Starting phenix.real_space_refine on Thu Jul 31 19:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhh_22337/07_2025/7jhh_22337.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhh_22337/07_2025/7jhh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jhh_22337/07_2025/7jhh_22337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhh_22337/07_2025/7jhh_22337.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhh_22337/07_2025/7jhh_22337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhh_22337/07_2025/7jhh_22337.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13418 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3074 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 8.10, per 1000 atoms: 0.60 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.72 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: 4.29 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4249 1.34 - 1.46: 3141 1.46 - 1.58: 6258 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13738 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.23e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.73e+01 bond pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.60e+01 ... (remaining 13733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 18542 3.76 - 7.52: 104 7.52 - 11.28: 11 11.28 - 15.04: 0 15.04 - 18.80: 2 Bond angle restraints: 18659 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.07 18.80 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 121.31 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.69 8.11 1.00e+00 1.00e+00 6.57e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.97 -7.93 1.15e+00 7.59e-01 4.77e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.59 5.10 1.00e+00 1.00e+00 2.60e+01 ... (remaining 18654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 8143 23.71 - 47.41: 127 47.41 - 71.12: 11 71.12 - 94.82: 6 94.82 - 118.53: 1 Dihedral angle restraints: 8288 sinusoidal: 3329 harmonic: 4959 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 19.66 73.34 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 58.53 -118.53 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA ASN A 69 " pdb=" C ASN A 69 " pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1850 0.079 - 0.159: 221 0.159 - 0.238: 13 0.238 - 0.318: 0 0.318 - 0.397: 2 Chirality restraints: 2086 Sorted by residual: chirality pdb=" C1 GLC C 2 " pdb=" O4 GLC C 1 " pdb=" C2 GLC C 2 " pdb=" O5 GLC C 2 " both_signs ideal model delta sigma weight residual False 2.40 2.31 0.09 2.00e-02 2.50e+03 1.88e+01 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C1 GLC C 1 " pdb=" C2 GLC C 1 " pdb=" O1 GLC C 1 " pdb=" O5 GLC C 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2083 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO L 9 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 430 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 431 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 144 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.028 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3867 2.82 - 3.34: 11216 3.34 - 3.86: 21641 3.86 - 4.38: 24291 4.38 - 4.90: 42444 Nonbonded interactions: 103459 Sorted by model distance: nonbonded pdb=" OE1 GLU M 111 " pdb=" O2 GLC C 1 " model vdw 2.300 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.310 3.040 nonbonded pdb=" OG1 THR G 89 " pdb=" O1B ADP G 402 " model vdw 2.347 3.040 nonbonded pdb=" OD2 ASP G 52 " pdb=" OG SER G 54 " model vdw 2.365 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.368 3.040 ... (remaining 103454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13745 Z= 0.206 Angle : 0.790 18.796 18675 Z= 0.447 Chirality : 0.051 0.397 2086 Planarity : 0.007 0.061 2359 Dihedral : 9.124 118.528 5088 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (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 TRP 0.020 0.002 TRP H 119 HIS 0.006 0.001 HIS G 36 PHE 0.029 0.002 PHE A 225 TYR 0.016 0.002 TYR H 102 ARG 0.012 0.001 ARG A 435 Details of bonding type rmsd link_TRANS : bond 0.00102 ( 1) link_TRANS : angle 0.48354 ( 3) link_ALPHA1-4 : bond 0.00850 ( 1) link_ALPHA1-4 : angle 1.33096 ( 3) hydrogen bonds : bond 0.20653 ( 452) hydrogen bonds : angle 8.83066 ( 1335) SS BOND : bond 0.00372 ( 5) SS BOND : angle 5.24720 ( 10) covalent geometry : bond 0.00352 (13738) covalent geometry : angle 0.78054 (18659) *********************** 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 : 1.565 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: 0.6341 (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: 0.7190 (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: 0.8783 (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: 0.8088 (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: 0.7944 (mt) REVERT: M 365 GLN cc_start: 0.8581 (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: 0.9073 (mt) cc_final: 0.8865 (mm) REVERT: L 203 SER cc_start: 0.7023 (t) cc_final: 0.5981 (p) REVERT: H 213 ASN cc_start: 0.8350 (m110) cc_final: 0.7655 (m-40) REVERT: N 45 TRP cc_start: 0.7203 (m100) cc_final: 0.6799 (m100) REVERT: N 82 ASP cc_start: 0.7148 (t70) cc_final: 0.6780 (t70) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.2811 time to fit residues: 179.2668 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 : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 139 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 HIS N 12 GLN N 86 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.090316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.068382 restraints weight = 56518.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070594 restraints weight = 32075.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.072046 restraints weight = 22296.348| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13745 Z= 0.162 Angle : 0.699 12.756 18675 Z= 0.353 Chirality : 0.045 0.269 2086 Planarity : 0.005 0.052 2359 Dihedral : 5.882 76.352 1937 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.32 % Allowed : 12.43 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1682 helix: -1.34 (0.21), residues: 448 sheet: -1.16 (0.28), residues: 329 loop : -1.43 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 10 HIS 0.006 0.001 HIS B 211 PHE 0.027 0.002 PHE M 279 TYR 0.022 0.002 TYR H 109 ARG 0.005 0.001 ARG L 143 Details of bonding type rmsd link_TRANS : bond 0.00265 ( 1) link_TRANS : angle 0.38817 ( 3) link_ALPHA1-4 : bond 0.00295 ( 1) link_ALPHA1-4 : angle 2.12663 ( 3) hydrogen bonds : bond 0.03717 ( 452) hydrogen bonds : angle 6.28524 ( 1335) SS BOND : bond 0.00597 ( 5) SS BOND : angle 1.75975 ( 10) covalent geometry : bond 0.00362 (13738) covalent geometry : angle 0.69788 (18659) *********************** 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 296 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.607 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: A 50 ASN cc_start: 0.6861 (t0) cc_final: 0.6558 (t0) REVERT: A 99 SER cc_start: 0.8352 (m) cc_final: 0.8151 (t) REVERT: A 105 ASP cc_start: 0.8177 (m-30) cc_final: 0.7968 (t70) REVERT: A 535 ILE cc_start: 0.9476 (mm) cc_final: 0.9187 (tp) REVERT: B 252 VAL cc_start: 0.8111 (t) cc_final: 0.7308 (t) REVERT: G 159 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7833 (tp30) REVERT: G 169 HIS cc_start: 0.8248 (m-70) cc_final: 0.7739 (m170) REVERT: G 259 ASP cc_start: 0.8368 (m-30) cc_final: 0.8082 (p0) REVERT: G 319 LEU cc_start: 0.9165 (mt) cc_final: 0.8596 (tp) REVERT: M 67 PHE cc_start: 0.8920 (m-10) cc_final: 0.8673 (m-80) REVERT: M 94 TRP cc_start: 0.7881 (m100) cc_final: 0.7239 (m100) REVERT: M 148 MET cc_start: 0.7470 (tpp) cc_final: 0.7138 (tpp) REVERT: M 321 MET cc_start: 0.8831 (mmm) cc_final: 0.8447 (mmp) REVERT: L 34 VAL cc_start: 0.9376 (t) cc_final: 0.9128 (m) REVERT: L 97 ILE cc_start: 0.9239 (mt) cc_final: 0.8995 (mm) REVERT: L 136 LEU cc_start: 0.9207 (tp) cc_final: 0.9000 (tt) REVERT: L 138 ASN cc_start: 0.8403 (t0) cc_final: 0.8070 (t0) REVERT: H 71 PHE cc_start: 0.6995 (m-10) cc_final: 0.6716 (m-10) REVERT: N 120 TRP cc_start: 0.6866 (p90) cc_final: 0.6240 (p90) outliers start: 34 outliers final: 22 residues processed: 287 average time/residue: 0.2537 time to fit residues: 105.0366 Evaluate side-chains 209 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 115 LEU 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 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 95 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 13 optimal weight: 0.0010 chunk 91 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.088967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069161 restraints weight = 56885.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069799 restraints weight = 34078.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.069685 restraints weight = 29953.207| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4312 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= 0.147 Angle : 0.658 8.589 18675 Z= 0.328 Chirality : 0.043 0.187 2086 Planarity : 0.004 0.046 2359 Dihedral : 5.659 62.527 1937 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.32 % Allowed : 15.30 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.20), residues: 1682 helix: -0.70 (0.24), residues: 438 sheet: -1.03 (0.27), residues: 341 loop : -1.09 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 45 HIS 0.006 0.001 HIS A 220 PHE 0.019 0.001 PHE M 279 TYR 0.026 0.001 TYR B 242 ARG 0.007 0.001 ARG A 459 Details of bonding type rmsd link_TRANS : bond 0.00115 ( 1) link_TRANS : angle 0.10928 ( 3) link_ALPHA1-4 : bond 0.00220 ( 1) link_ALPHA1-4 : angle 2.02030 ( 3) hydrogen bonds : bond 0.03377 ( 452) hydrogen bonds : angle 5.84830 ( 1335) SS BOND : bond 0.00719 ( 5) SS BOND : angle 0.97655 ( 10) covalent geometry : bond 0.00327 (13738) covalent geometry : angle 0.65695 (18659) *********************** 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 246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.568 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 99 SER cc_start: 0.8242 (m) cc_final: 0.8000 (t) REVERT: A 535 ILE cc_start: 0.9291 (mm) cc_final: 0.8944 (tp) REVERT: B 242 TYR cc_start: 0.6811 (m-80) cc_final: 0.6419 (m-80) REVERT: B 258 ARG cc_start: 0.8340 (tpt-90) cc_final: 0.7910 (tmt-80) REVERT: G 75 TRP cc_start: 0.7403 (t-100) cc_final: 0.7198 (t-100) REVERT: G 105 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: G 159 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7882 (tp30) REVERT: G 319 LEU cc_start: 0.9232 (mt) cc_final: 0.8782 (tp) REVERT: G 324 LEU cc_start: 0.7463 (mt) cc_final: 0.7137 (tp) REVERT: M 67 PHE cc_start: 0.8872 (m-10) cc_final: 0.8567 (m-80) REVERT: M 94 TRP cc_start: 0.7814 (m100) cc_final: 0.7144 (m100) REVERT: M 210 TYR cc_start: 0.6832 (t80) cc_final: 0.6387 (t80) REVERT: M 321 MET cc_start: 0.8814 (mmm) cc_final: 0.8576 (mmm) REVERT: L 34 VAL cc_start: 0.9364 (t) cc_final: 0.9097 (p) REVERT: L 83 ASP cc_start: 0.7652 (m-30) cc_final: 0.7413 (m-30) REVERT: L 97 ILE cc_start: 0.9300 (mt) cc_final: 0.9013 (mm) REVERT: N 12 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5133 (pp30) outliers start: 34 outliers final: 23 residues processed: 235 average time/residue: 0.2604 time to fit residues: 88.8358 Evaluate side-chains 204 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain M residue 255 SER Chi-restraints excluded: chain 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 187 TYR Chi-restraints excluded: chain N residue 12 GLN 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 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 127 optimal weight: 0.0570 chunk 140 optimal weight: 1.9990 chunk 85 optimal weight: 0.0060 chunk 42 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 overall best weight: 0.6516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN N 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.089356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066671 restraints weight = 56024.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068907 restraints weight = 31442.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.070384 restraints weight = 21780.702| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4633 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= 0.113 Angle : 0.637 7.755 18675 Z= 0.313 Chirality : 0.043 0.140 2086 Planarity : 0.004 0.053 2359 Dihedral : 5.471 53.707 1937 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.94 % Allowed : 15.37 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1682 helix: -0.58 (0.24), residues: 450 sheet: -0.81 (0.27), residues: 350 loop : -0.95 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 269 HIS 0.005 0.001 HIS A 220 PHE 0.021 0.001 PHE N 46 TYR 0.019 0.001 TYR G 107 ARG 0.007 0.001 ARG A 119 Details of bonding type rmsd link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.11180 ( 3) link_ALPHA1-4 : bond 0.00146 ( 1) link_ALPHA1-4 : angle 2.01065 ( 3) hydrogen bonds : bond 0.03052 ( 452) hydrogen bonds : angle 5.59853 ( 1335) SS BOND : bond 0.00502 ( 5) SS BOND : angle 0.71318 ( 10) covalent geometry : bond 0.00257 (13738) covalent geometry : angle 0.63683 (18659) *********************** 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 268 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 1.591 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 99 SER cc_start: 0.8235 (m) cc_final: 0.8034 (t) REVERT: A 105 ASP cc_start: 0.8524 (m-30) cc_final: 0.8271 (m-30) REVERT: A 256 MET cc_start: 0.8218 (mmm) cc_final: 0.7765 (tpp) REVERT: A 398 TRP cc_start: 0.6906 (m-10) cc_final: 0.6625 (m-10) REVERT: A 535 ILE cc_start: 0.9410 (mm) cc_final: 0.9033 (tp) REVERT: A 536 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8342 (tt0) REVERT: B 193 MET cc_start: 0.6640 (ppp) cc_final: 0.6398 (ppp) REVERT: B 242 TYR cc_start: 0.6963 (m-80) cc_final: 0.6493 (m-80) REVERT: G 159 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7857 (tp30) REVERT: G 324 LEU cc_start: 0.7471 (mt) cc_final: 0.7208 (tp) REVERT: M 42 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8350 (mmmt) REVERT: M 67 PHE cc_start: 0.8936 (m-10) cc_final: 0.8659 (m-80) REVERT: M 94 TRP cc_start: 0.7498 (m100) cc_final: 0.7056 (m100) REVERT: M 148 MET cc_start: 0.7907 (tpp) cc_final: 0.7640 (tpp) REVERT: M 210 TYR cc_start: 0.6937 (t80) cc_final: 0.6479 (t80) REVERT: M 321 MET cc_start: 0.8907 (mmm) cc_final: 0.8644 (mmm) REVERT: L 34 VAL cc_start: 0.9409 (t) cc_final: 0.9126 (p) REVERT: L 97 ILE cc_start: 0.9276 (mt) cc_final: 0.9021 (mm) REVERT: L 138 ASN cc_start: 0.8495 (t0) cc_final: 0.7641 (t0) REVERT: L 139 ASN cc_start: 0.8286 (m110) cc_final: 0.7582 (m110) REVERT: H 6 GLN cc_start: 0.7927 (mp10) cc_final: 0.7240 (pm20) REVERT: N 41 TYR cc_start: 0.6893 (m-80) cc_final: 0.6265 (m-80) REVERT: N 69 TYR cc_start: 0.6778 (m-10) cc_final: 0.6535 (m-10) REVERT: N 93 ASN cc_start: 0.8692 (m110) cc_final: 0.7629 (m-40) outliers start: 43 outliers final: 24 residues processed: 253 average time/residue: 0.2360 time to fit residues: 88.1584 Evaluate side-chains 205 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 422 LEU 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 105 GLN 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 187 TYR Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS G 105 GLN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 12 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.088214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067953 restraints weight = 56500.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068319 restraints weight = 33143.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.068595 restraints weight = 29965.732| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13745 Z= 0.131 Angle : 0.640 9.380 18675 Z= 0.315 Chirality : 0.042 0.152 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.430 46.995 1937 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.80 % Allowed : 16.73 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1682 helix: -0.22 (0.25), residues: 446 sheet: -0.65 (0.28), residues: 344 loop : -0.81 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 75 HIS 0.006 0.001 HIS G 268 PHE 0.026 0.002 PHE H 138 TYR 0.018 0.001 TYR L 50 ARG 0.006 0.001 ARG L 19 Details of bonding type rmsd link_TRANS : bond 0.00146 ( 1) link_TRANS : angle 0.11385 ( 3) link_ALPHA1-4 : bond 0.00169 ( 1) link_ALPHA1-4 : angle 2.01436 ( 3) hydrogen bonds : bond 0.03083 ( 452) hydrogen bonds : angle 5.38024 ( 1335) SS BOND : bond 0.00193 ( 5) SS BOND : angle 1.06837 ( 10) covalent geometry : bond 0.00299 (13738) covalent geometry : angle 0.63951 (18659) *********************** 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 239 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.540 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 398 TRP cc_start: 0.6966 (m-10) cc_final: 0.6664 (m-10) REVERT: B 193 MET cc_start: 0.6507 (ppp) cc_final: 0.6247 (ppp) REVERT: B 237 MET cc_start: 0.7859 (ptp) cc_final: 0.7526 (mpp) REVERT: B 251 MET cc_start: 0.7509 (tpp) cc_final: 0.7179 (tpp) REVERT: G 33 MET cc_start: 0.8663 (mmm) cc_final: 0.8264 (mmm) REVERT: G 159 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7931 (tp30) REVERT: G 324 LEU cc_start: 0.7456 (mt) cc_final: 0.7240 (tp) REVERT: M 67 PHE cc_start: 0.8822 (m-10) cc_final: 0.8412 (m-80) REVERT: M 210 TYR cc_start: 0.7074 (t80) cc_final: 0.6595 (t80) REVERT: M 321 MET cc_start: 0.8806 (mmm) cc_final: 0.8536 (mmm) REVERT: L 19 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7477 (ttp80) REVERT: L 34 VAL cc_start: 0.9402 (t) cc_final: 0.9165 (p) REVERT: L 97 ILE cc_start: 0.9334 (mt) cc_final: 0.9034 (mm) REVERT: L 126 LEU cc_start: 0.9148 (mt) cc_final: 0.8732 (pp) REVERT: L 138 ASN cc_start: 0.8429 (t0) cc_final: 0.8042 (t0) REVERT: N 36 ARG cc_start: 0.4448 (ptm-80) cc_final: 0.3386 (ptm160) REVERT: N 41 TYR cc_start: 0.7076 (m-80) cc_final: 0.6482 (m-80) REVERT: N 55 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8162 (mp0) REVERT: N 93 ASN cc_start: 0.8456 (m110) cc_final: 0.7922 (p0) outliers start: 41 outliers final: 29 residues processed: 226 average time/residue: 0.2260 time to fit residues: 77.4826 Evaluate side-chains 204 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU 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 240 ILE Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain 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 52 LYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 157 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 76 optimal weight: 0.0050 chunk 123 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** 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** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.087588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064441 restraints weight = 57188.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066649 restraints weight = 32339.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068062 restraints weight = 22505.037| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13745 Z= 0.130 Angle : 0.634 8.445 18675 Z= 0.313 Chirality : 0.042 0.154 2086 Planarity : 0.004 0.080 2359 Dihedral : 5.405 45.261 1937 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.80 % Allowed : 17.35 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1682 helix: -0.01 (0.25), residues: 442 sheet: -0.57 (0.28), residues: 339 loop : -0.71 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 75 HIS 0.006 0.001 HIS G 268 PHE 0.021 0.002 PHE H 138 TYR 0.017 0.001 TYR L 50 ARG 0.009 0.001 ARG N 28 Details of bonding type rmsd link_TRANS : bond 0.00140 ( 1) link_TRANS : angle 0.10335 ( 3) link_ALPHA1-4 : bond 0.00342 ( 1) link_ALPHA1-4 : angle 2.02603 ( 3) hydrogen bonds : bond 0.03005 ( 452) hydrogen bonds : angle 5.28037 ( 1335) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.04390 ( 10) covalent geometry : bond 0.00299 (13738) covalent geometry : angle 0.63353 (18659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 1.513 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: 0.8523 (OUTLIER) cc_final: 0.8290 (m) REVERT: B 192 GLU cc_start: 0.3113 (tp30) cc_final: 0.2354 (mm-30) REVERT: B 193 MET cc_start: 0.6399 (ppp) cc_final: 0.6095 (ppp) REVERT: B 237 MET cc_start: 0.8073 (ptp) cc_final: 0.7605 (ptp) REVERT: B 251 MET cc_start: 0.7681 (tpp) cc_final: 0.7303 (tpp) REVERT: G 159 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7911 (tp30) REVERT: G 324 LEU cc_start: 0.7570 (mt) cc_final: 0.7290 (tp) REVERT: M 67 PHE cc_start: 0.8899 (m-10) cc_final: 0.8412 (m-80) REVERT: M 94 TRP cc_start: 0.7017 (m100) cc_final: 0.5805 (m100) REVERT: M 148 MET cc_start: 0.7867 (tpp) cc_final: 0.7462 (tpp) REVERT: M 321 MET cc_start: 0.8914 (mmm) cc_final: 0.8564 (mmp) REVERT: L 34 VAL cc_start: 0.9424 (t) cc_final: 0.9170 (p) REVERT: L 97 ILE cc_start: 0.9323 (mt) cc_final: 0.9029 (mm) REVERT: L 138 ASN cc_start: 0.8522 (t0) cc_final: 0.8152 (t0) REVERT: H 54 ILE cc_start: 0.9258 (tt) cc_final: 0.8992 (pt) REVERT: N 36 ARG cc_start: 0.4192 (ptm-80) cc_final: 0.3123 (ptm160) REVERT: N 41 TYR cc_start: 0.7242 (m-80) cc_final: 0.7033 (m-80) REVERT: N 93 ASN cc_start: 0.8479 (m110) cc_final: 0.8109 (p0) outliers start: 41 outliers final: 34 residues processed: 219 average time/residue: 0.2227 time to fit residues: 74.6143 Evaluate side-chains 204 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 27 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 200 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.086489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.064006 restraints weight = 56748.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066102 restraints weight = 32789.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.067475 restraints weight = 23116.750| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13745 Z= 0.158 Angle : 0.662 10.196 18675 Z= 0.326 Chirality : 0.042 0.151 2086 Planarity : 0.004 0.075 2359 Dihedral : 5.434 43.698 1937 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.46 % Allowed : 18.44 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1682 helix: 0.21 (0.25), residues: 446 sheet: -0.52 (0.27), residues: 349 loop : -0.70 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 398 HIS 0.006 0.001 HIS G 268 PHE 0.020 0.002 PHE N 46 TYR 0.029 0.001 TYR L 87 ARG 0.008 0.001 ARG N 28 Details of bonding type rmsd link_TRANS : bond 0.00244 ( 1) link_TRANS : angle 0.14855 ( 3) link_ALPHA1-4 : bond 0.00082 ( 1) link_ALPHA1-4 : angle 1.95037 ( 3) hydrogen bonds : bond 0.02988 ( 452) hydrogen bonds : angle 5.24669 ( 1335) SS BOND : bond 0.00158 ( 5) SS BOND : angle 1.07106 ( 10) covalent geometry : bond 0.00358 (13738) covalent geometry : angle 0.66163 (18659) *********************** 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 213 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8275 (m) REVERT: B 193 MET cc_start: 0.6275 (ppp) cc_final: 0.6024 (ppp) REVERT: B 251 MET cc_start: 0.7554 (tpp) cc_final: 0.7216 (tpp) REVERT: G 159 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7923 (tp30) REVERT: G 267 GLN cc_start: 0.9025 (pm20) cc_final: 0.8484 (pm20) REVERT: G 320 GLN cc_start: 0.8632 (tp40) cc_final: 0.8191 (mm110) REVERT: G 324 LEU cc_start: 0.7541 (mt) cc_final: 0.7231 (tp) REVERT: M 67 PHE cc_start: 0.8859 (m-10) cc_final: 0.8330 (m-80) REVERT: M 94 TRP cc_start: 0.7076 (m100) cc_final: 0.5956 (m100) REVERT: M 148 MET cc_start: 0.7866 (tpp) cc_final: 0.7514 (tpp) REVERT: M 204 MET cc_start: 0.6113 (tpt) cc_final: 0.5913 (tpt) REVERT: M 321 MET cc_start: 0.8784 (mmm) cc_final: 0.8489 (mmp) REVERT: L 34 VAL cc_start: 0.9371 (t) cc_final: 0.9155 (p) REVERT: L 83 ASP cc_start: 0.7919 (t0) cc_final: 0.7652 (t0) REVERT: L 97 ILE cc_start: 0.9311 (mt) cc_final: 0.9031 (mm) REVERT: L 138 ASN cc_start: 0.8455 (t0) cc_final: 0.8118 (t0) REVERT: N 36 ARG cc_start: 0.4436 (ptm-80) cc_final: 0.3536 (ptm160) REVERT: N 41 TYR cc_start: 0.7348 (m-80) cc_final: 0.7070 (m-80) REVERT: N 93 ASN cc_start: 0.8328 (m110) cc_final: 0.8110 (p0) outliers start: 36 outliers final: 31 residues processed: 201 average time/residue: 0.2110 time to fit residues: 65.8618 Evaluate side-chains 203 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 197 ARG 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 173 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 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 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 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** L 200 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** N 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.086137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063505 restraints weight = 57122.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.065609 restraints weight = 33002.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.067001 restraints weight = 23247.462| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13745 Z= 0.145 Angle : 0.663 9.432 18675 Z= 0.323 Chirality : 0.042 0.212 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.409 42.221 1937 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.60 % Allowed : 18.99 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1682 helix: 0.44 (0.26), residues: 439 sheet: -0.48 (0.27), residues: 350 loop : -0.63 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 45 HIS 0.006 0.001 HIS G 268 PHE 0.017 0.002 PHE M 27 TYR 0.024 0.001 TYR L 87 ARG 0.008 0.001 ARG L 19 Details of bonding type rmsd link_TRANS : bond 0.00177 ( 1) link_TRANS : angle 0.10571 ( 3) link_ALPHA1-4 : bond 0.00002 ( 1) link_ALPHA1-4 : angle 1.85829 ( 3) hydrogen bonds : bond 0.02883 ( 452) hydrogen bonds : angle 5.21706 ( 1335) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.99460 ( 10) covalent geometry : bond 0.00332 (13738) covalent geometry : angle 0.66288 (18659) *********************** 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 217 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.549 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: 0.8558 (OUTLIER) cc_final: 0.8338 (m) REVERT: B 193 MET cc_start: 0.6210 (ppp) cc_final: 0.5962 (ppp) REVERT: B 265 THR cc_start: 0.8525 (p) cc_final: 0.8235 (t) REVERT: G 33 MET cc_start: 0.8499 (mmm) cc_final: 0.8177 (mmm) REVERT: G 159 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7929 (tp30) REVERT: G 267 GLN cc_start: 0.9003 (pm20) cc_final: 0.8408 (pm20) REVERT: G 320 GLN cc_start: 0.8648 (tp40) cc_final: 0.8321 (mm110) REVERT: M 67 PHE cc_start: 0.8896 (m-10) cc_final: 0.8479 (m-80) REVERT: M 94 TRP cc_start: 0.7155 (m100) cc_final: 0.6011 (m100) REVERT: M 148 MET cc_start: 0.7932 (tpp) cc_final: 0.7610 (tpp) REVERT: M 321 MET cc_start: 0.8788 (mmm) cc_final: 0.8487 (mmp) REVERT: M 330 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7938 (ttp) REVERT: L 83 ASP cc_start: 0.7881 (t0) cc_final: 0.7663 (t0) REVERT: L 97 ILE cc_start: 0.9301 (mt) cc_final: 0.8939 (mm) REVERT: L 138 ASN cc_start: 0.8373 (t0) cc_final: 0.8078 (t0) REVERT: H 54 ILE cc_start: 0.9249 (tt) cc_final: 0.8927 (pt) REVERT: N 22 GLN cc_start: 0.8266 (pp30) cc_final: 0.8043 (pp30) REVERT: N 36 ARG cc_start: 0.4505 (ptm-80) cc_final: 0.3740 (ptm160) REVERT: N 41 TYR cc_start: 0.7394 (m-80) cc_final: 0.7093 (m-80) REVERT: N 93 ASN cc_start: 0.8268 (m110) cc_final: 0.8067 (p0) outliers start: 38 outliers final: 31 residues processed: 205 average time/residue: 0.2203 time to fit residues: 69.5071 Evaluate side-chains 198 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 197 ARG 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 173 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 330 MET 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 52 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 18 optimal weight: 0.0070 chunk 70 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 132 optimal weight: 0.0000 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** 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** L 125 GLN ** L 200 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.086403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065143 restraints weight = 56329.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066348 restraints weight = 32833.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066578 restraints weight = 24739.947| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5994 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= 0.135 Angle : 0.672 9.414 18675 Z= 0.328 Chirality : 0.042 0.198 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.393 41.699 1937 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.25 % Allowed : 19.88 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1682 helix: 0.44 (0.26), residues: 445 sheet: -0.48 (0.27), residues: 350 loop : -0.61 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 398 HIS 0.008 0.001 HIS B 240 PHE 0.019 0.001 PHE N 46 TYR 0.021 0.001 TYR L 87 ARG 0.005 0.000 ARG L 19 Details of bonding type rmsd link_TRANS : bond 0.00111 ( 1) link_TRANS : angle 0.07960 ( 3) link_ALPHA1-4 : bond 0.00010 ( 1) link_ALPHA1-4 : angle 1.81826 ( 3) hydrogen bonds : bond 0.02969 ( 452) hydrogen bonds : angle 5.20343 ( 1335) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.95544 ( 10) covalent geometry : bond 0.00313 (13738) covalent geometry : angle 0.67117 (18659) *********************** 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 216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8364 (m) REVERT: B 193 MET cc_start: 0.6150 (ppp) cc_final: 0.5924 (ppp) REVERT: B 251 MET cc_start: 0.7566 (tpp) cc_final: 0.7210 (tpp) REVERT: B 265 THR cc_start: 0.8554 (p) cc_final: 0.8289 (t) REVERT: G 33 MET cc_start: 0.8531 (mmm) cc_final: 0.8143 (mmm) REVERT: G 159 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7939 (tp30) REVERT: G 206 MET cc_start: 0.8405 (mmm) cc_final: 0.8121 (mmm) REVERT: G 267 GLN cc_start: 0.9002 (pm20) cc_final: 0.8442 (pm20) REVERT: G 320 GLN cc_start: 0.8654 (tp40) cc_final: 0.8343 (mm110) REVERT: M 67 PHE cc_start: 0.8834 (m-10) cc_final: 0.8417 (m-80) REVERT: M 94 TRP cc_start: 0.7035 (m100) cc_final: 0.5980 (m100) REVERT: M 148 MET cc_start: 0.7953 (tpp) cc_final: 0.7612 (tpp) REVERT: M 321 MET cc_start: 0.8714 (mmm) cc_final: 0.8479 (mmp) REVERT: L 83 ASP cc_start: 0.7874 (t0) cc_final: 0.7583 (t0) REVERT: L 97 ILE cc_start: 0.9282 (mt) cc_final: 0.8882 (mm) REVERT: L 138 ASN cc_start: 0.8334 (t0) cc_final: 0.8003 (t0) REVERT: H 54 ILE cc_start: 0.9203 (tt) cc_final: 0.8871 (pt) REVERT: N 22 GLN cc_start: 0.8239 (pp30) cc_final: 0.8031 (pp30) REVERT: N 36 ARG cc_start: 0.4532 (ptm-80) cc_final: 0.3859 (ptm160) REVERT: N 41 TYR cc_start: 0.7454 (m-80) cc_final: 0.7167 (m-80) outliers start: 33 outliers final: 31 residues processed: 205 average time/residue: 0.2201 time to fit residues: 68.6348 Evaluate side-chains 203 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 197 ARG 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 173 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 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 93 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain N residue 31 CYS Chi-restraints excluded: chain N residue 52 LYS Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 15 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 27 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 overall best weight: 0.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.086699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064266 restraints weight = 56159.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066366 restraints weight = 32423.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067729 restraints weight = 22890.874| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13745 Z= 0.125 Angle : 0.675 9.356 18675 Z= 0.327 Chirality : 0.042 0.190 2086 Planarity : 0.004 0.042 2359 Dihedral : 5.316 41.290 1937 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.32 % Allowed : 19.67 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1682 helix: 0.52 (0.26), residues: 445 sheet: -0.42 (0.28), residues: 350 loop : -0.57 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 398 HIS 0.006 0.001 HIS B 257 PHE 0.020 0.001 PHE H 71 TYR 0.022 0.001 TYR H 161 ARG 0.011 0.000 ARG L 19 Details of bonding type rmsd link_TRANS : bond 0.00089 ( 1) link_TRANS : angle 0.07929 ( 3) link_ALPHA1-4 : bond 0.00166 ( 1) link_ALPHA1-4 : angle 1.66395 ( 3) hydrogen bonds : bond 0.02815 ( 452) hydrogen bonds : angle 5.14528 ( 1335) SS BOND : bond 0.00214 ( 5) SS BOND : angle 0.93397 ( 10) covalent geometry : bond 0.00299 (13738) covalent geometry : angle 0.67496 (18659) ********************** 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 210 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.615 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 193 MET cc_start: 0.6099 (ppp) cc_final: 0.5864 (ppp) REVERT: B 251 MET cc_start: 0.7488 (tpp) cc_final: 0.7234 (tpp) REVERT: B 265 THR cc_start: 0.8619 (p) cc_final: 0.8357 (t) REVERT: G 33 MET cc_start: 0.8401 (mmm) cc_final: 0.8175 (mmm) REVERT: G 206 MET cc_start: 0.8334 (mmm) cc_final: 0.8039 (mmm) REVERT: M 67 PHE cc_start: 0.8873 (m-10) cc_final: 0.8469 (m-80) REVERT: M 94 TRP cc_start: 0.7125 (m100) cc_final: 0.6074 (m100) REVERT: M 148 MET cc_start: 0.8011 (tpp) cc_final: 0.7606 (tpp) REVERT: M 321 MET cc_start: 0.8782 (mmm) cc_final: 0.8511 (mmp) REVERT: H 54 ILE cc_start: 0.9191 (tt) cc_final: 0.8899 (pt) REVERT: N 36 ARG cc_start: 0.4384 (ptm-80) cc_final: 0.3802 (ptm160) REVERT: N 41 TYR cc_start: 0.7479 (m-80) cc_final: 0.7199 (m-80) REVERT: N 53 GLU cc_start: 0.8327 (pm20) cc_final: 0.7921 (pm20) REVERT: N 55 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8275 (mp0) outliers start: 34 outliers final: 29 residues processed: 198 average time/residue: 0.2185 time to fit residues: 66.3586 Evaluate side-chains 193 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 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 456 VAL Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain H residue 93 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 136 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.0060 chunk 82 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 HIS ** M 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 ASN ** 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 = 0.3792 r_free = 0.3792 target = 0.085672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063159 restraints weight = 56975.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065252 restraints weight = 32692.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.066613 restraints weight = 23035.911| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13745 Z= 0.152 Angle : 0.694 12.526 18675 Z= 0.338 Chirality : 0.042 0.198 2086 Planarity : 0.004 0.047 2359 Dihedral : 5.349 40.105 1937 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.19 % Allowed : 20.42 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1682 helix: 0.53 (0.26), residues: 440 sheet: -0.41 (0.27), residues: 350 loop : -0.62 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 398 HIS 0.007 0.001 HIS G 268 PHE 0.018 0.002 PHE M 27 TYR 0.026 0.001 TYR H 109 ARG 0.011 0.001 ARG L 19 Details of bonding type rmsd link_TRANS : bond 0.00220 ( 1) link_TRANS : angle 0.11263 ( 3) link_ALPHA1-4 : bond 0.00064 ( 1) link_ALPHA1-4 : angle 1.72649 ( 3) hydrogen bonds : bond 0.02974 ( 452) hydrogen bonds : angle 5.20212 ( 1335) SS BOND : bond 0.00194 ( 5) SS BOND : angle 0.90966 ( 10) covalent geometry : bond 0.00351 (13738) covalent geometry : angle 0.69339 (18659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4526.71 seconds wall clock time: 79 minutes 23.53 seconds (4763.53 seconds total)