Starting phenix.real_space_refine on Mon Jul 6 02:53:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nz2_49948/07_2026/9nz2_49948_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nz2_49948/07_2026/9nz2_49948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nz2_49948/07_2026/9nz2_49948_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nz2_49948/07_2026/9nz2_49948_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nz2_49948/07_2026/9nz2_49948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nz2_49948/07_2026/9nz2_49948.map" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 S 87 5.16 5 C 9777 2.51 5 N 2613 2.21 5 O 3039 1.98 5 H 15447 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30963 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6800 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1801 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1706 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, F, I, G, H Time building chain proxies: 9.81, per 1000 atoms: 0.32 Number of scatterers: 30963 At special positions: 0 Unit cell: (150, 154.5, 106.5, 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 87 16.00 O 3039 8.00 N 2613 7.00 C 9777 6.00 H 15447 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.02 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.02 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 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 NAG-ASN " NAG A1000 " - " ASN A 459 " " NAG B1000 " - " ASN B 459 " " NAG C1000 " - " ASN C 459 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 878.3 milliseconds 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3732 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 33 sheets defined 30.9% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 60 through 66 removed outlier: 3.794A pdb=" N ARG A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN A 65 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 removed outlier: 3.714A pdb=" N PHE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.574A pdb=" N MET A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 96 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 119 through 142 removed outlier: 4.650A pdb=" N GLU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 removed outlier: 3.551A pdb=" N ASN A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.652A pdb=" N GLY A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 5.462A pdb=" N ASN A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.043A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.979A pdb=" N LEU A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.808A pdb=" N CYS A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.819A pdb=" N LYS A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 462 removed outlier: 3.648A pdb=" N ASN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 60 through 66 removed outlier: 3.794A pdb=" N ARG B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ASN B 65 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 removed outlier: 3.713A pdb=" N PHE B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.574A pdb=" N MET B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 119 through 142 removed outlier: 4.650A pdb=" N GLU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 removed outlier: 3.550A pdb=" N ASN B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.652A pdb=" N GLY B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 5.461A pdb=" N ASN B 183 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 209 Processing helix chain 'B' and resid 209 through 214 removed outlier: 4.043A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.979A pdb=" N LEU B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.809A pdb=" N CYS B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.818A pdb=" N LYS B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 385 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 455 through 462 removed outlier: 3.648A pdb=" N ASN B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 32 Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.794A pdb=" N ARG C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN C 65 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 100 removed outlier: 3.714A pdb=" N PHE C 71 " --> pdb=" O THR C 67 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.574A pdb=" N MET C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 96 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 119 through 142 removed outlier: 4.650A pdb=" N GLU C 134 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 removed outlier: 3.550A pdb=" N ASN C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.652A pdb=" N GLY C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 5.461A pdb=" N ASN C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 Processing helix chain 'C' and resid 209 through 214 removed outlier: 4.043A pdb=" N GLN C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 234 through 242 removed outlier: 3.978A pdb=" N LEU C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.808A pdb=" N CYS C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.818A pdb=" N LYS C 357 " --> pdb=" O ASP C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 385 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 455 through 462 removed outlier: 3.648A pdb=" N ASN C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.149A pdb=" N LEU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.150A pdb=" N LEU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.150A pdb=" N LEU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 279 through 282 removed outlier: 7.523A pdb=" N VAL A 333 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN A 40 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 282 removed outlier: 5.514A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 310 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE A 321 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 157 removed outlier: 8.061A pdb=" N THR A 163 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 51 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 165 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 55 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU A 276 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY A 259 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 7.067A pdb=" N MET A 110 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374 removed outlier: 3.729A pdb=" N ALA A 380 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 405 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 282 removed outlier: 7.523A pdb=" N VAL B 333 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 279 through 282 removed outlier: 5.513A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 310 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE B 321 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 157 removed outlier: 8.062A pdb=" N THR B 163 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 51 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 165 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 55 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP B 263 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 274 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE B 261 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU B 276 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 259 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AB3, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB4, first strand: chain 'B' and resid 371 through 374 removed outlier: 3.730A pdb=" N ALA B 380 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 405 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 279 through 282 removed outlier: 7.524A pdb=" N VAL C 333 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 279 through 282 removed outlier: 5.514A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE C 310 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE C 321 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 153 through 157 removed outlier: 8.061A pdb=" N THR C 163 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C 51 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 165 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 55 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP C 263 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU C 274 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE C 261 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU C 276 " --> pdb=" O GLY C 259 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY C 259 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB9, first strand: chain 'C' and resid 371 through 374 removed outlier: 3.729A pdb=" N ALA C 380 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 405 " --> pdb=" O ALA C 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.081A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU E 11 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU E 11 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR E 96 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.082A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.347A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.347A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR G 96 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.347A pdb=" N LEU H 11 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.347A pdb=" N LEU H 11 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H 96 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.081A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1617 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: 7.69 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15447 1.03 - 1.23: 20 1.23 - 1.42: 6457 1.42 - 1.62: 9177 1.62 - 1.82: 126 Bond restraints: 31227 Sorted by residual: bond pdb=" CA ASN C 100 " pdb=" C ASN C 100 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.72e-02 3.38e+03 9.27e-01 bond pdb=" CA ASN A 100 " pdb=" C ASN A 100 " ideal model delta sigma weight residual 1.522 1.505 0.016 1.72e-02 3.38e+03 9.04e-01 bond pdb=" CA ASN B 100 " pdb=" C ASN B 100 " ideal model delta sigma weight residual 1.522 1.506 0.016 1.72e-02 3.38e+03 8.81e-01 bond pdb=" CG GLN A 137 " pdb=" CD GLN A 137 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.16e-01 bond pdb=" CG GLN C 137 " pdb=" CD GLN C 137 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.09e-01 ... (remaining 31222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 53607 1.14 - 2.27: 2652 2.27 - 3.41: 126 3.41 - 4.55: 21 4.55 - 5.68: 6 Bond angle restraints: 56412 Sorted by residual: angle pdb=" N VAL C 364 " pdb=" CA VAL C 364 " pdb=" C VAL C 364 " ideal model delta sigma weight residual 113.71 110.21 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL A 364 " pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 113.71 110.21 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL B 364 " pdb=" CA VAL B 364 " pdb=" C VAL B 364 " ideal model delta sigma weight residual 113.71 110.24 3.47 9.50e-01 1.11e+00 1.33e+01 angle pdb=" N GLN C 137 " pdb=" CA GLN C 137 " pdb=" CB GLN C 137 " ideal model delta sigma weight residual 110.40 114.68 -4.28 1.63e+00 3.76e-01 6.88e+00 angle pdb=" N GLN B 137 " pdb=" CA GLN B 137 " pdb=" CB GLN B 137 " ideal model delta sigma weight residual 110.40 114.62 -4.22 1.63e+00 3.76e-01 6.70e+00 ... (remaining 56407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 13386 16.85 - 33.70: 1015 33.70 - 50.55: 260 50.55 - 67.40: 111 67.40 - 84.25: 21 Dihedral angle restraints: 14793 sinusoidal: 8163 harmonic: 6630 Sorted by residual: dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS B 109 " pdb=" CB CYS B 109 " ideal model delta sinusoidal sigma weight residual -86.00 -129.23 43.23 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS C 99 " pdb=" SG CYS C 99 " pdb=" SG CYS C 109 " pdb=" CB CYS C 109 " ideal model delta sinusoidal sigma weight residual -86.00 -129.21 43.21 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS A 99 " pdb=" SG CYS A 99 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual -86.00 -129.20 43.20 1 1.00e+01 1.00e-02 2.60e+01 ... (remaining 14790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1561 0.029 - 0.058: 610 0.058 - 0.087: 174 0.087 - 0.116: 159 0.116 - 0.145: 22 Chirality restraints: 2526 Sorted by residual: chirality pdb=" CA VAL D 11 " pdb=" N VAL D 11 " pdb=" C VAL D 11 " pdb=" CB VAL D 11 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL I 11 " pdb=" N VAL I 11 " pdb=" C VAL I 11 " pdb=" CB VAL I 11 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL F 11 " pdb=" N VAL F 11 " pdb=" C VAL F 11 " pdb=" CB VAL F 11 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2523 not shown) Planarity restraints: 4677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 42 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO E 43 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 42 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO H 43 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 43 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 43 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 42 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO G 43 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO G 43 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 43 " 0.019 5.00e-02 4.00e+02 ... (remaining 4674 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 14004 2.39 - 2.94: 70902 2.94 - 3.50: 76046 3.50 - 4.05: 100502 4.05 - 4.60: 144212 Nonbonded interactions: 405666 Sorted by model distance: nonbonded pdb=" H LYS C 69 " pdb=" HZ1 LYS C 69 " model vdw 1.841 2.100 nonbonded pdb=" H LYS B 69 " pdb=" HZ1 LYS B 69 " model vdw 1.841 2.100 nonbonded pdb=" H LYS A 69 " pdb=" HZ1 LYS A 69 " model vdw 1.841 2.100 nonbonded pdb=" H THR B 119 " pdb=" HG1 THR B 122 " model vdw 1.851 2.100 nonbonded pdb=" H THR A 119 " pdb=" HG1 THR A 122 " model vdw 1.851 2.100 ... (remaining 405661 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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: 0.010 Normalize map: mean=0, sd=1: 1.450 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: 0.230 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.090 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15801 Z= 0.142 Angle : 0.545 5.684 21495 Z= 0.324 Chirality : 0.041 0.145 2526 Planarity : 0.003 0.034 2733 Dihedral : 12.526 84.250 5778 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 2001 helix: 0.77 (0.27), residues: 438 sheet: -0.39 (0.23), residues: 498 loop : -1.24 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 27F TYR 0.010 0.001 TYR C 25 PHE 0.008 0.002 PHE A 71 TRP 0.016 0.001 TRP F 100 HIS 0.004 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (15780) covalent geometry : angle 0.54543 / 0.32 (21450) SS BOND : bond 0.00330 / 0.24 ( 18) SS BOND : angle 0.46214 / 0.35 ( 36) hydrogen bonds : bond 0.15651 / 10.18 ( 619) hydrogen bonds : angle 5.48830 / 3.79 ( 1617) link_NAG-ASN : bond 0.00295 / 0.15 ( 3) link_NAG-ASN : angle 0.85141 / 0.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.867 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 GLU cc_start: 0.7874 (mp0) cc_final: 0.7524 (tm-30) REVERT: B 74 TYR cc_start: 0.7875 (t80) cc_final: 0.7402 (t80) REVERT: B 76 ASN cc_start: 0.8849 (m110) cc_final: 0.8482 (m110) REVERT: B 291 LEU cc_start: 0.9155 (mt) cc_final: 0.8777 (mm) REVERT: B 383 LEU cc_start: 0.8121 (mm) cc_final: 0.7208 (mm) REVERT: B 432 GLU cc_start: 0.7877 (mp0) cc_final: 0.7569 (tm-30) REVERT: B 455 LEU cc_start: 0.9258 (mt) cc_final: 0.8854 (mp) REVERT: C 74 TYR cc_start: 0.7926 (t80) cc_final: 0.7512 (t80) REVERT: C 92 MET cc_start: 0.8831 (tpp) cc_final: 0.8371 (tpp) REVERT: C 455 LEU cc_start: 0.9322 (mt) cc_final: 0.9100 (mt) REVERT: D 67 VAL cc_start: 0.9023 (m) cc_final: 0.8747 (p) REVERT: E 37 GLN cc_start: 0.8548 (tt0) cc_final: 0.7873 (tt0) REVERT: E 52 SER cc_start: 0.8821 (m) cc_final: 0.8525 (p) REVERT: E 102 LYS cc_start: 0.9047 (tppt) cc_final: 0.8693 (tppt) REVERT: E 103 LEU cc_start: 0.9366 (tp) cc_final: 0.9121 (tp) REVERT: F 48 MET cc_start: 0.8170 (ptt) cc_final: 0.7665 (ptm) REVERT: I 34 MET cc_start: 0.6334 (tpt) cc_final: 0.6017 (tpt) REVERT: I 82 LEU cc_start: 0.7817 (tp) cc_final: 0.6984 (tp) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.2734 time to fit residues: 136.7158 Evaluate side-chains 239 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.073095 restraints weight = 160473.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076951 restraints weight = 81848.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079547 restraints weight = 51284.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081367 restraints weight = 36474.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082609 restraints weight = 28219.728| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15801 Z= 0.117 Angle : 0.505 6.012 21495 Z= 0.278 Chirality : 0.042 0.151 2526 Planarity : 0.004 0.035 2733 Dihedral : 4.318 15.178 2241 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.18), residues: 2001 helix: 0.84 (0.27), residues: 441 sheet: -0.50 (0.23), residues: 507 loop : -1.30 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 27F TYR 0.009 0.001 TYR B 249 PHE 0.014 0.001 PHE E 97 TRP 0.013 0.001 TRP F 100 HIS 0.005 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (15780) covalent geometry : angle 0.50456 / 0.28 (21450) SS BOND : bond 0.00538 / 0.41 ( 18) SS BOND : angle 0.39947 / 0.30 ( 36) hydrogen bonds : bond 0.04576 / 3.10 ( 619) hydrogen bonds : angle 4.88135 / 3.40 ( 1617) link_NAG-ASN : bond 0.00256 / 0.13 ( 3) link_NAG-ASN : angle 0.74454 / 0.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 0.877 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: 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: 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 52 MET cc_start: 0.8181 (ptt) cc_final: 0.7908 (ptt) REVERT: A 390 MET cc_start: 0.9119 (mmp) cc_final: 0.8739 (mmp) REVERT: A 432 GLU cc_start: 0.7886 (mp0) cc_final: 0.7550 (tm-30) REVERT: A 437 ASN cc_start: 0.7683 (p0) cc_final: 0.7333 (p0) REVERT: B 74 TYR cc_start: 0.7868 (t80) cc_final: 0.7405 (t80) REVERT: B 76 ASN cc_start: 0.8821 (m110) cc_final: 0.8405 (m110) REVERT: B 291 LEU cc_start: 0.9124 (mt) cc_final: 0.8761 (mm) REVERT: B 455 LEU cc_start: 0.9200 (mt) cc_final: 0.8908 (mp) REVERT: C 74 TYR cc_start: 0.7933 (t80) cc_final: 0.7522 (t80) REVERT: C 76 ASN cc_start: 0.8642 (m110) cc_final: 0.8287 (m110) REVERT: C 92 MET cc_start: 0.8844 (tpp) cc_final: 0.8370 (tpp) REVERT: C 390 MET cc_start: 0.9166 (mmm) cc_final: 0.8942 (mmp) REVERT: D 67 VAL cc_start: 0.9019 (m) cc_final: 0.8719 (p) REVERT: E 27 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8544 (tp-100) REVERT: E 37 GLN cc_start: 0.8543 (tt0) cc_final: 0.7911 (tt0) REVERT: E 52 SER cc_start: 0.8821 (m) cc_final: 0.8542 (p) REVERT: F 32 TYR cc_start: 0.7956 (m-80) cc_final: 0.7657 (m-80) REVERT: F 48 MET cc_start: 0.8344 (ptt) cc_final: 0.7752 (ptm) REVERT: F 69 MET cc_start: 0.9165 (ptp) cc_final: 0.8884 (ptp) REVERT: G 27 GLN cc_start: 0.8849 (tp40) cc_final: 0.8552 (tp40) REVERT: G 102 LYS cc_start: 0.8814 (tppt) cc_final: 0.8433 (tppt) REVERT: H 27 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8614 (tp-100) REVERT: I 34 MET cc_start: 0.6742 (tpt) cc_final: 0.6366 (tpt) outliers start: 1 outliers final: 1 residues processed: 305 average time/residue: 0.2577 time to fit residues: 119.2677 Evaluate side-chains 238 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.070835 restraints weight = 161585.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074368 restraints weight = 85436.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076795 restraints weight = 54733.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078488 restraints weight = 39525.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.079658 restraints weight = 30987.016| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15801 Z= 0.167 Angle : 0.531 6.187 21495 Z= 0.290 Chirality : 0.042 0.164 2526 Planarity : 0.004 0.035 2733 Dihedral : 4.411 16.632 2241 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.18), residues: 2001 helix: 0.78 (0.26), residues: 441 sheet: -0.57 (0.22), residues: 513 loop : -1.48 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27F TYR 0.019 0.002 TYR C 415 PHE 0.020 0.001 PHE E 97 TRP 0.015 0.001 TRP I 100 HIS 0.004 0.002 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (15780) covalent geometry : angle 0.53037 / 0.29 (21450) SS BOND : bond 0.00349 / 0.25 ( 18) SS BOND : angle 0.65481 / 0.43 ( 36) hydrogen bonds : bond 0.03908 / 2.62 ( 619) hydrogen bonds : angle 4.82446 / 3.36 ( 1617) link_NAG-ASN : bond 0.00360 / 0.18 ( 3) link_NAG-ASN : angle 1.02852 / 0.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.738 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: 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 432 GLU cc_start: 0.8018 (mp0) cc_final: 0.7443 (tm-30) REVERT: B 92 MET cc_start: 0.9121 (tpp) cc_final: 0.8742 (tpp) REVERT: B 291 LEU cc_start: 0.9110 (mt) cc_final: 0.8746 (mm) REVERT: C 74 TYR cc_start: 0.8096 (t80) cc_final: 0.7839 (t80) REVERT: C 76 ASN cc_start: 0.8772 (m110) cc_final: 0.8421 (m110) REVERT: C 92 MET cc_start: 0.8866 (tpp) cc_final: 0.8412 (tpp) REVERT: C 390 MET cc_start: 0.9266 (mmm) cc_final: 0.9009 (mmp) REVERT: D 67 VAL cc_start: 0.9029 (m) cc_final: 0.8754 (p) REVERT: D 86 ASP cc_start: 0.8864 (m-30) cc_final: 0.8437 (m-30) REVERT: E 27 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8634 (tp-100) REVERT: E 32 TYR cc_start: 0.5927 (m-80) cc_final: 0.5476 (m-10) REVERT: E 37 GLN cc_start: 0.8667 (tt0) cc_final: 0.7978 (tt0) REVERT: E 52 SER cc_start: 0.8961 (m) cc_final: 0.8728 (p) REVERT: F 32 TYR cc_start: 0.8186 (m-80) cc_final: 0.7887 (m-80) REVERT: F 48 MET cc_start: 0.8611 (ptt) cc_final: 0.8065 (ptm) REVERT: F 64 GLN cc_start: 0.9142 (tp40) cc_final: 0.8870 (tp-100) REVERT: F 69 MET cc_start: 0.9230 (ptp) cc_final: 0.8922 (ptp) REVERT: G 27 GLN cc_start: 0.9023 (tp40) cc_final: 0.8710 (tp-100) REVERT: G 32 TYR cc_start: 0.5989 (m-80) cc_final: 0.5575 (m-10) REVERT: H 27 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8712 (tp-100) REVERT: I 34 MET cc_start: 0.7092 (tpt) cc_final: 0.6744 (tpt) REVERT: I 81 GLU cc_start: 0.6430 (tp30) cc_final: 0.6220 (tm-30) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.2541 time to fit residues: 116.1650 Evaluate side-chains 229 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 137 optimal weight: 0.3980 chunk 173 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 HIS C 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.070264 restraints weight = 159750.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.073847 restraints weight = 83356.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.076303 restraints weight = 53049.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078024 restraints weight = 38162.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.079203 restraints weight = 29859.131| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15801 Z= 0.152 Angle : 0.529 6.147 21495 Z= 0.288 Chirality : 0.042 0.152 2526 Planarity : 0.003 0.034 2733 Dihedral : 4.507 16.581 2241 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 2001 helix: 0.47 (0.26), residues: 462 sheet: -0.64 (0.22), residues: 513 loop : -1.60 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 27F TYR 0.019 0.001 TYR D 79 PHE 0.007 0.001 PHE E 97 TRP 0.014 0.001 TRP D 100 HIS 0.006 0.002 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (15780) covalent geometry : angle 0.52596 / 0.29 (21450) SS BOND : bond 0.00532 / 0.37 ( 18) SS BOND : angle 1.34736 / 0.71 ( 36) hydrogen bonds : bond 0.03709 / 2.49 ( 619) hydrogen bonds : angle 4.83352 / 3.38 ( 1617) link_NAG-ASN : bond 0.00325 / 0.16 ( 3) link_NAG-ASN : angle 1.02561 / 0.48 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.772 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 HIS cc_start: 0.8720 (m90) cc_final: 0.8327 (m-70) REVERT: A 52 MET cc_start: 0.8385 (ptt) cc_final: 0.8098 (ptt) REVERT: A 437 ASN cc_start: 0.8018 (p0) cc_final: 0.7722 (p0) REVERT: B 92 MET cc_start: 0.9114 (tpp) cc_final: 0.8723 (tpp) REVERT: B 291 LEU cc_start: 0.9119 (mt) cc_final: 0.8768 (mm) REVERT: C 76 ASN cc_start: 0.8789 (m110) cc_final: 0.8431 (m110) REVERT: C 92 MET cc_start: 0.8870 (tpp) cc_final: 0.8410 (tpp) REVERT: D 67 VAL cc_start: 0.9082 (m) cc_final: 0.8771 (p) REVERT: E 27 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8643 (tp-100) REVERT: E 32 TYR cc_start: 0.5978 (m-80) cc_final: 0.5488 (m-10) REVERT: E 37 GLN cc_start: 0.8670 (tt0) cc_final: 0.8130 (tt0) REVERT: E 52 SER cc_start: 0.8931 (m) cc_final: 0.8637 (p) REVERT: F 32 TYR cc_start: 0.8011 (m-80) cc_final: 0.7739 (m-80) REVERT: F 48 MET cc_start: 0.8660 (ptt) cc_final: 0.8117 (ptm) REVERT: F 64 GLN cc_start: 0.9183 (tp40) cc_final: 0.8930 (tp-100) REVERT: F 66 ARG cc_start: 0.9397 (ttp80) cc_final: 0.8996 (ttp80) REVERT: F 69 MET cc_start: 0.9219 (ptp) cc_final: 0.8918 (ptp) REVERT: F 80 MET cc_start: 0.8173 (tmm) cc_final: 0.7853 (tmm) REVERT: G 27 GLN cc_start: 0.9061 (tp40) cc_final: 0.8734 (tp-100) REVERT: G 32 TYR cc_start: 0.6014 (m-80) cc_final: 0.5589 (m-10) REVERT: H 27 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8532 (tp-100) REVERT: I 29 PHE cc_start: 0.7344 (t80) cc_final: 0.7138 (t80) REVERT: I 34 MET cc_start: 0.7115 (tpt) cc_final: 0.6808 (tpt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2545 time to fit residues: 111.3410 Evaluate side-chains 230 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.069889 restraints weight = 159319.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073587 restraints weight = 81310.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076109 restraints weight = 51171.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077857 restraints weight = 36544.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.079061 restraints weight = 28503.302| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15801 Z= 0.131 Angle : 0.513 6.118 21495 Z= 0.278 Chirality : 0.042 0.154 2526 Planarity : 0.003 0.035 2733 Dihedral : 4.463 16.955 2241 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 2001 helix: 0.51 (0.26), residues: 462 sheet: -0.63 (0.22), residues: 513 loop : -1.61 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 27F TYR 0.015 0.001 TYR I 100A PHE 0.024 0.001 PHE E 97 TRP 0.016 0.001 TRP I 100 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15780) covalent geometry : angle 0.51190 / 0.28 (21450) SS BOND : bond 0.00569 / 0.45 ( 18) SS BOND : angle 1.02252 / 0.60 ( 36) hydrogen bonds : bond 0.03574 / 2.39 ( 619) hydrogen bonds : angle 4.72832 / 3.31 ( 1617) link_NAG-ASN : bond 0.00311 / 0.16 ( 3) link_NAG-ASN : angle 0.96878 / 0.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.842 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: 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: symmetry clash REVERT: A 24 HIS cc_start: 0.8726 (m90) cc_final: 0.8331 (m-70) REVERT: B 92 MET cc_start: 0.9107 (tpp) cc_final: 0.8701 (tpp) REVERT: B 142 MET cc_start: 0.8512 (mmp) cc_final: 0.8062 (mmp) REVERT: B 291 LEU cc_start: 0.9122 (mt) cc_final: 0.8797 (mm) REVERT: B 390 MET cc_start: 0.9226 (mmm) cc_final: 0.8709 (mmm) REVERT: C 92 MET cc_start: 0.8879 (tpp) cc_final: 0.8398 (tpp) REVERT: C 343 MET cc_start: 0.8101 (ttm) cc_final: 0.7475 (tpp) REVERT: D 67 VAL cc_start: 0.9107 (m) cc_final: 0.8777 (p) REVERT: D 86 ASP cc_start: 0.8934 (m-30) cc_final: 0.8614 (m-30) REVERT: E 21 MET cc_start: 0.9466 (pmm) cc_final: 0.9200 (pmm) REVERT: E 27 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8641 (tp-100) REVERT: E 32 TYR cc_start: 0.6010 (m-80) cc_final: 0.5518 (m-10) REVERT: E 37 GLN cc_start: 0.8675 (tt0) cc_final: 0.8133 (tt0) REVERT: E 52 SER cc_start: 0.8918 (m) cc_final: 0.8624 (p) REVERT: E 102 LYS cc_start: 0.8989 (tppt) cc_final: 0.8712 (tppt) REVERT: F 32 TYR cc_start: 0.8059 (m-80) cc_final: 0.7746 (m-80) REVERT: F 48 MET cc_start: 0.8655 (ptt) cc_final: 0.8129 (ptm) REVERT: F 64 GLN cc_start: 0.9183 (tp40) cc_final: 0.8898 (tp-100) REVERT: F 69 MET cc_start: 0.9085 (ptp) cc_final: 0.8799 (ptp) REVERT: G 21 MET cc_start: 0.9550 (pmm) cc_final: 0.9320 (pmm) REVERT: G 27 GLN cc_start: 0.9082 (tp40) cc_final: 0.8723 (tp-100) REVERT: G 32 TYR cc_start: 0.5957 (m-80) cc_final: 0.5476 (m-10) REVERT: H 27 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8526 (tp-100) REVERT: H 87 TYR cc_start: 0.8861 (m-80) cc_final: 0.8436 (m-80) REVERT: I 29 PHE cc_start: 0.7214 (t80) cc_final: 0.6976 (t80) REVERT: I 34 MET cc_start: 0.7110 (tpt) cc_final: 0.6831 (tpt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2451 time to fit residues: 106.4961 Evaluate side-chains 230 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.070500 restraints weight = 156510.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074222 restraints weight = 79782.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076755 restraints weight = 50060.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.078529 restraints weight = 35783.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079688 restraints weight = 27824.662| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15801 Z= 0.103 Angle : 0.505 6.074 21495 Z= 0.272 Chirality : 0.042 0.152 2526 Planarity : 0.003 0.036 2733 Dihedral : 4.369 15.568 2241 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2001 helix: 0.62 (0.26), residues: 462 sheet: -0.59 (0.23), residues: 513 loop : -1.58 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 27F TYR 0.009 0.001 TYR B 201 PHE 0.010 0.001 PHE E 97 TRP 0.012 0.001 TRP D 100 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (15780) covalent geometry : angle 0.50471 / 0.27 (21450) SS BOND : bond 0.00334 / 0.25 ( 18) SS BOND : angle 0.73174 / 0.41 ( 36) hydrogen bonds : bond 0.03423 / 2.29 ( 619) hydrogen bonds : angle 4.65015 / 3.25 ( 1617) link_NAG-ASN : bond 0.00302 / 0.15 ( 3) link_NAG-ASN : angle 0.90667 / 0.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.871 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: 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 24 HIS cc_start: 0.8735 (m90) cc_final: 0.8373 (m-70) REVERT: A 52 MET cc_start: 0.8399 (ptt) cc_final: 0.8129 (ptt) REVERT: A 343 MET cc_start: 0.8299 (ttm) cc_final: 0.7787 (tpp) REVERT: A 437 ASN cc_start: 0.7974 (p0) cc_final: 0.7676 (p0) REVERT: B 92 MET cc_start: 0.9063 (tpp) cc_final: 0.8501 (tpp) REVERT: B 291 LEU cc_start: 0.9152 (mt) cc_final: 0.8799 (mm) REVERT: B 390 MET cc_start: 0.9235 (mmm) cc_final: 0.8743 (mmm) REVERT: C 92 MET cc_start: 0.8872 (tpp) cc_final: 0.8400 (tpp) REVERT: C 390 MET cc_start: 0.9199 (mmm) cc_final: 0.8924 (mmp) REVERT: D 67 VAL cc_start: 0.9266 (m) cc_final: 0.8989 (p) REVERT: D 86 ASP cc_start: 0.8940 (m-30) cc_final: 0.8626 (m-30) REVERT: E 21 MET cc_start: 0.9531 (pmm) cc_final: 0.9303 (pmm) REVERT: E 27 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8630 (tp-100) REVERT: E 32 TYR cc_start: 0.5983 (m-80) cc_final: 0.5489 (m-10) REVERT: E 37 GLN cc_start: 0.8657 (tt0) cc_final: 0.8122 (tt0) REVERT: E 52 SER cc_start: 0.8884 (m) cc_final: 0.8579 (p) REVERT: E 102 LYS cc_start: 0.8967 (tppt) cc_final: 0.8720 (tppt) REVERT: F 32 TYR cc_start: 0.8059 (m-80) cc_final: 0.7749 (m-80) REVERT: F 48 MET cc_start: 0.8615 (ptt) cc_final: 0.8257 (ptm) REVERT: F 64 GLN cc_start: 0.9192 (tp40) cc_final: 0.8894 (tp-100) REVERT: F 69 MET cc_start: 0.9162 (ptp) cc_final: 0.8820 (ptp) REVERT: G 21 MET cc_start: 0.9552 (pmm) cc_final: 0.9301 (pmm) REVERT: G 27 GLN cc_start: 0.9059 (tp40) cc_final: 0.8707 (tp-100) REVERT: G 32 TYR cc_start: 0.5920 (m-80) cc_final: 0.5413 (m-10) REVERT: G 102 LYS cc_start: 0.9003 (tppt) cc_final: 0.8637 (tppt) REVERT: H 27 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8503 (tp-100) REVERT: I 29 PHE cc_start: 0.7250 (t80) cc_final: 0.7000 (t80) REVERT: I 34 MET cc_start: 0.7095 (tpt) cc_final: 0.6811 (tpt) REVERT: I 86 ASP cc_start: 0.9132 (m-30) cc_final: 0.8789 (m-30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2538 time to fit residues: 108.4720 Evaluate side-chains 230 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 0.0770 chunk 160 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 146 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.070668 restraints weight = 157725.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.074394 restraints weight = 80461.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076972 restraints weight = 50515.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078737 restraints weight = 35919.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079965 restraints weight = 27957.704| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15801 Z= 0.103 Angle : 0.499 6.085 21495 Z= 0.268 Chirality : 0.042 0.155 2526 Planarity : 0.003 0.036 2733 Dihedral : 4.300 15.434 2241 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 2001 helix: 0.66 (0.26), residues: 462 sheet: -0.57 (0.23), residues: 513 loop : -1.58 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 27F TYR 0.015 0.001 TYR I 100A PHE 0.009 0.001 PHE E 97 TRP 0.016 0.001 TRP I 100 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (15780) covalent geometry : angle 0.49727 / 0.27 (21450) SS BOND : bond 0.00590 / 0.34 ( 18) SS BOND : angle 0.99740 / 0.62 ( 36) hydrogen bonds : bond 0.03302 / 2.20 ( 619) hydrogen bonds : angle 4.57320 / 3.20 ( 1617) link_NAG-ASN : bond 0.00297 / 0.15 ( 3) link_NAG-ASN : angle 0.85542 / 0.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.056 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: 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 24 HIS cc_start: 0.8726 (m90) cc_final: 0.8334 (m-70) REVERT: A 52 MET cc_start: 0.8407 (ptt) cc_final: 0.8138 (ptt) REVERT: A 437 ASN cc_start: 0.8069 (p0) cc_final: 0.7789 (p0) REVERT: B 92 MET cc_start: 0.8988 (tpp) cc_final: 0.8436 (tpp) REVERT: B 142 MET cc_start: 0.8656 (mmp) cc_final: 0.8297 (mmp) REVERT: B 390 MET cc_start: 0.9233 (mmm) cc_final: 0.8752 (mmm) REVERT: C 92 MET cc_start: 0.8923 (tpp) cc_final: 0.8431 (tpp) REVERT: D 67 VAL cc_start: 0.9274 (m) cc_final: 0.9009 (p) REVERT: D 86 ASP cc_start: 0.8964 (m-30) cc_final: 0.8651 (m-30) REVERT: E 21 MET cc_start: 0.9529 (pmm) cc_final: 0.9300 (pmm) REVERT: E 27 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8618 (tp-100) REVERT: E 32 TYR cc_start: 0.5998 (m-80) cc_final: 0.5502 (m-10) REVERT: E 37 GLN cc_start: 0.8647 (tt0) cc_final: 0.8134 (tt0) REVERT: E 52 SER cc_start: 0.8783 (m) cc_final: 0.8465 (p) REVERT: F 32 TYR cc_start: 0.8109 (m-80) cc_final: 0.7812 (m-80) REVERT: F 48 MET cc_start: 0.8613 (ptt) cc_final: 0.8264 (ptm) REVERT: F 64 GLN cc_start: 0.9198 (tp40) cc_final: 0.8896 (tp-100) REVERT: F 69 MET cc_start: 0.9171 (ptp) cc_final: 0.8820 (ptp) REVERT: F 86 ASP cc_start: 0.9230 (m-30) cc_final: 0.8946 (m-30) REVERT: G 21 MET cc_start: 0.9565 (pmm) cc_final: 0.9299 (pmm) REVERT: G 27 GLN cc_start: 0.9059 (tp40) cc_final: 0.8695 (tp-100) REVERT: G 32 TYR cc_start: 0.5898 (m-80) cc_final: 0.5606 (m-10) REVERT: H 27 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8507 (tp-100) REVERT: H 87 TYR cc_start: 0.8895 (m-80) cc_final: 0.8430 (m-80) REVERT: I 29 PHE cc_start: 0.7290 (t80) cc_final: 0.7050 (t80) REVERT: I 34 MET cc_start: 0.7111 (tpt) cc_final: 0.6804 (tpt) REVERT: I 86 ASP cc_start: 0.9158 (m-30) cc_final: 0.8818 (m-30) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2771 time to fit residues: 120.5789 Evaluate side-chains 230 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069731 restraints weight = 157284.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.073414 restraints weight = 80109.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.075928 restraints weight = 50253.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077678 restraints weight = 35872.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.078877 restraints weight = 27933.389| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15801 Z= 0.126 Angle : 0.512 7.947 21495 Z= 0.276 Chirality : 0.042 0.171 2526 Planarity : 0.003 0.035 2733 Dihedral : 4.317 16.227 2241 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2001 helix: 0.60 (0.26), residues: 462 sheet: -0.59 (0.23), residues: 513 loop : -1.63 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 27F TYR 0.011 0.001 TYR C 415 PHE 0.014 0.001 PHE F 29 TRP 0.012 0.001 TRP F 100 HIS 0.004 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (15780) covalent geometry : angle 0.51003 / 0.28 (21450) SS BOND : bond 0.00518 / 0.32 ( 18) SS BOND : angle 1.16376 / 0.74 ( 36) hydrogen bonds : bond 0.03391 / 2.26 ( 619) hydrogen bonds : angle 4.59834 / 3.22 ( 1617) link_NAG-ASN : bond 0.00304 / 0.15 ( 3) link_NAG-ASN : angle 0.87335 / 0.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.862 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: 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 437 ASN cc_start: 0.8088 (p0) cc_final: 0.7796 (p0) REVERT: B 92 MET cc_start: 0.9000 (tpp) cc_final: 0.8634 (tpp) REVERT: B 390 MET cc_start: 0.9266 (mmm) cc_final: 0.8770 (mmm) REVERT: C 92 MET cc_start: 0.8974 (tpp) cc_final: 0.8508 (tpp) REVERT: C 343 MET cc_start: 0.8047 (ttm) cc_final: 0.7244 (tpp) REVERT: D 67 VAL cc_start: 0.9310 (m) cc_final: 0.9023 (p) REVERT: D 86 ASP cc_start: 0.8935 (m-30) cc_final: 0.8618 (m-30) REVERT: E 21 MET cc_start: 0.9501 (pmm) cc_final: 0.9278 (pmm) REVERT: E 27 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8484 (tp-100) REVERT: E 37 GLN cc_start: 0.8675 (tt0) cc_final: 0.8167 (tt0) REVERT: E 52 SER cc_start: 0.8832 (m) cc_final: 0.8507 (p) REVERT: F 32 TYR cc_start: 0.8118 (m-80) cc_final: 0.7819 (m-80) REVERT: F 48 MET cc_start: 0.8680 (ptt) cc_final: 0.8336 (ptm) REVERT: F 69 MET cc_start: 0.9195 (ptp) cc_final: 0.8821 (ptp) REVERT: F 86 ASP cc_start: 0.9200 (m-30) cc_final: 0.8913 (m-30) REVERT: G 21 MET cc_start: 0.9561 (pmm) cc_final: 0.9317 (pmm) REVERT: G 27 GLN cc_start: 0.9086 (tp40) cc_final: 0.8714 (tp-100) REVERT: G 32 TYR cc_start: 0.5933 (m-80) cc_final: 0.5624 (m-10) REVERT: H 27 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8475 (tp-100) REVERT: H 87 TYR cc_start: 0.8925 (m-80) cc_final: 0.8450 (m-80) REVERT: I 34 MET cc_start: 0.7136 (tpt) cc_final: 0.6931 (tpt) REVERT: I 86 ASP cc_start: 0.9115 (m-30) cc_final: 0.8763 (m-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2644 time to fit residues: 111.6740 Evaluate side-chains 228 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 194 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 0.0270 chunk 81 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.071407 restraints weight = 157650.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.075126 restraints weight = 80536.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077660 restraints weight = 50622.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079431 restraints weight = 36170.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080642 restraints weight = 28173.825| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15801 Z= 0.095 Angle : 0.503 6.770 21495 Z= 0.269 Chirality : 0.042 0.159 2526 Planarity : 0.003 0.036 2733 Dihedral : 4.212 15.133 2241 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 2001 helix: 0.76 (0.26), residues: 462 sheet: -0.52 (0.23), residues: 513 loop : -1.56 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 57 TYR 0.019 0.001 TYR H 87 PHE 0.013 0.001 PHE F 29 TRP 0.013 0.001 TRP D 100 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (15780) covalent geometry : angle 0.50056 / 0.27 (21450) SS BOND : bond 0.00450 / 0.30 ( 18) SS BOND : angle 1.30762 / 0.73 ( 36) hydrogen bonds : bond 0.03190 / 2.13 ( 619) hydrogen bonds : angle 4.45657 / 3.13 ( 1617) link_NAG-ASN : bond 0.00292 / 0.15 ( 3) link_NAG-ASN : angle 0.78297 / 0.37 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.875 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: 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 343 MET cc_start: 0.8000 (ttm) cc_final: 0.7744 (ttm) REVERT: A 437 ASN cc_start: 0.8176 (p0) cc_final: 0.7911 (p0) REVERT: B 92 MET cc_start: 0.8984 (tpp) cc_final: 0.8451 (tpp) REVERT: B 142 MET cc_start: 0.8633 (mmp) cc_final: 0.8305 (mmp) REVERT: B 390 MET cc_start: 0.9196 (mmm) cc_final: 0.8701 (mmm) REVERT: B 421 LEU cc_start: 0.9050 (mp) cc_final: 0.8815 (mp) REVERT: C 92 MET cc_start: 0.8976 (tpp) cc_final: 0.8495 (tpp) REVERT: C 292 MET cc_start: 0.8669 (mtm) cc_final: 0.6922 (mtm) REVERT: D 67 VAL cc_start: 0.9311 (m) cc_final: 0.9003 (p) REVERT: D 86 ASP cc_start: 0.8996 (m-30) cc_final: 0.8696 (m-30) REVERT: E 27 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8624 (tp-100) REVERT: E 37 GLN cc_start: 0.8637 (tt0) cc_final: 0.8029 (tt0) REVERT: E 52 SER cc_start: 0.8720 (m) cc_final: 0.8388 (p) REVERT: F 32 TYR cc_start: 0.8240 (m-80) cc_final: 0.7973 (m-80) REVERT: F 48 MET cc_start: 0.8648 (ptt) cc_final: 0.8295 (ptm) REVERT: F 64 GLN cc_start: 0.9182 (tp40) cc_final: 0.8881 (tp-100) REVERT: F 69 MET cc_start: 0.9146 (ptp) cc_final: 0.8783 (ptp) REVERT: F 86 ASP cc_start: 0.9209 (m-30) cc_final: 0.8922 (m-30) REVERT: G 21 MET cc_start: 0.9559 (pmm) cc_final: 0.9292 (pmm) REVERT: G 27 GLN cc_start: 0.9042 (tp40) cc_final: 0.8686 (tp-100) REVERT: G 32 TYR cc_start: 0.5839 (m-80) cc_final: 0.5312 (m-10) REVERT: H 27 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8376 (tp-100) REVERT: I 29 PHE cc_start: 0.7320 (t80) cc_final: 0.7075 (t80) REVERT: I 34 MET cc_start: 0.7190 (tpt) cc_final: 0.6965 (tpt) REVERT: I 48 MET cc_start: 0.8895 (ptt) cc_final: 0.8606 (ptm) REVERT: I 86 ASP cc_start: 0.9175 (m-30) cc_final: 0.8840 (m-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2694 time to fit residues: 113.6651 Evaluate side-chains 229 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.089860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069699 restraints weight = 158013.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073345 restraints weight = 80527.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075862 restraints weight = 50670.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077585 restraints weight = 36180.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078775 restraints weight = 28202.813| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15801 Z= 0.129 Angle : 0.512 6.948 21495 Z= 0.275 Chirality : 0.041 0.158 2526 Planarity : 0.003 0.034 2733 Dihedral : 4.260 16.577 2241 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.18), residues: 2001 helix: 0.68 (0.26), residues: 462 sheet: -0.60 (0.23), residues: 513 loop : -1.62 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 27F TYR 0.016 0.001 TYR H 87 PHE 0.019 0.001 PHE F 29 TRP 0.017 0.001 TRP I 100 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15780) covalent geometry : angle 0.50998 / 0.27 (21450) SS BOND : bond 0.00448 / 0.28 ( 18) SS BOND : angle 1.06820 / 0.64 ( 36) hydrogen bonds : bond 0.03370 / 2.24 ( 619) hydrogen bonds : angle 4.57453 / 3.20 ( 1617) link_NAG-ASN : bond 0.00289 / 0.14 ( 3) link_NAG-ASN : angle 0.85157 / 0.40 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4002 Ramachandran restraints generated. 2001 Oldfield, 0 Emsley, 2001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.819 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: 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: B 92 MET cc_start: 0.9000 (tpp) cc_final: 0.8633 (tpp) REVERT: B 390 MET cc_start: 0.9155 (mmm) cc_final: 0.8638 (mmm) REVERT: B 421 LEU cc_start: 0.9117 (mp) cc_final: 0.8867 (mp) REVERT: C 92 MET cc_start: 0.8964 (tpp) cc_final: 0.8467 (tpp) REVERT: C 290 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 343 MET cc_start: 0.8008 (ttm) cc_final: 0.7235 (tpp) REVERT: D 67 VAL cc_start: 0.9293 (m) cc_final: 0.9008 (p) REVERT: D 69 MET cc_start: 0.8859 (ptt) cc_final: 0.8571 (ptt) REVERT: D 86 ASP cc_start: 0.8980 (m-30) cc_final: 0.8660 (m-30) REVERT: E 27 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8463 (tp-100) REVERT: E 37 GLN cc_start: 0.8672 (tt0) cc_final: 0.8194 (tt0) REVERT: E 52 SER cc_start: 0.8754 (m) cc_final: 0.8436 (p) REVERT: F 48 MET cc_start: 0.8733 (ptt) cc_final: 0.8413 (ptm) REVERT: F 69 MET cc_start: 0.9111 (ptp) cc_final: 0.8793 (ptp) REVERT: F 86 ASP cc_start: 0.9202 (m-30) cc_final: 0.8913 (m-30) REVERT: G 27 GLN cc_start: 0.9064 (tp40) cc_final: 0.8671 (tp-100) REVERT: G 32 TYR cc_start: 0.5950 (m-80) cc_final: 0.5621 (m-10) REVERT: H 27 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8466 (tp-100) REVERT: H 87 TYR cc_start: 0.9050 (m-80) cc_final: 0.8578 (m-80) REVERT: I 33 TYR cc_start: 0.7754 (m-80) cc_final: 0.7299 (m-10) REVERT: I 86 ASP cc_start: 0.9091 (m-30) cc_final: 0.8730 (m-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2612 time to fit residues: 107.2549 Evaluate side-chains 222 residues out of total 1731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 73 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068764 restraints weight = 159917.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072367 restraints weight = 82183.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074841 restraints weight = 51788.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.076570 restraints weight = 37147.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077754 restraints weight = 29053.333| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15801 Z= 0.158 Angle : 0.534 6.705 21495 Z= 0.292 Chirality : 0.042 0.155 2526 Planarity : 0.003 0.034 2733 Dihedral : 4.391 17.577 2241 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 2001 helix: 0.51 (0.25), residues: 462 sheet: -0.59 (0.23), residues: 543 loop : -1.66 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 27F TYR 0.013 0.002 TYR H 87 PHE 0.017 0.001 PHE F 29 TRP 0.013 0.001 TRP D 100 HIS 0.004 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (15780) covalent geometry : angle 0.53281 / 0.29 (21450) SS BOND : bond 0.00461 / 0.29 ( 18) SS BOND : angle 0.99450 / 0.61 ( 36) hydrogen bonds : bond 0.03552 / 2.34 ( 619) hydrogen bonds : angle 4.79717 / 3.35 ( 1617) link_NAG-ASN : bond 0.00331 / 0.17 ( 3) link_NAG-ASN : angle 0.87570 / 0.41 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.91 seconds wall clock time: 76 minutes 15.68 seconds (4575.68 seconds total)