Starting phenix.real_space_refine on Sat Oct 24 18:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29yb_57442/10_2026/29yb_57442.cif Found real_map, /net/cci-nas-00/data/ceres_data/29yb_57442/10_2026/29yb_57442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29yb_57442/10_2026/29yb_57442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29yb_57442/10_2026/29yb_57442.map" model { file = "/net/cci-nas-00/data/ceres_data/29yb_57442/10_2026/29yb_57442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29yb_57442/10_2026/29yb_57442.cif" } resolution = 2.74 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= 0.007 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 9196 2.51 5 N 2222 2.21 5 O 2480 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: 13988 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1343 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "B" Number of atoms: 3516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 436, 3500 Classifications: {'peptide': 436} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 405} Conformer: "B" Number of residues, atoms: 436, 3500 Classifications: {'peptide': 436} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 405} bond proxies already assigned to first conformer: 3618 Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1848 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FES': 1, 'UMQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 206 Unusual residues: {'HEM': 2, 'UMQ': 3, 'UQ1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, E, F List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 911 SG CYS A 133 85.345 61.609 68.228 1.00106.79 S ATOM 1057 SG CYS A 153 86.079 58.065 68.480 1.00113.67 S ATOM 7618 SG CYS D 133 28.083 29.535 68.410 1.00111.99 S ATOM 7764 SG CYS D 153 27.326 33.075 68.657 1.00113.20 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS B 8 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS B 8 " occ=0.47 residue: pdb=" N AHIS E 8 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS E 8 " occ=0.47 Time building chain proxies: 4.72, per 1000 atoms: 0.34 Number of scatterers: 13988 At special positions: 0 Unit cell: (114.156, 92.1704, 108.237, 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 2480 8.00 N 2222 7.00 C 9196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 155 " 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: 1.28 Conformation dependent library (CDL) restraints added in 764.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 501 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 135 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 156 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 133 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 153 " pdb=" FES D 501 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 135 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 156 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 133 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 153 " Number of angles added : 6 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3116 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 56.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.552A pdb=" N ALA A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.603A pdb=" N GLU A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.513A pdb=" N ARG A 113 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 114 " --> pdb=" O GLU A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 114' Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.787A pdb=" N LYS B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.589A 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: 3.719A 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: 3.989A pdb=" N ALA B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 147 removed outlier: 3.554A pdb=" N TRP B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.740A pdb=" N ILE B 169 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 187 through 220 Proline residue: B 202 - end of helix removed outlier: 3.562A pdb=" N THR B 218 " --> pdb=" O TRP B 214 " (cutoff:3.500A) removed outlier: 3.922A 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 246 through 270 removed outlier: 3.910A pdb=" N LYS B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.539A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 4.008A 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: 3.839A pdb=" N GLY B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 356 through 359 removed outlier: 3.906A 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: 4.362A pdb=" N MET B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.640A pdb=" N LEU B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.874A pdb=" N GLY B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.715A 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: 3.523A pdb=" N ALA C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.518A pdb=" N ARG C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 removed outlier: 3.528A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 201 through 218 Processing helix chain 'C' and resid 220 through 250 removed outlier: 3.549A pdb=" N ARG C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'D' and resid 14 through 37 removed outlier: 3.552A pdb=" N ALA D 18 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 78 through 88 removed outlier: 3.603A pdb=" N GLU D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.513A pdb=" N ARG D 113 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 114' Processing helix chain 'E' and resid 13 through 21 removed outlier: 3.787A pdb=" N LYS E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.589A 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: 3.719A 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: 3.989A pdb=" N ALA E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 147 removed outlier: 3.554A pdb=" N TRP E 129 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.740A pdb=" N ILE E 169 " --> pdb=" O PHE E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 182 Processing helix chain 'E' and resid 187 through 220 Proline residue: E 202 - end of helix removed outlier: 3.562A pdb=" N THR E 218 " --> pdb=" O TRP E 214 " (cutoff:3.500A) removed outlier: 3.923A 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 246 through 270 removed outlier: 3.910A pdb=" N LYS E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 266 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.538A pdb=" N ILE E 304 " --> pdb=" O PRO E 300 " (cutoff:3.500A) removed outlier: 4.008A 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: 3.839A pdb=" N GLY E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 356 through 359 removed outlier: 3.907A 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: 4.362A pdb=" N MET E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP E 366 " --> pdb=" O LYS E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 removed outlier: 3.640A pdb=" N LEU E 394 " --> pdb=" O ASP E 390 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE E 404 " --> pdb=" O TRP E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.874A pdb=" N GLY E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 433 removed outlier: 3.716A 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: 3.523A pdb=" N ALA F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 removed outlier: 3.518A pdb=" N ARG F 107 " --> pdb=" O MET F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 136 removed outlier: 3.528A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 201 through 218 Processing helix chain 'F' and resid 220 through 250 removed outlier: 3.549A pdb=" N ARG F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.692A pdb=" N ALA A 181 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145 removed outlier: 4.502A pdb=" N ASP A 143 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY A 150 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 158 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS A 159 " --> pdb=" O ARG A 167 " (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 50 through 53 removed outlier: 3.692A pdb=" N ALA D 181 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 66 Processing sheet with id=AA9, first strand: chain 'D' and resid 141 through 145 removed outlier: 4.502A pdb=" N ASP D 143 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY D 150 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 158 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS D 159 " --> pdb=" O ARG D 167 " (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 155 652 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.69 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: 6123 1.41 - 1.60: 8179 1.60 - 1.80: 123 1.80 - 2.00: 13 2.00 - 2.20: 32 Bond restraints: 14470 Sorted by residual: bond pdb=" C GLU E 295 " pdb=" CA BGLU E 295 " ideal model delta sigma weight residual 1.527 1.599 -0.073 1.34e-02 5.57e+03 2.95e+01 bond pdb=" C GLU B 295 " pdb=" CA BGLU B 295 " ideal model delta sigma weight residual 1.527 1.599 -0.072 1.34e-02 5.57e+03 2.89e+01 bond pdb=" N SER E 2 " pdb=" CA SER E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N SER B 2 " pdb=" CA SER B 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" CG ASP D 184 " pdb=" OD1 ASP D 184 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.17e+00 ... (remaining 14465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 19261 1.28 - 2.55: 408 2.55 - 3.83: 145 3.83 - 5.11: 10 5.11 - 6.38: 4 Bond angle restraints: 19828 Sorted by residual: angle pdb=" N GLU B 295 " pdb=" CA BGLU B 295 " pdb=" C GLU B 295 " ideal model delta sigma weight residual 110.43 106.37 4.06 1.31e+00 5.83e-01 9.59e+00 angle pdb=" N GLU E 295 " pdb=" CA BGLU E 295 " pdb=" C GLU E 295 " ideal model delta sigma weight residual 110.43 106.38 4.05 1.31e+00 5.83e-01 9.53e+00 angle pdb=" N GLU E 295 " pdb=" CA BGLU E 295 " pdb=" CB BGLU E 295 " ideal model delta sigma weight residual 110.26 114.25 -3.99 1.43e+00 4.89e-01 7.77e+00 angle pdb=" N GLU B 295 " pdb=" CA BGLU B 295 " pdb=" CB BGLU B 295 " ideal model delta sigma weight residual 110.26 114.21 -3.95 1.43e+00 4.89e-01 7.63e+00 angle pdb=" C THR D 123 " pdb=" N GLY D 124 " pdb=" CA GLY D 124 " ideal model delta sigma weight residual 121.41 125.78 -4.37 1.96e+00 2.60e-01 4.96e+00 ... (remaining 19823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 7987 15.69 - 31.37: 363 31.37 - 47.06: 104 47.06 - 62.75: 28 62.75 - 78.43: 22 Dihedral angle restraints: 8504 sinusoidal: 3608 harmonic: 4896 Sorted by residual: dihedral pdb=" CA LEU E 200 " pdb=" C LEU E 200 " pdb=" N LEU E 201 " pdb=" CA LEU E 201 " ideal model delta harmonic sigma weight residual 180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LEU B 200 " pdb=" C LEU B 200 " pdb=" N LEU B 201 " pdb=" CA LEU B 201 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C2D HEM E 502 " pdb=" C3D HEM E 502 " pdb=" CAD HEM E 502 " pdb=" CBD HEM E 502 " ideal model delta sinusoidal sigma weight residual -180.00 -103.46 -76.54 2 2.00e+01 2.50e-03 1.14e+01 ... (remaining 8501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1222 0.027 - 0.054: 562 0.054 - 0.081: 205 0.081 - 0.108: 86 0.108 - 0.135: 49 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE A 50 " pdb=" N ILE A 50 " pdb=" C ILE A 50 " pdb=" CB ILE A 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-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 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 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 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 2121 not shown) Planarity restraints: 2446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 16 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C TYR A 16 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR A 16 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS A 17 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 16 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C TYR D 16 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR D 16 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS D 17 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 201 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 202 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 202 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 202 " 0.023 5.00e-02 4.00e+02 ... (remaining 2443 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2563 2.77 - 3.30: 13258 3.30 - 3.83: 22489 3.83 - 4.37: 27219 4.37 - 4.90: 46779 Nonbonded interactions: 112308 Sorted by model distance: nonbonded pdb=" NE2 HIS F 38 " pdb="FE HEC F 501 " model vdw 2.233 3.080 nonbonded pdb=" NE2 HIS C 38 " pdb="FE HEC C 501 " model vdw 2.233 3.080 nonbonded pdb=" NE2 HIS E 97 " pdb="FE HEM E 501 " model vdw 2.238 3.080 nonbonded pdb=" NE2 HIS B 97 " pdb="FE HEM B 501 " model vdw 2.238 3.080 nonbonded pdb=" O ASN D 122 " pdb=" OG1 THR D 123 " model vdw 2.327 3.040 ... (remaining 112303 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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=0.47 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: 3.340 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.660 Find NCS groups from input model: 0.110 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 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 0.153 14492 Z= 0.285 Angle : 0.566 16.737 19842 Z= 0.269 Chirality : 0.040 0.135 2124 Planarity : 0.004 0.041 2446 Dihedral : 11.192 78.433 5376 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.29 (0.21), residues: 1698 helix: 1.53 (0.19), residues: 814 sheet: -2.46 (0.52), residues: 86 loop : -0.91 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 224 TYR 0.011 0.001 TYR B 399 PHE 0.021 0.001 PHE E 216 TRP 0.011 0.001 TRP E 157 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (14470) covalent geometry : angle 0.52098 / 0.27 (19828) SS BOND : bond 0.00271 / 0.14 ( 4) SS BOND : angle 0.54880 / 0.31 ( 8) hydrogen bonds : bond 0.17684 / 11.58 ( 652) hydrogen bonds : angle 5.46965 / 3.81 ( 1842) metal coordination : bond 0.01592 / 0.89 ( 8) metal coordination : angle 12.72270 / 7.82 ( 6) Misc. bond : bond 0.12984 / 7.60 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.8965 (mmp) cc_final: 0.8631 (mmp) REVERT: B 234 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8666 (ttmt) REVERT: B 362 LYS cc_start: 0.8752 (mttm) cc_final: 0.8524 (mmmt) REVERT: B 410 LEU cc_start: 0.8762 (tt) cc_final: 0.8448 (mp) REVERT: C 10 SER cc_start: 0.9301 (p) cc_final: 0.9044 (t) REVERT: C 74 LYS cc_start: 0.8946 (mtpm) cc_final: 0.8460 (mmtm) REVERT: C 257 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7657 (ttmt) REVERT: D 159 HIS cc_start: 0.8019 (m90) cc_final: 0.7789 (m90) REVERT: D 177 ILE cc_start: 0.9407 (mt) cc_final: 0.9129 (mp) REVERT: E 154 MET cc_start: 0.8996 (mmp) cc_final: 0.8690 (mmp) REVERT: E 234 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8693 (ttmt) REVERT: E 353 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8637 (mptt) REVERT: E 362 LYS cc_start: 0.8764 (mttm) cc_final: 0.8532 (mmmt) REVERT: E 410 LEU cc_start: 0.8752 (tt) cc_final: 0.8448 (mp) REVERT: F 74 LYS cc_start: 0.8937 (mtpm) cc_final: 0.8447 (mmtm) REVERT: F 257 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7572 (ttmt) outliers start: 9 outliers final: 7 residues processed: 200 average time/residue: 0.5643 time to fit residues: 124.0856 Evaluate side-chains 142 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.0070 chunk 149 optimal weight: 2.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 HIS A B 429 ASN C 141 ASN E 8 HIS A E 429 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.063210 restraints weight = 73279.326| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.85 r_work: 0.2606 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.374 14492 Z= 0.119 Angle : 0.647 13.447 19842 Z= 0.284 Chirality : 0.042 0.158 2124 Planarity : 0.005 0.046 2446 Dihedral : 8.865 76.124 2404 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.23 % Allowed : 8.82 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1698 helix: 1.69 (0.18), residues: 838 sheet: -2.20 (0.49), residues: 86 loop : -0.78 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.007 0.001 TYR B 399 PHE 0.018 0.001 PHE E 216 TRP 0.013 0.001 TRP E 157 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14470) covalent geometry : angle 0.62571 / 0.28 (19828) SS BOND : bond 0.00454 / 0.22 ( 4) SS BOND : angle 0.87608 / 0.44 ( 8) hydrogen bonds : bond 0.05430 / 3.57 ( 652) hydrogen bonds : angle 4.16481 / 2.94 ( 1842) metal coordination : bond 0.00843 / 0.42 ( 8) metal coordination : angle 9.43247 / 5.55 ( 6) Misc. bond : bond 0.17933 / 12.60 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 LEU cc_start: 0.8983 (tt) cc_final: 0.8673 (mp) REVERT: C 10 SER cc_start: 0.9251 (p) cc_final: 0.9007 (t) REVERT: C 74 LYS cc_start: 0.9074 (mtpm) cc_final: 0.8506 (mmtm) REVERT: C 257 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7490 (ttmt) REVERT: D 68 ARG cc_start: 0.8410 (mpt-90) cc_final: 0.7862 (mpp80) REVERT: D 76 ARG cc_start: 0.5846 (mtt180) cc_final: 0.5466 (mtp85) REVERT: D 159 HIS cc_start: 0.7970 (m90) cc_final: 0.7550 (m90) REVERT: E 410 LEU cc_start: 0.8988 (tt) cc_final: 0.8680 (mp) REVERT: F 74 LYS cc_start: 0.9047 (mtpm) cc_final: 0.8490 (mmtm) REVERT: F 183 MET cc_start: 0.9196 (ttt) cc_final: 0.8909 (ttt) REVERT: F 257 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7449 (ttmt) outliers start: 15 outliers final: 5 residues processed: 151 average time/residue: 0.6149 time to fit residues: 101.2391 Evaluate side-chains 125 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain F residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [145, 30, 38, 93, 44, 92, 164, 149, 59, 103, 62] chunk 145 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 103 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN E 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.064705 restraints weight = 50610.425| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.27 r_work: 0.2647 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 14492 Z= 0.109 Angle : 0.589 11.541 19842 Z= 0.261 Chirality : 0.041 0.139 2124 Planarity : 0.005 0.039 2446 Dihedral : 8.570 77.968 2400 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.30 % Allowed : 9.75 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.75 (0.21), residues: 1698 helix: 1.83 (0.18), residues: 838 sheet: -1.91 (0.47), residues: 86 loop : -0.70 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 113 TYR 0.009 0.001 TYR B 399 PHE 0.019 0.001 PHE E 216 TRP 0.011 0.001 TRP E 157 HIS 0.003 0.001 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14470) covalent geometry : angle 0.56942 / 0.26 (19828) SS BOND : bond 0.00216 / 0.11 ( 4) SS BOND : angle 0.66794 / 0.33 ( 8) hydrogen bonds : bond 0.04752 / 3.15 ( 652) hydrogen bonds : angle 3.89277 / 2.74 ( 1842) metal coordination : bond 0.00778 / 0.38 ( 8) metal coordination : angle 8.69860 / 4.78 ( 6) Misc. bond : bond 0.14722 / 10.42 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8280 (mpp80) cc_final: 0.7938 (mpp80) REVERT: B 410 LEU cc_start: 0.8969 (tt) cc_final: 0.8710 (mm) REVERT: C 10 SER cc_start: 0.9239 (p) cc_final: 0.9013 (t) REVERT: C 74 LYS cc_start: 0.9081 (mtpm) cc_final: 0.8501 (mmtm) REVERT: C 183 MET cc_start: 0.9201 (ttt) cc_final: 0.8899 (ttt) REVERT: C 257 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7451 (ttmt) REVERT: D 76 ARG cc_start: 0.5905 (mtt180) cc_final: 0.5551 (mtp85) REVERT: D 83 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8643 (mt-10) REVERT: D 111 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8254 (tm-30) REVERT: D 141 MET cc_start: 0.8629 (ptm) cc_final: 0.8074 (ppp) REVERT: D 159 HIS cc_start: 0.7895 (m90) cc_final: 0.7524 (m90) REVERT: E 410 LEU cc_start: 0.8974 (tt) cc_final: 0.8725 (mm) REVERT: F 74 LYS cc_start: 0.9036 (mtpm) cc_final: 0.8486 (mmtm) REVERT: F 183 MET cc_start: 0.9187 (ttt) cc_final: 0.8914 (ttt) REVERT: F 257 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7461 (ttmt) outliers start: 16 outliers final: 9 residues processed: 138 average time/residue: 0.5974 time to fit residues: 90.4039 Evaluate side-chains 126 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [99, 125, 104, 113, 62, 164, 36, 110, 13, 101, 91] chunk 99 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 164 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN E 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.065521 restraints weight = 56022.414| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.40 r_work: 0.2666 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.287 14492 Z= 0.100 Angle : 0.554 9.539 19842 Z= 0.248 Chirality : 0.040 0.140 2124 Planarity : 0.004 0.038 2446 Dihedral : 8.381 78.417 2400 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.52 % Allowed : 10.55 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.91 (0.21), residues: 1698 helix: 1.95 (0.18), residues: 840 sheet: -1.71 (0.49), residues: 86 loop : -0.62 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 113 TYR 0.008 0.001 TYR B 399 PHE 0.016 0.001 PHE E 216 TRP 0.012 0.001 TRP B 157 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14470) covalent geometry : angle 0.53787 / 0.25 (19828) SS BOND : bond 0.00160 / 0.08 ( 4) SS BOND : angle 0.50064 / 0.29 ( 8) hydrogen bonds : bond 0.04141 / 2.75 ( 652) hydrogen bonds : angle 3.71816 / 2.61 ( 1842) metal coordination : bond 0.00568 / 0.28 ( 8) metal coordination : angle 7.61748 / 4.27 ( 6) Misc. bond : bond 0.14242 / 9.81 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 LEU cc_start: 0.8943 (tt) cc_final: 0.8729 (mm) REVERT: C 10 SER cc_start: 0.9238 (p) cc_final: 0.9016 (t) REVERT: C 74 LYS cc_start: 0.9097 (mtpm) cc_final: 0.8510 (mmtm) REVERT: C 183 MET cc_start: 0.9217 (ttt) cc_final: 0.8921 (ttt) REVERT: C 257 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7453 (ttmt) REVERT: D 76 ARG cc_start: 0.5931 (mtt180) cc_final: 0.5681 (mtp85) REVERT: D 111 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8204 (tm-30) REVERT: D 159 HIS cc_start: 0.7899 (m90) cc_final: 0.7441 (m90) REVERT: E 410 LEU cc_start: 0.8946 (tt) cc_final: 0.8741 (mm) REVERT: F 74 LYS cc_start: 0.9062 (mtpm) cc_final: 0.8506 (mmtm) REVERT: F 183 MET cc_start: 0.9169 (ttt) cc_final: 0.8860 (ttt) REVERT: F 257 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7438 (ttmt) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 0.6015 time to fit residues: 90.1597 Evaluate side-chains 127 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [15, 118, 66, 83, 74, 125, 140, 122, 4, 24, 103] chunk 15 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 122 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN E 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.063573 restraints weight = 59175.242| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.46 r_work: 0.2621 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.345 14492 Z= 0.125 Angle : 0.589 11.693 19842 Z= 0.262 Chirality : 0.041 0.132 2124 Planarity : 0.005 0.047 2446 Dihedral : 8.394 79.314 2398 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.59 % Allowed : 10.12 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 (0.21), residues: 1698 helix: 1.91 (0.18), residues: 836 sheet: -1.55 (0.50), residues: 86 loop : -0.64 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 68 TYR 0.011 0.001 TYR B 399 PHE 0.020 0.001 PHE E 216 TRP 0.048 0.001 TRP D 67 HIS 0.005 0.001 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.12 (14470) covalent geometry : angle 0.57527 / 0.26 (19828) SS BOND : bond 0.00217 / 0.11 ( 4) SS BOND : angle 0.38251 / 0.21 ( 8) hydrogen bonds : bond 0.04884 / 3.26 ( 652) hydrogen bonds : angle 3.75131 / 2.63 ( 1842) metal coordination : bond 0.00728 / 0.37 ( 8) metal coordination : angle 7.25305 / 3.92 ( 6) Misc. bond : bond 0.16377 / 11.64 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 SER cc_start: 0.9205 (p) cc_final: 0.8998 (t) REVERT: C 74 LYS cc_start: 0.9136 (mtpm) cc_final: 0.8568 (mmtm) REVERT: C 257 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7409 (ttmt) REVERT: D 76 ARG cc_start: 0.5950 (mtt180) cc_final: 0.5573 (mtp85) REVERT: D 159 HIS cc_start: 0.7884 (m90) cc_final: 0.7359 (m90) REVERT: F 74 LYS cc_start: 0.9082 (mtpm) cc_final: 0.8502 (mmtm) REVERT: F 257 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7382 (ttmt) outliers start: 20 outliers final: 10 residues processed: 134 average time/residue: 0.6047 time to fit residues: 88.5362 Evaluate side-chains 122 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 14 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [105, 147, 64, 106, 79, 124, 2, 129, 22, 65, 152] chunk 105 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN E 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.064277 restraints weight = 69514.184| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.75 r_work: 0.2631 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 14492 Z= 0.104 Angle : 0.559 10.370 19842 Z= 0.249 Chirality : 0.040 0.135 2124 Planarity : 0.004 0.037 2446 Dihedral : 8.279 79.800 2398 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.88 % Allowed : 10.33 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1698 helix: 1.97 (0.18), residues: 836 sheet: -1.37 (0.52), residues: 86 loop : -0.65 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 113 TYR 0.009 0.001 TYR B 399 PHE 0.017 0.001 PHE B 216 TRP 0.011 0.001 TRP B 157 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.10 (14470) covalent geometry : angle 0.54756 / 0.25 (19828) SS BOND : bond 0.00179 / 0.09 ( 4) SS BOND : angle 0.30837 / 0.17 ( 8) hydrogen bonds : bond 0.04344 / 2.89 ( 652) hydrogen bonds : angle 3.67688 / 2.58 ( 1842) metal coordination : bond 0.00574 / 0.29 ( 8) metal coordination : angle 6.52695 / 3.55 ( 6) Misc. bond : bond 0.12547 / 8.52 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8473 (mppt) REVERT: A 125 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: C 10 SER cc_start: 0.9208 (p) cc_final: 0.9003 (t) REVERT: C 74 LYS cc_start: 0.9148 (mtpm) cc_final: 0.8637 (mptp) REVERT: C 183 MET cc_start: 0.9172 (ttt) cc_final: 0.8770 (ttt) REVERT: C 257 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7422 (ttmt) REVERT: D 76 ARG cc_start: 0.5944 (mtt180) cc_final: 0.5607 (mtp85) REVERT: D 112 ASN cc_start: 0.7985 (m-40) cc_final: 0.7552 (p0) REVERT: D 125 GLU cc_start: 0.6927 (tp30) cc_final: 0.6708 (tp30) REVERT: D 159 HIS cc_start: 0.7914 (m90) cc_final: 0.7366 (m90) REVERT: E 429 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8252 (t0) REVERT: F 74 LYS cc_start: 0.9111 (mtpm) cc_final: 0.8520 (mmtm) REVERT: F 183 MET cc_start: 0.9161 (ttt) cc_final: 0.8775 (ttt) REVERT: F 257 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7318 (ttmt) outliers start: 24 outliers final: 13 residues processed: 136 average time/residue: 0.6128 time to fit residues: 91.1380 Evaluate side-chains 131 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 429 ASN Chi-restraints excluded: chain F residue 14 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [62, 156, 66, 70, 162, 119, 13, 164, 24, 11, 58] chunk 62 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.061248 restraints weight = 67481.180| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.65 r_work: 0.2568 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.406 14492 Z= 0.172 Angle : 0.624 12.847 19842 Z= 0.279 Chirality : 0.043 0.139 2124 Planarity : 0.005 0.041 2446 Dihedral : 8.461 81.740 2398 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.02 % Allowed : 10.19 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1698 helix: 1.82 (0.18), residues: 836 sheet: -1.36 (0.51), residues: 86 loop : -0.71 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.013 0.001 TYR B 399 PHE 0.025 0.002 PHE B 216 TRP 0.009 0.001 TRP E 47 HIS 0.007 0.001 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.17 (14470) covalent geometry : angle 0.61456 / 0.28 (19828) SS BOND : bond 0.00270 / 0.14 ( 4) SS BOND : angle 0.47934 / 0.26 ( 8) hydrogen bonds : bond 0.05746 / 3.84 ( 652) hydrogen bonds : angle 3.87679 / 2.73 ( 1842) metal coordination : bond 0.00886 / 0.46 ( 8) metal coordination : angle 6.41390 / 3.36 ( 6) Misc. bond : bond 0.18808 / 13.54 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6585 (tm-30) REVERT: C 74 LYS cc_start: 0.9174 (mtpm) cc_final: 0.8595 (mptp) REVERT: C 257 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7423 (ttmt) REVERT: D 76 ARG cc_start: 0.5861 (mtt180) cc_final: 0.5525 (mtp85) REVERT: D 125 GLU cc_start: 0.7022 (tp30) cc_final: 0.6792 (tp30) REVERT: D 159 HIS cc_start: 0.8007 (m90) cc_final: 0.7357 (m90) REVERT: E 429 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8397 (t0) REVERT: F 74 LYS cc_start: 0.9152 (mtpm) cc_final: 0.8591 (mptp) REVERT: F 257 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7358 (ttmt) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.5797 time to fit residues: 87.5939 Evaluate side-chains 127 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 429 ASN Chi-restraints excluded: chain F residue 14 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [76, 62, 49, 109, 142, 95, 165, 27, 124, 13, 146] chunk 76 optimal weight: 0.0060 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 109 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.065099 restraints weight = 62169.945| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.56 r_work: 0.2650 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14492 Z= 0.099 Angle : 0.557 9.204 19842 Z= 0.251 Chirality : 0.040 0.124 2124 Planarity : 0.004 0.038 2446 Dihedral : 8.219 81.648 2398 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.98 (0.21), residues: 1698 helix: 2.01 (0.18), residues: 838 sheet: -1.29 (0.51), residues: 86 loop : -0.64 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 68 TYR 0.007 0.001 TYR B 399 PHE 0.015 0.001 PHE B 216 TRP 0.023 0.001 TRP D 67 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (14470) covalent geometry : angle 0.54991 / 0.25 (19828) SS BOND : bond 0.00170 / 0.09 ( 4) SS BOND : angle 0.30742 / 0.17 ( 8) hydrogen bonds : bond 0.04071 / 2.71 ( 652) hydrogen bonds : angle 3.66182 / 2.58 ( 1842) metal coordination : bond 0.00388 / 0.19 ( 8) metal coordination : angle 5.31208 / 2.86 ( 6) Misc. bond : bond 0.10561 / 6.81 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8404 (mpp80) cc_final: 0.8029 (mpp80) REVERT: A 70 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8452 (mppt) REVERT: B 429 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8278 (t0) REVERT: C 74 LYS cc_start: 0.9174 (mtpm) cc_final: 0.8631 (mptp) REVERT: C 183 MET cc_start: 0.9113 (ttt) cc_final: 0.8615 (ttt) REVERT: C 257 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7417 (ttmt) REVERT: D 76 ARG cc_start: 0.5916 (mtt180) cc_final: 0.5656 (mtp85) REVERT: D 112 ASN cc_start: 0.8355 (m-40) cc_final: 0.7628 (p0) REVERT: D 159 HIS cc_start: 0.7913 (m90) cc_final: 0.7248 (m90) REVERT: E 429 ASN cc_start: 0.8598 (m-40) cc_final: 0.8291 (t0) REVERT: F 74 LYS cc_start: 0.9155 (mtpm) cc_final: 0.8597 (mptp) REVERT: F 183 MET cc_start: 0.9113 (ttt) cc_final: 0.8645 (ttt) REVERT: F 257 LYS cc_start: 0.7599 (ttmt) cc_final: 0.7306 (ttmt) outliers start: 18 outliers final: 12 residues processed: 133 average time/residue: 0.6206 time to fit residues: 90.0709 Evaluate side-chains 133 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 125 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [109, 4, 163, 132, 122, 90, 24, 150, 152, 45, 17] chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 163 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 122 optimal weight: 0.0570 chunk 90 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.101889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.063100 restraints weight = 68604.245| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.68 r_work: 0.2605 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.313 14492 Z= 0.128 Angle : 0.595 11.356 19842 Z= 0.270 Chirality : 0.041 0.130 2124 Planarity : 0.005 0.040 2446 Dihedral : 8.234 81.775 2398 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.08 % Allowed : 11.92 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1698 helix: 1.97 (0.18), residues: 836 sheet: -1.16 (0.52), residues: 86 loop : -0.68 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 68 TYR 0.012 0.001 TYR B 399 PHE 0.027 0.001 PHE A 152 TRP 0.017 0.001 TRP D 67 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 (14470) covalent geometry : angle 0.58736 / 0.27 (19828) SS BOND : bond 0.00215 / 0.11 ( 4) SS BOND : angle 0.35466 / 0.19 ( 8) hydrogen bonds : bond 0.04813 / 3.21 ( 652) hydrogen bonds : angle 3.69588 / 2.59 ( 1842) metal coordination : bond 0.00642 / 0.33 ( 8) metal coordination : angle 5.49935 / 2.84 ( 6) Misc. bond : bond 0.15126 / 10.64 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8452 (mpp80) cc_final: 0.7842 (mpp80) REVERT: A 70 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8446 (mppt) REVERT: B 429 ASN cc_start: 0.8697 (m-40) cc_final: 0.8296 (t0) REVERT: C 74 LYS cc_start: 0.9189 (mtpm) cc_final: 0.8611 (mptp) REVERT: C 183 MET cc_start: 0.9165 (ttt) cc_final: 0.8832 (ttt) REVERT: C 257 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7376 (ttmt) REVERT: D 76 ARG cc_start: 0.6100 (mtt180) cc_final: 0.5730 (mtp85) REVERT: D 83 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8303 (mp0) REVERT: D 159 HIS cc_start: 0.7934 (m90) cc_final: 0.7286 (m90) REVERT: E 429 ASN cc_start: 0.8620 (m-40) cc_final: 0.8278 (t0) REVERT: F 74 LYS cc_start: 0.9162 (mtpm) cc_final: 0.8579 (mptp) REVERT: F 183 MET cc_start: 0.9172 (ttt) cc_final: 0.8851 (ttt) REVERT: F 257 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7304 (ttmt) outliers start: 13 outliers final: 12 residues processed: 125 average time/residue: 0.6307 time to fit residues: 85.8571 Evaluate side-chains 128 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [141, 149, 62, 35, 119, 70, 116, 69, 64, 30, 68] chunk 141 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 119 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.064151 restraints weight = 54541.092| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.33 r_work: 0.2632 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 14492 Z= 0.115 Angle : 0.586 10.814 19842 Z= 0.266 Chirality : 0.041 0.127 2124 Planarity : 0.005 0.039 2446 Dihedral : 8.185 82.110 2398 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.16 % Allowed : 11.71 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 0.97 (0.21), residues: 1698 helix: 1.98 (0.18), residues: 836 sheet: -1.15 (0.52), residues: 86 loop : -0.64 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 68 TYR 0.010 0.001 TYR B 399 PHE 0.019 0.001 PHE E 216 TRP 0.027 0.001 TRP D 67 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.11 (14470) covalent geometry : angle 0.57901 / 0.27 (19828) SS BOND : bond 0.00192 / 0.10 ( 4) SS BOND : angle 0.31416 / 0.18 ( 8) hydrogen bonds : bond 0.04580 / 3.05 ( 652) hydrogen bonds : angle 3.66138 / 2.57 ( 1842) metal coordination : bond 0.00560 / 0.28 ( 8) metal coordination : angle 5.33984 / 2.79 ( 6) Misc. bond : bond 0.14443 / 10.09 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8452 (mpp80) cc_final: 0.7809 (mpp80) REVERT: A 70 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8389 (mppt) REVERT: B 429 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8285 (t0) REVERT: C 74 LYS cc_start: 0.9184 (mtpm) cc_final: 0.8609 (mptp) REVERT: C 183 MET cc_start: 0.9156 (ttt) cc_final: 0.8780 (ttt) REVERT: C 257 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7324 (ttmt) REVERT: D 83 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8333 (mp0) REVERT: D 112 ASN cc_start: 0.8354 (m-40) cc_final: 0.7567 (p0) REVERT: D 159 HIS cc_start: 0.7906 (m90) cc_final: 0.7197 (m90) REVERT: E 429 ASN cc_start: 0.8636 (m-40) cc_final: 0.8289 (t0) REVERT: F 74 LYS cc_start: 0.9171 (mtpm) cc_final: 0.8590 (mptp) REVERT: F 183 MET cc_start: 0.9175 (ttt) cc_final: 0.8842 (ttt) REVERT: F 257 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7310 (ttmt) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.6202 time to fit residues: 84.5096 Evaluate side-chains 126 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 217 HIS Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: [74, 155, 2, 41, 26, 40, 72, 105, 49, 141, 126] chunk 74 optimal weight: 0.2980 chunk 155 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.102405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.064151 restraints weight = 58184.007| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.43 r_work: 0.2628 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.294 14492 Z= 0.169 Angle : 0.800 59.199 19842 Z= 0.441 Chirality : 0.045 0.914 2124 Planarity : 0.005 0.061 2446 Dihedral : 8.234 82.097 2398 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 1.16 % Allowed : 11.92 % Favored : 86.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.96 (0.21), residues: 1698 helix: 1.97 (0.18), residues: 836 sheet: -1.15 (0.52), residues: 86 loop : -0.64 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.010 0.001 TYR B 399 PHE 0.019 0.001 PHE B 216 TRP 0.020 0.001 TRP D 67 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (14470) covalent geometry : angle 0.79440 / 0.44 (19828) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 0.29177 / 0.17 ( 8) hydrogen bonds : bond 0.04586 / 3.02 ( 652) hydrogen bonds : angle 3.68808 / 2.58 ( 1842) metal coordination : bond 0.00546 / 0.28 ( 8) metal coordination : angle 5.33931 / 2.78 ( 6) Misc. bond : bond 0.14411 / 10.06 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4546.65 seconds wall clock time: 78 minutes 2.13 seconds (4682.13 seconds total)