REVERT: L 34 VAL cc_start: 0.9368 (t) cc_final: 0.9111 (p) REVERT: L 83 ASP cc_start: 0.7661 (m-30) cc_final: 0.7352 (m-30) REVERT: L 97 ILE cc_start: 0.9304 (mt) cc_final: 0.9059 (mm) REVERT: L 138 ASN cc_start: 0.8612 (t0) cc_final: 0.8270 (t0) REVERT: N 12 GLN cc_start: 0.5993 (OUTLIER) cc_final: 0.4985 (pp30) REVERT: N 36 ARG cc_start: 0.3850 (ptm-80) cc_final: 0.3438 (ptm160) REVERT: N 41 TYR cc_start: 0.6965 (m-80) cc_final: 0.4941 (m-80) REVERT: N 48 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7385 (tp-100) outliers start: 41 outliers final: 20 residues processed: 255 average time/residue: 0.1074 time to fit residues: 40.9722 Evaluate side-chains 212 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 105 ASP 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 256 MET 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 105 GLN 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 48 GLN Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 100 THR 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: 8.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 50.0000 chunk 136 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS ** 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** M 365 GLN N 12 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 = 0.3835 r_free = 0.3835 target = 0.087310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.067208 restraints weight = 56498.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067907 restraints weight = 32848.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.067815 restraints weight = 29143.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069217 restraints weight = 25225.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069010 restraints weight = 20659.382| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13745 Z= 0.135 Angle : 0.644 7.716 18675 Z= 0.318 Chirality : 0.043 0.219 2086 Planarity : 0.004 0.044 2359 Dihedral : 5.125 59.192 1879 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.35 % Allowed : 15.78 % Favored : 80.87 % 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: -1.11 (0.20), residues: 1682 helix: -0.27 (0.25), residues: 429 sheet: -0.84 (0.27), residues: 359 loop : -0.85 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 119 TYR 0.019 0.001 TYR H 109 PHE 0.021 0.002 PHE H 138 TRP 0.016 0.001 TRP A 269 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13738) covalent geometry : angle 0.64298 / 0.32 (18659) SS BOND : bond 0.00949 / 0.45 ( 5) SS BOND : angle 0.86516 / 0.50 ( 10) hydrogen bonds : bond 0.03109 / 2.05 ( 452) hydrogen bonds : angle 5.64620 / 3.88 ( 1335) link_ALPHA1-4 : bond 0.00382 / 0.20 ( 1) link_ALPHA1-4 : angle 1.96552 / 0.99 ( 3) link_TRANS : bond 0.00109 / 0.06 ( 1) link_TRANS : angle 0.11722 / 0.06 ( 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 258 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.524 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: 0.8520 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 96 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 256 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7726 (mmm) REVERT: A 535 ILE cc_start: 0.9341 (mm) cc_final: 0.9022 (tp) REVERT: B 237 MET cc_start: 0.7852 (ptp) cc_final: 0.7492 (ptp) REVERT: B 242 TYR cc_start: 0.6936 (m-80) cc_final: 0.6451 (m-80) REVERT: G 105 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: G 159 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7879 (tp30) REVERT: M 41 ASP cc_start: 0.8252 (t0) cc_final: 0.8047 (p0) REVERT: M 57 PRO cc_start: 0.7183 (Cg_endo) cc_final: 0.6979 (Cg_exo) REVERT: M 67 PHE cc_start: 0.8842 (m-10) cc_final: 0.8424 (m-80) REVERT: M 94 TRP cc_start: 0.7442 (m100) cc_final: 0.7083 (m100) REVERT: M 148 MET cc_start: 0.7871 (tpp) cc_final: 0.7492 (tpp) REVERT: M 210 TYR cc_start: 0.7060 (t80) cc_final: 0.6615 (t80) REVERT: L 19 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7509 (ttp80) REVERT: L 34 VAL cc_start: 0.9333 (t) cc_final: 0.9097 (p) REVERT: L 97 ILE cc_start: 0.9334 (mt) cc_final: 0.9057 (mm) REVERT: L 138 ASN cc_start: 0.8409 (t0) cc_final: 0.8071 (t0) REVERT: N 12 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5211 (pp30) REVERT: N 48 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7503 (tp40) REVERT: N 74 GLN cc_start: 0.7596 (pm20) cc_final: 0.7390 (pm20) outliers start: 49 outliers final: 29 residues processed: 241 average time/residue: 0.0985 time to fit residues: 36.5421 Evaluate side-chains 209 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 105 ASP 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 256 MET 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 B residue 253 LEU Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 228 LEU 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 L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 48 GLN Chi-restraints excluded: chain N residue 100 THR 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 169 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** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.087497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066268 restraints weight = 57283.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067232 restraints weight = 32921.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.067620 restraints weight = 25258.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067932 restraints weight = 23378.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068031 restraints weight = 21553.760| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13745 Z= 0.127 Angle : 0.643 12.992 18675 Z= 0.315 Chirality : 0.042 0.170 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.036 55.338 1879 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.07 % Allowed : 16.87 % Favored : 80.05 % 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: -0.89 (0.21), residues: 1682 helix: -0.09 (0.25), residues: 435 sheet: -0.70 (0.27), residues: 355 loop : -0.71 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.017 0.001 TYR L 50 PHE 0.027 0.002 PHE H 138 TRP 0.035 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13738) covalent geometry : angle 0.64241 / 0.32 (18659) SS BOND : bond 0.00225 / 0.11 ( 5) SS BOND : angle 1.02226 / 0.55 ( 10) hydrogen bonds : bond 0.03018 / 1.97 ( 452) hydrogen bonds : angle 5.45428 / 3.76 ( 1335) link_ALPHA1-4 : bond 0.00071 / 0.04 ( 1) link_ALPHA1-4 : angle 2.04984 / 1.04 ( 3) link_TRANS : bond 0.00110 / 0.06 ( 1) link_TRANS : angle 0.10712 / 0.06 ( 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 248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.497 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: 0.8541 (OUTLIER) cc_final: 0.8305 (m) REVERT: A 535 ILE cc_start: 0.9349 (mm) cc_final: 0.9121 (tp) REVERT: B 192 GLU cc_start: 0.3887 (OUTLIER) cc_final: 0.3665 (tp30) REVERT: B 242 TYR cc_start: 0.7168 (m-80) cc_final: 0.6884 (m-80) REVERT: B 251 MET cc_start: 0.7531 (tpp) cc_final: 0.7160 (tpp) REVERT: G 159 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7892 (tp30) REVERT: M 67 PHE cc_start: 0.8851 (m-10) cc_final: 0.8428 (m-80) REVERT: M 94 TRP cc_start: 0.7569 (m100) cc_final: 0.7080 (m100) REVERT: M 210 TYR cc_start: 0.7064 (t80) cc_final: 0.6579 (t80) REVERT: M 321 MET cc_start: 0.8864 (mmm) cc_final: 0.8554 (mmp) REVERT: L 19 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7338 (ttp80) REVERT: L 34 VAL cc_start: 0.9394 (t) cc_final: 0.9167 (p) REVERT: L 97 ILE cc_start: 0.9339 (mt) cc_final: 0.9046 (mm) REVERT: L 126 LEU cc_start: 0.9173 (mt) cc_final: 0.8725 (pp) REVERT: L 138 ASN cc_start: 0.8328 (t0) cc_final: 0.8033 (t0) REVERT: N 90 LEU cc_start: 0.8043 (tp) cc_final: 0.6898 (tp) REVERT: N 93 ASN cc_start: 0.8578 (m-40) cc_final: 0.7751 (p0) outliers start: 45 outliers final: 31 residues processed: 231 average time/residue: 0.0998 time to fit residues: 35.2702 Evaluate side-chains 211 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 105 ASP 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 A residue 536 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 234 ASN 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 213 VAL 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 L residue 187 TYR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 95 LEU 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: 5.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 0.0050 chunk 119 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.083972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062764 restraints weight = 56823.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063641 restraints weight = 33127.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.063665 restraints weight = 25999.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063986 restraints weight = 24803.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064099 restraints weight = 23326.492| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13745 Z= 0.218 Angle : 0.706 9.968 18675 Z= 0.350 Chirality : 0.043 0.205 2086 Planarity : 0.005 0.045 2359 Dihedral : 5.246 54.941 1879 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.14 % Allowed : 17.14 % Favored : 79.71 % 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: -0.84 (0.21), residues: 1682 helix: 0.05 (0.25), residues: 447 sheet: -0.70 (0.27), residues: 355 loop : -0.72 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 208 TYR 0.021 0.002 TYR L 50 PHE 0.033 0.002 PHE H 71 TRP 0.055 0.003 TRP A 398 HIS 0.009 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (13738) covalent geometry : angle 0.70509 / 0.35 (18659) SS BOND : bond 0.00296 / 0.14 ( 5) SS BOND : angle 1.07005 / 0.58 ( 10) hydrogen bonds : bond 0.03308 / 2.22 ( 452) hydrogen bonds : angle 5.49373 / 3.77 ( 1335) link_ALPHA1-4 : bond 0.00178 / 0.09 ( 1) link_ALPHA1-4 : angle 2.13716 / 1.09 ( 3) link_TRANS : bond 0.00408 / 0.21 ( 1) link_TRANS : angle 0.23784 / 0.11 ( 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 226 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.592 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 256 MET cc_start: 0.8212 (mmm) cc_final: 0.7664 (tpp) REVERT: B 237 MET cc_start: 0.7678 (ptp) cc_final: 0.7380 (mpp) REVERT: B 240 HIS cc_start: 0.7695 (m-70) cc_final: 0.7425 (m90) REVERT: B 251 MET cc_start: 0.7721 (tpp) cc_final: 0.7383 (tpp) REVERT: B 265 THR cc_start: 0.8783 (m) cc_final: 0.8468 (p) REVERT: G 159 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7900 (tp30) REVERT: M 41 ASP cc_start: 0.8519 (t0) cc_final: 0.8019 (p0) REVERT: M 67 PHE cc_start: 0.8886 (m-10) cc_final: 0.8402 (m-80) REVERT: M 94 TRP cc_start: 0.7787 (m100) cc_final: 0.7302 (m100) REVERT: M 148 MET cc_start: 0.7943 (tpp) cc_final: 0.7581 (tpp) REVERT: M 321 MET cc_start: 0.8794 (mmm) cc_final: 0.8524 (mmp) REVERT: M 355 GLN cc_start: 0.8257 (mt0) cc_final: 0.8040 (mm-40) REVERT: L 97 ILE cc_start: 0.9371 (mt) cc_final: 0.9071 (mm) REVERT: L 138 ASN cc_start: 0.8319 (t0) cc_final: 0.8069 (t0) REVERT: N 12 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.5600 (pp30) outliers start: 46 outliers final: 36 residues processed: 211 average time/residue: 0.1072 time to fit residues: 34.6377 Evaluate side-chains 200 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 105 ASP 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 456 VAL Chi-restraints excluded: chain B residue 234 ASN 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 105 GLN Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 213 VAL 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 G residue 317 ASP Chi-restraints excluded: chain M residue 365 GLN 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 N residue 12 GLN Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 164 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS M 323 ASN ** M 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.082780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060666 restraints weight = 56990.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062344 restraints weight = 36467.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062685 restraints weight = 25000.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062996 restraints weight = 24275.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.063180 restraints weight = 22059.325| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.6196 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= 0.238 Angle : 0.717 9.509 18675 Z= 0.357 Chirality : 0.043 0.214 2086 Planarity : 0.005 0.047 2359 Dihedral : 5.374 56.002 1879 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.55 % Allowed : 17.76 % Favored : 78.69 % 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: -0.78 (0.21), residues: 1682 helix: 0.10 (0.25), residues: 447 sheet: -0.70 (0.26), residues: 363 loop : -0.67 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 19 TYR 0.021 0.002 TYR H 97 PHE 0.022 0.002 PHE H 138 TRP 0.019 0.002 TRP A 398 HIS 0.008 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (13738) covalent geometry : angle 0.71598 / 0.36 (18659) SS BOND : bond 0.00216 / 0.09 ( 5) SS BOND : angle 1.12360 / 0.59 ( 10) hydrogen bonds : bond 0.03315 / 2.24 ( 452) hydrogen bonds : angle 5.57181 / 3.83 ( 1335) link_ALPHA1-4 : bond 0.00252 / 0.13 ( 1) link_ALPHA1-4 : angle 2.21890 / 1.12 ( 3) link_TRANS : bond 0.00412 / 0.22 ( 1) link_TRANS : angle 0.27498 / 0.13 ( 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 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.552 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 256 MET cc_start: 0.8172 (mmm) cc_final: 0.7821 (tpp) REVERT: B 251 MET cc_start: 0.7880 (tpp) cc_final: 0.7615 (tpp) REVERT: B 265 THR cc_start: 0.8828 (m) cc_final: 0.8528 (p) REVERT: G 105 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8261 (pp30) REVERT: G 159 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7934 (tp30) REVERT: M 41 ASP cc_start: 0.8567 (t0) cc_final: 0.8096 (p0) REVERT: M 67 PHE cc_start: 0.8990 (m-10) cc_final: 0.8507 (m-80) REVERT: M 94 TRP cc_start: 0.8098 (m100) cc_final: 0.7402 (m100) REVERT: M 115 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8867 (tm) REVERT: M 148 MET cc_start: 0.8180 (tpp) cc_final: 0.7759 (tpp) REVERT: M 321 MET cc_start: 0.8837 (mmm) cc_final: 0.8517 (mmp) REVERT: M 355 GLN cc_start: 0.8209 (mt0) cc_final: 0.8001 (mm-40) REVERT: L 83 ASP cc_start: 0.8067 (m-30) cc_final: 0.7865 (t70) REVERT: L 97 ILE cc_start: 0.9337 (mt) cc_final: 0.9041 (mm) REVERT: L 126 LEU cc_start: 0.9256 (mt) cc_final: 0.8852 (pp) REVERT: N 46 PHE cc_start: 0.8208 (m-80) cc_final: 0.7955 (t80) outliers start: 52 outliers final: 45 residues processed: 204 average time/residue: 0.1022 time to fit residues: 32.4129 Evaluate side-chains 206 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 165 MET 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 398 TRP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 197 ARG 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 104 VAL Chi-restraints excluded: chain G residue 105 GLN 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 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 G residue 317 ASP Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain L residue 34 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 L residue 118 ILE 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 N residue 31 CYS Chi-restraints excluded: chain N residue 78 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 108 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS G 105 GLN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.084629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.063483 restraints weight = 55901.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064334 restraints weight = 33060.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064512 restraints weight = 26067.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.064875 restraints weight = 25072.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064989 restraints weight = 22289.017| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6181 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= 0.126 Angle : 0.673 10.585 18675 Z= 0.329 Chirality : 0.043 0.246 2086 Planarity : 0.004 0.050 2359 Dihedral : 5.196 50.922 1879 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.94 % Allowed : 17.90 % Favored : 79.17 % 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: -0.65 (0.21), residues: 1682 helix: 0.27 (0.25), residues: 446 sheet: -0.63 (0.26), residues: 370 loop : -0.63 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 258 TYR 0.024 0.001 TYR H 161 PHE 0.016 0.001 PHE N 46 TRP 0.019 0.002 TRP A 398 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13738) covalent geometry : angle 0.67221 / 0.33 (18659) SS BOND : bond 0.00232 / 0.11 ( 5) SS BOND : angle 0.92905 / 0.49 ( 10) hydrogen bonds : bond 0.02930 / 1.98 ( 452) hydrogen bonds : angle 5.37902 / 3.70 ( 1335) link_ALPHA1-4 : bond 0.00122 / 0.06 ( 1) link_ALPHA1-4 : angle 1.95450 / 1.00 ( 3) link_TRANS : bond 0.00039 / 0.02 ( 1) link_TRANS : angle 0.07926 / 0.05 ( 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 228 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.541 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: B 242 TYR cc_start: 0.7906 (m-80) cc_final: 0.7528 (t80) REVERT: B 251 MET cc_start: 0.7731 (tpp) cc_final: 0.7505 (tpp) REVERT: B 265 THR cc_start: 0.8848 (m) cc_final: 0.8560 (p) REVERT: G 105 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8165 (pp30) REVERT: G 159 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7891 (tp30) REVERT: M 41 ASP cc_start: 0.8571 (t0) cc_final: 0.8124 (p0) REVERT: M 67 PHE cc_start: 0.8917 (m-10) cc_final: 0.8510 (m-80) REVERT: M 94 TRP cc_start: 0.7763 (m100) cc_final: 0.6950 (m100) REVERT: M 148 MET cc_start: 0.8006 (tpp) cc_final: 0.7602 (tpp) REVERT: L 19 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7195 (ttp80) REVERT: L 97 ILE cc_start: 0.9299 (mt) cc_final: 0.8899 (mm) REVERT: L 126 LEU cc_start: 0.9181 (mt) cc_final: 0.8833 (pp) REVERT: L 139 ASN cc_start: 0.8182 (m110) cc_final: 0.7856 (m-40) REVERT: H 194 LEU cc_start: 0.9196 (tp) cc_final: 0.8878 (tt) REVERT: N 12 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5587 (pp30) REVERT: N 22 GLN cc_start: 0.8370 (pp30) cc_final: 0.8127 (pp30) outliers start: 43 outliers final: 38 residues processed: 217 average time/residue: 0.1027 time to fit residues: 34.7229 Evaluate side-chains 207 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 ASP 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 432 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 173 LEU 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 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 M residue 365 GLN Chi-restraints excluded: chain L residue 34 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 L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL 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 105 CYS Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 136 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 96 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** M 365 GLN ** 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.085146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.064010 restraints weight = 56430.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064950 restraints weight = 32626.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065056 restraints weight = 25433.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065364 restraints weight = 24457.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065474 restraints weight = 22588.024| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13745 Z= 0.126 Angle : 0.692 10.962 18675 Z= 0.337 Chirality : 0.044 0.224 2086 Planarity : 0.004 0.043 2359 Dihedral : 5.131 45.817 1879 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.94 % Allowed : 18.92 % Favored : 78.14 % 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: -0.59 (0.21), residues: 1682 helix: 0.32 (0.25), residues: 443 sheet: -0.56 (0.27), residues: 360 loop : -0.59 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 19 TYR 0.022 0.001 TYR L 87 PHE 0.020 0.001 PHE N 46 TRP 0.018 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13738) covalent geometry : angle 0.69174 / 0.34 (18659) SS BOND : bond 0.00250 / 0.12 ( 5) SS BOND : angle 1.00420 / 0.52 ( 10) hydrogen bonds : bond 0.02968 / 2.02 ( 452) hydrogen bonds : angle 5.29245 / 3.65 ( 1335) link_ALPHA1-4 : bond 0.00215 / 0.11 ( 1) link_ALPHA1-4 : angle 1.92217 / 0.98 ( 3) link_TRANS : bond 0.00085 / 0.04 ( 1) link_TRANS : angle 0.08060 / 0.05 ( 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 221 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.534 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: B 242 TYR cc_start: 0.7851 (m-80) cc_final: 0.7233 (t80) REVERT: B 251 MET cc_start: 0.7691 (tpp) cc_final: 0.7465 (tpp) REVERT: B 265 THR cc_start: 0.8836 (m) cc_final: 0.8507 (t) REVERT: G 159 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7927 (tp30) REVERT: G 267 GLN cc_start: 0.9005 (pm20) cc_final: 0.8451 (pm20) REVERT: M 41 ASP cc_start: 0.8560 (t0) cc_final: 0.8124 (p0) REVERT: M 67 PHE cc_start: 0.8874 (m-10) cc_final: 0.8473 (m-80) REVERT: M 94 TRP cc_start: 0.7737 (m100) cc_final: 0.6956 (m100) REVERT: M 148 MET cc_start: 0.8019 (tpp) cc_final: 0.7632 (tpp) REVERT: M 359 GLU cc_start: 0.8261 (pt0) cc_final: 0.7954 (pt0) REVERT: L 19 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7197 (ttp80) REVERT: L 97 ILE cc_start: 0.9293 (mt) cc_final: 0.8895 (mm) REVERT: L 106 GLU cc_start: 0.7372 (tp30) cc_final: 0.7162 (tp30) REVERT: L 126 LEU cc_start: 0.9212 (mt) cc_final: 0.8868 (pp) REVERT: L 139 ASN cc_start: 0.8156 (m110) cc_final: 0.7920 (m-40) REVERT: L 140 PHE cc_start: 0.8738 (p90) cc_final: 0.8287 (p90) REVERT: H 86 MET cc_start: 0.7278 (mmm) cc_final: 0.6745 (mmm) REVERT: H 194 LEU cc_start: 0.9179 (tp) cc_final: 0.8860 (tt) REVERT: N 22 GLN cc_start: 0.8326 (pp30) cc_final: 0.8090 (pp30) REVERT: N 36 ARG cc_start: 0.4490 (ptm-80) cc_final: 0.3616 (ptm160) outliers start: 43 outliers final: 40 residues processed: 211 average time/residue: 0.0993 time to fit residues: 32.6366 Evaluate side-chains 210 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 ASP 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 432 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU 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 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain L residue 34 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 L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL 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 Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.083936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062675 restraints weight = 56345.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063582 restraints weight = 32887.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063946 restraints weight = 24787.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064459 restraints weight = 23600.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064438 restraints weight = 21324.567| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13745 Z= 0.168 Angle : 0.709 11.431 18675 Z= 0.346 Chirality : 0.044 0.218 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.191 43.917 1879 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.94 % Allowed : 19.26 % Favored : 77.80 % 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: -0.53 (0.21), residues: 1682 helix: 0.35 (0.25), residues: 442 sheet: -0.41 (0.27), residues: 360 loop : -0.61 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 90 TYR 0.022 0.002 TYR L 87 PHE 0.030 0.002 PHE H 71 TRP 0.039 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (13738) covalent geometry : angle 0.70851 / 0.35 (18659) SS BOND : bond 0.00252 / 0.11 ( 5) SS BOND : angle 0.97727 / 0.51 ( 10) hydrogen bonds : bond 0.03074 / 2.09 ( 452) hydrogen bonds : angle 5.39255 / 3.72 ( 1335) link_ALPHA1-4 : bond 0.00169 / 0.09 ( 1) link_ALPHA1-4 : angle 2.03528 / 1.03 ( 3) link_TRANS : bond 0.00258 / 0.14 ( 1) link_TRANS : angle 0.14844 / 0.07 ( 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 212 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.543 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: B 265 THR cc_start: 0.8857 (m) cc_final: 0.8528 (t) REVERT: G 33 MET cc_start: 0.8387 (mtm) cc_final: 0.7961 (ttm) REVERT: G 159 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7937 (tp30) REVERT: G 267 GLN cc_start: 0.9018 (pm20) cc_final: 0.8447 (pm20) REVERT: M 41 ASP cc_start: 0.8565 (t0) cc_final: 0.8114 (p0) REVERT: M 67 PHE cc_start: 0.8911 (m-10) cc_final: 0.8506 (m-80) REVERT: M 94 TRP cc_start: 0.7881 (m100) cc_final: 0.7304 (m100) REVERT: M 148 MET cc_start: 0.8155 (tpp) cc_final: 0.7757 (tpp) REVERT: M 359 GLU cc_start: 0.8409 (pt0) cc_final: 0.8153 (pt0) REVERT: L 97 ILE cc_start: 0.9284 (mt) cc_final: 0.8875 (mm) REVERT: L 140 PHE cc_start: 0.8809 (p90) cc_final: 0.8358 (p90) REVERT: N 12 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5791 (pp30) REVERT: N 22 GLN cc_start: 0.8363 (pp30) cc_final: 0.8120 (pp30) REVERT: N 36 ARG cc_start: 0.4405 (ptm-80) cc_final: 0.3720 (ptm160) outliers start: 43 outliers final: 39 residues processed: 201 average time/residue: 0.0984 time to fit residues: 30.7669 Evaluate side-chains 201 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 105 ASP 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 251 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 197 ARG 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 105 GLN Chi-restraints excluded: chain G residue 173 LEU 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 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain M residue 365 GLN Chi-restraints excluded: chain L residue 34 VAL 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 N residue 12 GLN 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 Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain N residue 127 THR Chi-restraints excluded: chain N residue 128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 143 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN ** 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** N 12 GLN ** N 22 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 = 0.3759 r_free = 0.3759 target = 0.083903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061463 restraints weight = 56957.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063456 restraints weight = 32728.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064771 restraints weight = 23116.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065583 restraints weight = 18603.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.066100 restraints weight = 16188.758| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.322 13745 Z= 0.320 Angle : 1.033 59.200 18675 Z= 0.604 Chirality : 0.048 0.895 2086 Planarity : 0.006 0.170 2359 Dihedral : 5.191 43.914 1879 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.35 % Allowed : 19.19 % Favored : 77.46 % Cbeta Deviations : 0.13 % 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: -0.53 (0.21), residues: 1682 helix: 0.37 (0.25), residues: 441 sheet: -0.41 (0.27), residues: 360 loop : -0.62 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 90 TYR 0.040 0.002 TYR B 242 PHE 0.030 0.002 PHE N 46 TRP 0.019 0.002 TRP N 45 HIS 0.006 0.001 HIS G 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.32 (13738) covalent geometry : angle 1.03332 / 0.60 (18659) SS BOND : bond 0.00255 / 0.11 ( 5) SS BOND : angle 0.94022 / 0.49 ( 10) hydrogen bonds : bond 0.03068 / 2.09 ( 452) hydrogen bonds : angle 5.39415 / 3.72 ( 1335) link_ALPHA1-4 : bond 0.00149 / 0.08 ( 1) link_ALPHA1-4 : angle 2.04259 / 1.04 ( 3) link_TRANS : bond 0.00249 / 0.13 ( 1) link_TRANS : angle 0.15493 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.02 seconds wall clock time: 40 minutes 58.08 seconds (2458.08 seconds total)