Starting phenix.real_space_refine on Sat Oct 24 19:23:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29ye_57445/10_2026/29ye_57445.cif Found real_map, /net/cci-nas-00/data/ceres_data/29ye_57445/10_2026/29ye_57445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29ye_57445/10_2026/29ye_57445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29ye_57445/10_2026/29ye_57445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29ye_57445/10_2026/29ye_57445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29ye_57445/10_2026/29ye_57445.map" } resolution = 2.41 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= 0.006 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 Fe 10 7.16 5 S 80 5.16 5 C 9310 2.51 5 N 2220 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14106 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1353 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "B" Number of atoms: 3490 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 402} Conformer: "B" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 402} bond proxies already assigned to first conformer: 3585 Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1856 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 223} Chain breaks: 1 Chain: "E" Number of atoms: 3490 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 402} Conformer: "B" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 402} bond proxies already assigned to first conformer: 3585 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 272 Unusual residues: {'HEM': 2, 'LMT': 3, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 272 Unusual residues: {'HEM': 2, 'LMT': 3, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Restraints were copied for chains: D, F List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 921 SG CYS A 135 28.081 29.517 68.310 1.00103.63 S ATOM 1067 SG CYS A 155 27.305 33.169 68.694 1.00103.47 S ATOM 7620 SG CYS D 135 85.230 61.808 68.310 1.00103.53 S ATOM 7766 SG CYS D 155 86.006 58.156 68.695 1.00103.18 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS B 8 " occ=0.46 ... (18 atoms not shown) pdb=" NE2BHIS B 8 " occ=0.54 residue: pdb=" N AGLU B 295 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU B 295 " occ=0.50 residue: pdb=" N AHIS E 8 " occ=0.46 ... (18 atoms not shown) pdb=" NE2BHIS E 8 " occ=0.54 residue: pdb=" N AGLU E 295 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU E 295 " occ=0.49 Time building chain proxies: 4.71, per 1000 atoms: 0.33 Number of scatterers: 14106 At special positions: 0 Unit cell: (114.156, 92.1704, 107.391, 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) Fe 10 26.01 S 80 16.00 O 2486 8.00 N 2220 7.00 C 9310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 167 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 770.5 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 501 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 158 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 137 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 155 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 135 " pdb=" FES D 501 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 158 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 137 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 155 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 135 " Number of angles added : 6 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3112 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 56.9% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 37 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.584A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.554A pdb=" N SER A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 6.041A pdb=" N GLY A 93 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.527A pdb=" N ARG A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.616A pdb=" N LEU B 28 " --> pdb=" O PRO B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 66 removed outlier: 3.623A pdb=" N VAL B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 89 through 118 removed outlier: 3.682A pdb=" N ALA B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 147 Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.110A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 187 through 220 removed outlier: 3.508A pdb=" N SER B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Proline residue: B 202 - end of helix removed outlier: 3.600A pdb=" N PHE B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 244 through 270 removed outlier: 6.875A pdb=" N VAL B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.722A pdb=" N ARG B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 327 through 345 removed outlier: 3.641A pdb=" N VAL B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 356 through 359 removed outlier: 3.856A pdb=" N TYR B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 359' Processing helix chain 'B' and resid 360 through 381 removed outlier: 4.140A pdb=" N MET B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.728A pdb=" N LEU B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.811A pdb=" N GLY B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.758A pdb=" N HIS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 34 through 37 Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.533A pdb=" N GLY C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.556A pdb=" N ARG C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 removed outlier: 3.561A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 218 Processing helix chain 'C' and resid 220 through 255 removed outlier: 3.830A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Proline residue: C 252 - end of helix Processing helix chain 'D' and resid 14 through 37 Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 41 through 48 removed outlier: 3.584A pdb=" N ALA D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 removed outlier: 3.554A pdb=" N SER D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 6.042A pdb=" N GLY D 93 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.527A pdb=" N ARG D 115 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.615A pdb=" N LEU E 28 " --> pdb=" O PRO E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 46 through 66 removed outlier: 3.623A pdb=" N VAL E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 89 through 118 removed outlier: 3.682A pdb=" N ALA E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 108 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 147 Processing helix chain 'E' and resid 152 through 167 removed outlier: 4.110A pdb=" N PHE E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY E 167 " --> pdb=" O THR E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 187 through 220 removed outlier: 3.508A pdb=" N SER E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Proline residue: E 202 - end of helix removed outlier: 3.600A pdb=" N PHE E 216 " --> pdb=" O HIS E 212 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 244 through 270 removed outlier: 6.875A pdb=" N VAL E 249 " --> pdb=" O TRP E 245 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 295 through 297 No H-bonds generated for 'chain 'E' and resid 295 through 297' Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.722A pdb=" N ARG E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 327 through 345 removed outlier: 3.641A pdb=" N VAL E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 356 through 359 removed outlier: 3.856A pdb=" N TYR E 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 360 through 381 removed outlier: 4.140A pdb=" N MET E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP E 366 " --> pdb=" O LYS E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.728A pdb=" N LEU E 394 " --> pdb=" O ASP E 390 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE E 404 " --> pdb=" O TRP E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.811A pdb=" N GLY E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 433 removed outlier: 3.758A pdb=" N HIS E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 34 through 37 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.533A pdb=" N GLY F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 removed outlier: 3.573A pdb=" N ARG F 107 " --> pdb=" O MET F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 136 removed outlier: 3.561A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 218 Processing helix chain 'F' and resid 220 through 255 removed outlier: 3.830A pdb=" N LEU F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.673A pdb=" N THR A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 183 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 147 removed outlier: 4.460A pdb=" N ASP A 145 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY A 152 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 153 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 160 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS A 161 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 55 removed outlier: 6.673A pdb=" N THR D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 183 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 69 Processing sheet with id=AA9, first strand: chain 'D' and resid 143 through 147 removed outlier: 4.459A pdb=" N ASP D 145 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY D 152 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP D 153 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER D 160 " --> pdb=" O CYS D 155 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS D 161 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 36 through 38 Processing sheet with id=AB2, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 153 through 155 660 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6203 1.41 - 1.61: 8215 1.61 - 1.81: 121 1.81 - 2.01: 15 2.01 - 2.20: 32 Bond restraints: 14586 Sorted by residual: bond pdb=" C1 U10 E 506 " pdb=" C6 U10 E 506 " ideal model delta sigma weight residual 1.345 1.485 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C1 U10 B 505 " pdb=" C6 U10 B 505 " ideal model delta sigma weight residual 1.345 1.484 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C3 U10 E 506 " pdb=" C4 U10 E 506 " ideal model delta sigma weight residual 1.341 1.467 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C3 U10 B 505 " pdb=" C4 U10 B 505 " ideal model delta sigma weight residual 1.341 1.467 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" N SER B 2 " pdb=" CA SER B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 ... (remaining 14581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 19635 1.81 - 3.63: 234 3.63 - 5.44: 65 5.44 - 7.25: 16 7.25 - 9.06: 18 Bond angle restraints: 19968 Sorted by residual: angle pdb=" C32 U10 E 506 " pdb=" C33 U10 E 506 " pdb=" C34 U10 E 506 " ideal model delta sigma weight residual 128.34 119.28 9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" C32 U10 B 505 " pdb=" C33 U10 B 505 " pdb=" C34 U10 B 505 " ideal model delta sigma weight residual 128.34 119.28 9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" C37 U10 E 506 " pdb=" C38 U10 E 506 " pdb=" C39 U10 E 506 " ideal model delta sigma weight residual 128.42 119.38 9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" C37 U10 B 505 " pdb=" C38 U10 B 505 " pdb=" C39 U10 B 505 " ideal model delta sigma weight residual 128.42 119.39 9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" C47 U10 B 505 " pdb=" C48 U10 B 505 " pdb=" C49 U10 B 505 " ideal model delta sigma weight residual 128.73 119.76 8.97 3.00e+00 1.11e-01 8.94e+00 ... (remaining 19963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8088 17.52 - 35.05: 340 35.05 - 52.57: 109 52.57 - 70.10: 31 70.10 - 87.62: 12 Dihedral angle restraints: 8580 sinusoidal: 3690 harmonic: 4890 Sorted by residual: dihedral pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " pdb=" CAD HEC C 501 " pdb=" CBD HEC C 501 " ideal model delta sinusoidal sigma weight residual 0.00 87.62 -87.62 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2D HEC F 501 " pdb=" C3D HEC F 501 " pdb=" CAD HEC F 501 " pdb=" CBD HEC F 501 " ideal model delta sinusoidal sigma weight residual 0.00 87.58 -87.58 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM B 501 " pdb=" C2A HEM B 501 " pdb=" CAA HEM B 501 " pdb=" CBA HEM B 501 " ideal model delta sinusoidal sigma weight residual -0.00 -86.10 86.10 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 8577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1381 0.029 - 0.058: 466 0.058 - 0.087: 158 0.087 - 0.116: 84 0.116 - 0.145: 33 Chirality restraints: 2122 Sorted by residual: chirality pdb=" CA ILE B 35 " pdb=" N ILE B 35 " pdb=" C ILE B 35 " pdb=" CB ILE B 35 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE E 35 " pdb=" N ILE E 35 " pdb=" C ILE E 35 " pdb=" CB ILE E 35 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 169 " pdb=" N ILE B 169 " pdb=" C ILE B 169 " pdb=" CB ILE B 169 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2119 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 171 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO D 172 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 171 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 172 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 201 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO E 202 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 202 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 202 " -0.018 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3599 2.80 - 3.33: 12381 3.33 - 3.85: 21852 3.85 - 4.38: 27292 4.38 - 4.90: 45656 Nonbonded interactions: 110780 Sorted by model distance: nonbonded pdb=" NE2 HIS B 198 " pdb="FE HEM B 501 " model vdw 2.277 3.080 nonbonded pdb=" NE2 HIS E 198 " pdb="FE HEM E 502 " model vdw 2.277 3.080 nonbonded pdb=" NE2 HIS B 111 " pdb="FE HEM B 502 " model vdw 2.378 3.080 nonbonded pdb=" NE2 HIS E 111 " pdb="FE HEM E 503 " model vdw 2.378 3.080 nonbonded pdb=" SD MET F 183 " pdb="FE HEC F 501 " model vdw 2.419 3.360 ... (remaining 110775 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 2 through 7 or resid 9 through 294 or resid 296 through 43 \ 3 or resid 502 or resid 504)) selection = (chain 'E' and (resid 2 through 7 or resid 9 through 294 or resid 296 through 43 \ 3 or resid 502 or resid 504)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.410 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 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 : 0.005 0.182 14608 Z= 0.278 Angle : 0.614 9.064 19982 Z= 0.262 Chirality : 0.039 0.145 2122 Planarity : 0.004 0.037 2464 Dihedral : 12.054 87.622 5456 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.67 (0.20), residues: 1700 helix: -0.10 (0.17), residues: 846 sheet: -0.89 (0.59), residues: 86 loop : -0.65 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 94 TYR 0.010 0.001 TYR E 302 PHE 0.020 0.001 PHE B 104 TRP 0.018 0.001 TRP E 45 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (14586) covalent geometry : angle 0.60914 / 0.26 (19968) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 1.96814 / 1.31 ( 8) hydrogen bonds : bond 0.29322 / 19.90 ( 660) hydrogen bonds : angle 6.53561 / 4.92 ( 1878) metal coordination : bond 0.06927 / 3.17 ( 8) metal coordination : angle 3.97911 / 1.84 ( 6) Misc. bond : bond 0.13543 / 7.88 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.536 Fit side-chains REVERT: A 81 GLU cc_start: 0.8730 (tp30) cc_final: 0.7289 (tp30) REVERT: A 127 GLU cc_start: 0.8658 (pt0) cc_final: 0.8337 (pt0) REVERT: C 183 MET cc_start: 0.9237 (ttt) cc_final: 0.8820 (ttt) REVERT: D 81 GLU cc_start: 0.8731 (tp30) cc_final: 0.7281 (tp30) REVERT: D 127 GLU cc_start: 0.8667 (pt0) cc_final: 0.8345 (pt0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.7642 time to fit residues: 100.5102 Evaluate side-chains 104 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 226 GLN F 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.068836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.045356 restraints weight = 78232.949| |-----------------------------------------------------------------------------| r_work (start): 0.2461 rms_B_bonded: 3.89 r_work: 0.2298 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2306 r_free = 0.2306 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2306 r_free = 0.2306 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 14608 Z= 0.122 Angle : 0.577 12.297 19982 Z= 0.273 Chirality : 0.042 0.138 2122 Planarity : 0.005 0.038 2464 Dihedral : 10.933 85.450 2486 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 4.35 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.56 (0.21), residues: 1700 helix: 1.23 (0.18), residues: 868 sheet: -0.51 (0.60), residues: 86 loop : -0.47 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.007 0.001 TYR B 302 PHE 0.018 0.001 PHE B 104 TRP 0.014 0.001 TRP E 157 HIS 0.004 0.001 HIS E 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14586) covalent geometry : angle 0.57277 / 0.27 (19968) SS BOND : bond 0.01168 / 0.57 ( 4) SS BOND : angle 1.57243 / 1.01 ( 8) hydrogen bonds : bond 0.06900 / 4.72 ( 660) hydrogen bonds : angle 4.18484 / 3.07 ( 1878) metal coordination : bond 0.00434 / 0.23 ( 8) metal coordination : angle 3.52112 / 1.69 ( 6) Misc. bond : bond 0.05642 / 3.84 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.540 Fit side-chains REVERT: A 127 GLU cc_start: 0.8540 (pt0) cc_final: 0.8310 (pt0) REVERT: A 187 GLU cc_start: 0.8754 (tp30) cc_final: 0.8554 (tp30) REVERT: D 127 GLU cc_start: 0.8547 (pt0) cc_final: 0.8319 (pt0) REVERT: F 183 MET cc_start: 0.9151 (ttt) cc_final: 0.8210 (ttt) outliers start: 7 outliers final: 0 residues processed: 102 average time/residue: 0.7837 time to fit residues: 86.1043 Evaluate side-chains 98 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [126, 101, 148, 163, 92, 3, 7, 18, 154, 68, 72] chunk 126 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3015 r_free = 0.3015 target = 0.068895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.045469 restraints weight = 79765.310| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 3.85 r_work: 0.2331 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2359 r_free = 0.2359 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2359 r_free = 0.2359 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 14608 Z= 0.125 Angle : 0.576 14.116 19982 Z= 0.264 Chirality : 0.042 0.138 2122 Planarity : 0.005 0.038 2464 Dihedral : 10.495 85.741 2486 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.22 % Allowed : 5.29 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.07 (0.21), residues: 1700 helix: 1.71 (0.18), residues: 872 sheet: -0.34 (0.61), residues: 86 loop : -0.33 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.007 0.001 TYR B 302 PHE 0.017 0.001 PHE E 104 TRP 0.014 0.001 TRP E 157 HIS 0.003 0.000 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 (14586) covalent geometry : angle 0.57200 / 0.26 (19968) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 1.13215 / 0.80 ( 8) hydrogen bonds : bond 0.06318 / 4.31 ( 660) hydrogen bonds : angle 3.90473 / 2.87 ( 1878) metal coordination : bond 0.00483 / 0.26 ( 8) metal coordination : angle 3.76910 / 1.87 ( 6) Misc. bond : bond 0.06387 / 4.14 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.475 Fit side-chains REVERT: A 81 GLU cc_start: 0.7960 (pm20) cc_final: 0.7656 (pm20) REVERT: A 82 LYS cc_start: 0.9163 (tppp) cc_final: 0.8810 (mmmm) REVERT: A 85 GLU cc_start: 0.8556 (mp0) cc_final: 0.8353 (mm-30) REVERT: A 127 GLU cc_start: 0.8615 (pt0) cc_final: 0.8353 (pt0) REVERT: A 187 GLU cc_start: 0.8779 (tp30) cc_final: 0.8542 (tp30) REVERT: C 183 MET cc_start: 0.9228 (ttt) cc_final: 0.8098 (ttt) REVERT: D 81 GLU cc_start: 0.7960 (pm20) cc_final: 0.7659 (pm20) REVERT: D 82 LYS cc_start: 0.9157 (tppp) cc_final: 0.8806 (mmmm) REVERT: D 85 GLU cc_start: 0.8548 (mp0) cc_final: 0.8346 (mm-30) REVERT: D 127 GLU cc_start: 0.8621 (pt0) cc_final: 0.8363 (pt0) REVERT: F 183 MET cc_start: 0.9358 (ttt) cc_final: 0.8481 (ttt) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.7462 time to fit residues: 80.5211 Evaluate side-chains 98 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [65, 27, 29, 10, 134, 128, 76, 44, 67, 136, 34] chunk 65 optimal weight: 0.0980 chunk 27 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.072272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.049416 restraints weight = 72299.252| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.75 r_work: 0.2459 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2467 r_free = 0.2467 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14608 Z= 0.096 Angle : 0.508 9.452 19982 Z= 0.237 Chirality : 0.040 0.134 2122 Planarity : 0.004 0.040 2464 Dihedral : 9.975 82.586 2486 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.29 % Allowed : 5.80 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.31 (0.21), residues: 1700 helix: 1.96 (0.18), residues: 872 sheet: -0.02 (0.62), residues: 86 loop : -0.31 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 115 TYR 0.006 0.001 TYR E 297 PHE 0.016 0.001 PHE B 216 TRP 0.014 0.001 TRP B 157 HIS 0.002 0.000 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14586) covalent geometry : angle 0.50488 / 0.24 (19968) SS BOND : bond 0.00026 / 0.01 ( 4) SS BOND : angle 0.70999 / 0.52 ( 8) hydrogen bonds : bond 0.04512 / 3.09 ( 660) hydrogen bonds : angle 3.60126 / 2.64 ( 1878) metal coordination : bond 0.00210 / 0.12 ( 8) metal coordination : angle 3.40948 / 1.87 ( 6) Misc. bond : bond 0.04746 / 2.87 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.526 Fit side-chains REVERT: A 45 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8533 (mtpp) REVERT: A 81 GLU cc_start: 0.8075 (pm20) cc_final: 0.7757 (pm20) REVERT: A 82 LYS cc_start: 0.9159 (tppp) cc_final: 0.8841 (mmmm) REVERT: A 85 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8347 (mm-30) REVERT: A 127 GLU cc_start: 0.8608 (pt0) cc_final: 0.8373 (pt0) REVERT: A 187 GLU cc_start: 0.8775 (tp30) cc_final: 0.8520 (tp30) REVERT: D 45 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8540 (mtpp) REVERT: D 81 GLU cc_start: 0.8081 (pm20) cc_final: 0.7762 (pm20) REVERT: D 82 LYS cc_start: 0.9154 (tppp) cc_final: 0.8839 (mmmm) REVERT: D 85 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: D 127 GLU cc_start: 0.8616 (pt0) cc_final: 0.8382 (pt0) REVERT: F 183 MET cc_start: 0.9092 (ttt) cc_final: 0.8082 (ttt) outliers start: 4 outliers final: 0 residues processed: 104 average time/residue: 0.6987 time to fit residues: 78.7985 Evaluate side-chains 100 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain D residue 85 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [150, 122, 151, 30, 91, 18, 108, 157, 137, 63, 159] chunk 150 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.2987 r_free = 0.2987 target = 0.067239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.043609 restraints weight = 84809.361| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 3.94 r_work: 0.2289 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2322 r_free = 0.2322 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2322 r_free = 0.2322 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 14608 Z= 0.157 Angle : 0.603 14.826 19982 Z= 0.274 Chirality : 0.043 0.136 2122 Planarity : 0.005 0.037 2464 Dihedral : 10.301 88.644 2486 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.29 % Allowed : 6.16 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.22 (0.21), residues: 1700 helix: 1.88 (0.18), residues: 870 sheet: 0.32 (0.67), residues: 74 loop : -0.38 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.010 0.001 TYR E 302 PHE 0.017 0.001 PHE E 216 TRP 0.012 0.001 TRP B 157 HIS 0.004 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (14586) covalent geometry : angle 0.59850 / 0.27 (19968) SS BOND : bond 0.00085 / 0.04 ( 4) SS BOND : angle 1.18977 / 0.82 ( 8) hydrogen bonds : bond 0.06921 / 4.73 ( 660) hydrogen bonds : angle 3.88368 / 2.85 ( 1878) metal coordination : bond 0.00527 / 0.27 ( 8) metal coordination : angle 3.86579 / 2.08 ( 6) Misc. bond : bond 0.06453 / 4.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8196 (pm20) cc_final: 0.7974 (pm20) REVERT: A 82 LYS cc_start: 0.9166 (tppp) cc_final: 0.8858 (mmmm) REVERT: A 85 GLU cc_start: 0.8652 (mp0) cc_final: 0.8405 (mm-30) REVERT: A 127 GLU cc_start: 0.8616 (pt0) cc_final: 0.8368 (pt0) REVERT: A 187 GLU cc_start: 0.8895 (tp30) cc_final: 0.8629 (tp30) REVERT: B 94 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.7640 (ttt90) REVERT: D 81 GLU cc_start: 0.8202 (pm20) cc_final: 0.7982 (pm20) REVERT: D 82 LYS cc_start: 0.9162 (tppp) cc_final: 0.8855 (mmmm) REVERT: D 85 GLU cc_start: 0.8661 (mp0) cc_final: 0.8412 (mm-30) REVERT: D 127 GLU cc_start: 0.8615 (pt0) cc_final: 0.8368 (pt0) REVERT: E 94 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.7644 (ttt90) REVERT: F 183 MET cc_start: 0.9444 (ttt) cc_final: 0.8763 (ttt) outliers start: 4 outliers final: 0 residues processed: 102 average time/residue: 0.7992 time to fit residues: 87.5789 Evaluate side-chains 98 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain E residue 94 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [21, 11, 68, 29, 60, 103, 5, 70, 95, 131, 114] chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3001 r_free = 0.3001 target = 0.067983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.044290 restraints weight = 92415.564| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 4.08 r_work: 0.2298 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2334 r_free = 0.2334 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2334 r_free = 0.2334 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14608 Z= 0.134 Angle : 0.574 12.579 19982 Z= 0.263 Chirality : 0.042 0.133 2122 Planarity : 0.004 0.038 2464 Dihedral : 10.179 88.808 2486 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.29 % Allowed : 6.38 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.25 (0.21), residues: 1700 helix: 1.90 (0.18), residues: 872 sheet: 0.44 (0.67), residues: 74 loop : -0.39 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 355 TYR 0.008 0.001 TYR B 302 PHE 0.017 0.001 PHE E 216 TRP 0.013 0.001 TRP E 157 HIS 0.004 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.13 (14586) covalent geometry : angle 0.56995 / 0.26 (19968) SS BOND : bond 0.00067 / 0.03 ( 4) SS BOND : angle 1.08487 / 0.77 ( 8) hydrogen bonds : bond 0.06243 / 4.27 ( 660) hydrogen bonds : angle 3.78945 / 2.78 ( 1878) metal coordination : bond 0.00506 / 0.27 ( 8) metal coordination : angle 3.92689 / 2.10 ( 6) Misc. bond : bond 0.05602 / 3.58 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: A 127 GLU cc_start: 0.8617 (pt0) cc_final: 0.8383 (pt0) REVERT: A 187 GLU cc_start: 0.8930 (tp30) cc_final: 0.8667 (tp30) REVERT: B 94 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.7693 (ttt90) REVERT: D 85 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8440 (mm-30) REVERT: D 127 GLU cc_start: 0.8617 (pt0) cc_final: 0.8385 (pt0) REVERT: E 94 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.7695 (ttt90) outliers start: 4 outliers final: 0 residues processed: 98 average time/residue: 0.7848 time to fit residues: 82.7496 Evaluate side-chains 100 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 94 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [33, 78, 47, 91, 163, 49, 101, 87, 165, 36, 53] chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3033 r_free = 0.3033 target = 0.069695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.046433 restraints weight = 83456.248| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 3.92 r_work: 0.2382 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2359 r_free = 0.2359 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2359 r_free = 0.2359 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 14608 Z= 0.110 Angle : 0.540 10.235 19982 Z= 0.252 Chirality : 0.041 0.129 2122 Planarity : 0.004 0.038 2464 Dihedral : 9.969 88.063 2486 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.29 % Allowed : 6.88 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.38 (0.21), residues: 1700 helix: 2.01 (0.18), residues: 872 sheet: 0.53 (0.68), residues: 74 loop : -0.33 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 182 TYR 0.007 0.001 TYR E 297 PHE 0.017 0.001 PHE B 216 TRP 0.014 0.001 TRP E 157 HIS 0.003 0.000 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (14586) covalent geometry : angle 0.53605 / 0.25 (19968) SS BOND : bond 0.00046 / 0.02 ( 4) SS BOND : angle 0.85481 / 0.62 ( 8) hydrogen bonds : bond 0.05268 / 3.60 ( 660) hydrogen bonds : angle 3.63369 / 2.66 ( 1878) metal coordination : bond 0.00360 / 0.19 ( 8) metal coordination : angle 3.57842 / 1.89 ( 6) Misc. bond : bond 0.04658 / 2.61 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: A 127 GLU cc_start: 0.8605 (pt0) cc_final: 0.8388 (pt0) REVERT: A 187 GLU cc_start: 0.8922 (tp30) cc_final: 0.8664 (tp30) REVERT: B 94 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.7595 (ttt90) REVERT: C 239 SER cc_start: 0.8878 (m) cc_final: 0.8664 (m) REVERT: D 85 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (mm-30) REVERT: D 127 GLU cc_start: 0.8603 (pt0) cc_final: 0.8390 (pt0) REVERT: E 94 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7596 (ttt90) REVERT: F 239 SER cc_start: 0.8881 (m) cc_final: 0.8671 (m) outliers start: 4 outliers final: 0 residues processed: 102 average time/residue: 0.7707 time to fit residues: 84.8391 Evaluate side-chains 102 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 94 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [52, 47, 31, 61, 72, 33, 43, 167, 144, 73, 101] chunk 52 optimal weight: 0.0870 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.049546 restraints weight = 70766.821| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 3.73 r_work: 0.2464 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14608 Z= 0.096 Angle : 0.505 8.597 19982 Z= 0.236 Chirality : 0.040 0.129 2122 Planarity : 0.004 0.037 2464 Dihedral : 9.693 85.401 2486 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.43 % Allowed : 6.81 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.53 (0.21), residues: 1700 helix: 2.16 (0.18), residues: 872 sheet: 0.49 (0.65), residues: 86 loop : -0.29 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 115 TYR 0.006 0.001 TYR E 297 PHE 0.016 0.001 PHE B 216 TRP 0.014 0.001 TRP E 157 HIS 0.003 0.000 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (14586) covalent geometry : angle 0.50141 / 0.24 (19968) SS BOND : bond 0.00018 / 0.01 ( 4) SS BOND : angle 0.63678 / 0.46 ( 8) hydrogen bonds : bond 0.04264 / 2.91 ( 660) hydrogen bonds : angle 3.46334 / 2.54 ( 1878) metal coordination : bond 0.00181 / 0.10 ( 8) metal coordination : angle 3.42535 / 1.93 ( 6) Misc. bond : bond 0.04809 / 2.61 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8786 (ttt180) cc_final: 0.8368 (tpp80) REVERT: A 85 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8439 (mm-30) REVERT: A 127 GLU cc_start: 0.8574 (pt0) cc_final: 0.8263 (pt0) REVERT: A 187 GLU cc_start: 0.8926 (tp30) cc_final: 0.8660 (tp30) REVERT: B 94 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7487 (ttt90) REVERT: C 239 SER cc_start: 0.8899 (m) cc_final: 0.8698 (m) REVERT: D 78 ARG cc_start: 0.8782 (ttt180) cc_final: 0.8367 (tpp80) REVERT: D 85 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8458 (mm-30) REVERT: D 127 GLU cc_start: 0.8576 (pt0) cc_final: 0.8264 (pt0) REVERT: E 94 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7492 (ttt90) REVERT: F 239 SER cc_start: 0.8901 (m) cc_final: 0.8700 (m) outliers start: 6 outliers final: 0 residues processed: 106 average time/residue: 0.8272 time to fit residues: 94.1491 Evaluate side-chains 106 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 94 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [166, 107, 160, 91, 98, 151, 25, 126, 143, 136, 20] chunk 166 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 160 optimal weight: 0.1980 chunk 91 optimal weight: 0.0060 chunk 98 optimal weight: 10.0000 chunk 151 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 0.0870 chunk 143 optimal weight: 0.1980 chunk 136 optimal weight: 0.0070 chunk 20 optimal weight: 2.9990 overall best weight: 0.0992 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.077462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.055648 restraints weight = 60974.804| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.53 r_work: 0.2615 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14608 Z= 0.092 Angle : 0.480 8.614 19982 Z= 0.226 Chirality : 0.039 0.130 2122 Planarity : 0.004 0.038 2464 Dihedral : 9.290 82.911 2486 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.43 % Allowed : 7.46 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.82 (0.22), residues: 1700 helix: 2.30 (0.18), residues: 874 sheet: 0.69 (0.66), residues: 86 loop : -0.02 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 88 TYR 0.005 0.000 TYR B 109 PHE 0.017 0.001 PHE B 216 TRP 0.014 0.001 TRP E 157 HIS 0.002 0.000 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.09 (14586) covalent geometry : angle 0.47546 / 0.23 (19968) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.52775 / 0.37 ( 8) hydrogen bonds : bond 0.03130 / 2.14 ( 660) hydrogen bonds : angle 3.28983 / 2.42 ( 1878) metal coordination : bond 0.00136 / 0.07 ( 8) metal coordination : angle 3.73829 / 2.09 ( 6) Misc. bond : bond 0.04761 / 2.79 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.537 Fit side-chains REVERT: A 45 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8504 (mtpp) REVERT: A 78 ARG cc_start: 0.8775 (ttt180) cc_final: 0.8369 (tpp80) REVERT: A 85 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8471 (mm-30) REVERT: A 127 GLU cc_start: 0.8679 (pt0) cc_final: 0.8417 (pt0) REVERT: A 187 GLU cc_start: 0.8918 (tp30) cc_final: 0.8690 (tp30) REVERT: C 183 MET cc_start: 0.8659 (ttt) cc_final: 0.8026 (ttt) REVERT: C 227 MET cc_start: 0.8879 (tmt) cc_final: 0.8583 (pp-130) REVERT: C 239 SER cc_start: 0.8882 (m) cc_final: 0.8676 (m) REVERT: D 45 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8502 (mtpp) REVERT: D 78 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8373 (tpp80) REVERT: D 85 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (mm-30) REVERT: D 127 GLU cc_start: 0.8676 (pt0) cc_final: 0.8412 (pt0) REVERT: F 183 MET cc_start: 0.8647 (ttt) cc_final: 0.8281 (ttt) REVERT: F 227 MET cc_start: 0.8880 (tmt) cc_final: 0.8592 (pp-130) REVERT: F 239 SER cc_start: 0.8883 (m) cc_final: 0.8678 (m) outliers start: 6 outliers final: 0 residues processed: 112 average time/residue: 0.7729 time to fit residues: 93.5068 Evaluate side-chains 105 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain D residue 85 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [26, 32, 109, 153, 119, 78, 97, 108, 93, 116, 14] chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 78 optimal weight: 0.0970 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.074452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.051772 restraints weight = 80704.437| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 3.91 r_work: 0.2497 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14608 Z= 0.093 Angle : 0.504 10.480 19982 Z= 0.232 Chirality : 0.039 0.129 2122 Planarity : 0.004 0.039 2464 Dihedral : 9.317 85.048 2486 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.88 (0.22), residues: 1700 helix: 2.43 (0.18), residues: 860 sheet: 1.04 (0.72), residues: 74 loop : -0.09 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 88 TYR 0.008 0.001 TYR E 297 PHE 0.017 0.001 PHE E 216 TRP 0.015 0.001 TRP E 157 HIS 0.002 0.000 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.09 (14586) covalent geometry : angle 0.50095 / 0.23 (19968) SS BOND : bond 0.00035 / 0.02 ( 4) SS BOND : angle 0.67887 / 0.51 ( 8) hydrogen bonds : bond 0.03977 / 2.71 ( 660) hydrogen bonds : angle 3.32653 / 2.45 ( 1878) metal coordination : bond 0.00182 / 0.11 ( 8) metal coordination : angle 3.23302 / 1.74 ( 6) Misc. bond : bond 0.04466 / 2.43 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8454 (mtpp) REVERT: A 78 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8345 (tpp80) REVERT: A 85 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: A 127 GLU cc_start: 0.8679 (pt0) cc_final: 0.8428 (pt0) REVERT: A 187 GLU cc_start: 0.8970 (tp30) cc_final: 0.8741 (tp30) REVERT: C 227 MET cc_start: 0.8911 (tmt) cc_final: 0.8610 (pp-130) REVERT: D 45 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8466 (mtpp) REVERT: D 78 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8346 (tpp80) REVERT: D 85 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: D 127 GLU cc_start: 0.8680 (pt0) cc_final: 0.8430 (pt0) REVERT: F 183 MET cc_start: 0.8914 (ttt) cc_final: 0.8015 (ttt) REVERT: F 227 MET cc_start: 0.8918 (tmt) cc_final: 0.8617 (pp-130) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.7403 time to fit residues: 83.3955 Evaluate side-chains 106 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain D residue 85 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [120, 125, 22, 106, 103, 139, 43, 124, 119, 29, 23] chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3037 r_free = 0.3037 target = 0.070013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.046645 restraints weight = 78151.019| |-----------------------------------------------------------------------------| r_work (start): 0.2514 rms_B_bonded: 3.86 r_work: 0.2360 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2387 r_free = 0.2387 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14608 Z= 0.118 Angle : 0.563 12.925 19982 Z= 0.257 Chirality : 0.041 0.130 2122 Planarity : 0.004 0.037 2464 Dihedral : 9.639 86.883 2486 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.14 % Allowed : 8.26 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.69 (0.21), residues: 1700 helix: 2.27 (0.18), residues: 870 sheet: 0.97 (0.71), residues: 74 loop : -0.21 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 88 TYR 0.008 0.001 TYR E 297 PHE 0.017 0.001 PHE E 216 TRP 0.012 0.001 TRP B 157 HIS 0.003 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (14586) covalent geometry : angle 0.55983 / 0.26 (19968) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.86359 / 0.62 ( 8) hydrogen bonds : bond 0.05457 / 3.74 ( 660) hydrogen bonds : angle 3.57757 / 2.63 ( 1878) metal coordination : bond 0.00347 / 0.19 ( 8) metal coordination : angle 3.53227 / 1.88 ( 6) Misc. bond : bond 0.05230 / 3.03 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.25 seconds wall clock time: 88 minutes 18.01 seconds (5298.01 seconds total)