Starting phenix.real_space_refine on Mon Jun 16 02:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yei_39196/06_2025/8yei_39196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yei_39196/06_2025/8yei_39196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yei_39196/06_2025/8yei_39196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yei_39196/06_2025/8yei_39196.map" model { file = "/net/cci-nas-00/data/ceres_data/8yei_39196/06_2025/8yei_39196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yei_39196/06_2025/8yei_39196.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.131 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 11528 2.51 5 N 3099 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18253 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 837 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3294 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 25, 'TRANS': 393} Chain breaks: 1 Chain: "B" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3294 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 25, 'TRANS': 393} Chain breaks: 1 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3294 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 25, 'TRANS': 393} Chain breaks: 1 Chain: "E" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3294 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 25, 'TRANS': 393} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3294 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 25, 'TRANS': 393} Chain breaks: 1 Time building chain proxies: 12.83, per 1000 atoms: 0.70 Number of scatterers: 18253 At special positions: 0 Unit cell: (115.44, 121.68, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 3522 8.00 N 3099 7.00 C 11528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.9 seconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 24 sheets defined 16.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.649A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.720A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.591A pdb=" N ILE A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 91 " --> pdb=" O THR A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.913A pdb=" N ARG A 283 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.639A pdb=" N GLN A 462 " --> pdb=" O ASP A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.731A pdb=" N ILE B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.782A pdb=" N TYR B 276 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.743A pdb=" N ARG B 283 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 385 through 396 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 459 through 462 Processing helix chain 'B' and resid 463 through 473 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.583A pdb=" N ILE D 90 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR D 91 " --> pdb=" O THR D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 209 through 214 removed outlier: 3.539A pdb=" N GLN D 214 " --> pdb=" O PHE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.701A pdb=" N TYR D 276 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 385 through 396 Processing helix chain 'D' and resid 396 through 404 removed outlier: 4.384A pdb=" N LEU D 400 " --> pdb=" O ASN D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 462 removed outlier: 3.590A pdb=" N GLN D 462 " --> pdb=" O ASP D 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 459 through 462' Processing helix chain 'D' and resid 463 through 473 Processing helix chain 'E' and resid 23 through 26 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.969A pdb=" N TYR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.535A pdb=" N GLN E 214 " --> pdb=" O PHE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.523A pdb=" N ARG E 283 " --> pdb=" O THR E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 385 through 396 Processing helix chain 'E' and resid 397 through 404 Processing helix chain 'E' and resid 463 through 473 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.998A pdb=" N TYR C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.638A pdb=" N GLN C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.560A pdb=" N TYR C 276 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'C' and resid 396 through 404 removed outlier: 4.418A pdb=" N LEU C 400 " --> pdb=" O ASN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 462 removed outlier: 3.572A pdb=" N GLN C 462 " --> pdb=" O ASP C 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 462' Processing helix chain 'C' and resid 463 through 473 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 109 through 112 Processing sheet with id=AA3, first strand: chain 'L' and resid 3 through 4 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 3 through 4 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 98 through 102 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 38 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 38 current: chain 'A' and resid 310 through 312 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 310 through 312 current: chain 'A' and resid 361 through 383 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 76 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 76 current: chain 'A' and resid 248 through 261 removed outlier: 6.197A pdb=" N SER A 294 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE A 260 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER A 292 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 123 removed outlier: 4.134A pdb=" N PHE A 122 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP A 145 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 188 through 194 removed outlier: 5.343A pdb=" N TRP A 169 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N CYS A 229 " --> pdb=" O TRP A 169 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET A 200 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 266 through 267 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 266 through 267 current: chain 'B' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 311 through 312 current: chain 'B' and resid 361 through 383 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 301 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 300 through 301 current: chain 'C' and resid 248 through 262 removed outlier: 5.483A pdb=" N ALA C 257 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER C 296 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS C 259 " --> pdb=" O SER C 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 76 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 76 current: chain 'B' and resid 248 through 262 removed outlier: 5.416A pdb=" N ALA B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER B 296 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS B 259 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 118 through 123 removed outlier: 4.289A pdb=" N PHE B 122 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASP B 145 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 188 through 194 removed outlier: 5.436A pdb=" N TRP B 169 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N CYS B 229 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N MET B 200 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 267 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 266 through 267 current: chain 'D' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 311 through 312 current: chain 'D' and resid 361 through 383 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 76 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 71 through 76 current: chain 'D' and resid 248 through 262 removed outlier: 6.176A pdb=" N SER D 294 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE D 260 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER D 292 " --> pdb=" O PHE D 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 118 through 123 removed outlier: 4.984A pdb=" N GLY D 119 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 149 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL D 147 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 188 through 194 removed outlier: 5.421A pdb=" N TRP D 169 " --> pdb=" O CYS D 229 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS D 229 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N MET D 200 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 266 through 267 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 266 through 267 current: chain 'E' and resid 311 through 312 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 311 through 312 current: chain 'E' and resid 361 through 383 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 71 through 76 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 76 current: chain 'E' and resid 248 through 262 removed outlier: 5.560A pdb=" N ALA E 257 " --> pdb=" O SER E 296 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER E 296 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS E 259 " --> pdb=" O SER E 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 118 through 123 removed outlier: 4.281A pdb=" N PHE E 122 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP E 145 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 188 through 194 removed outlier: 5.452A pdb=" N TRP E 169 " --> pdb=" O CYS E 229 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N CYS E 229 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET E 200 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 266 through 267 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 266 through 267 current: chain 'C' and resid 310 through 312 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 310 through 312 current: chain 'C' and resid 361 through 383 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 118 through 123 removed outlier: 4.133A pdb=" N PHE C 122 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASP C 145 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 188 through 194 removed outlier: 5.340A pdb=" N TRP C 169 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS C 229 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N MET C 200 " --> pdb=" O LYS C 230 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 642 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: 8.46 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5959 1.34 - 1.46: 4367 1.46 - 1.58: 8260 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 18730 Sorted by residual: bond pdb=" C SER C 350 " pdb=" N PRO C 351 " ideal model delta sigma weight residual 1.334 1.357 -0.023 1.11e-02 8.12e+03 4.42e+00 bond pdb=" C SER A 350 " pdb=" N PRO A 351 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.28e-02 6.10e+03 3.99e+00 bond pdb=" C TYR E 463 " pdb=" N PRO E 464 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.75e+00 bond pdb=" N ASN C 404 " pdb=" CA ASN C 404 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.66e+00 bond pdb=" N ASN E 404 " pdb=" CA ASN E 404 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.59e+00 ... (remaining 18725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 24799 1.83 - 3.65: 572 3.65 - 5.48: 76 5.48 - 7.31: 25 7.31 - 9.14: 13 Bond angle restraints: 25485 Sorted by residual: angle pdb=" C LEU E 400 " pdb=" N GLU E 401 " pdb=" CA GLU E 401 " ideal model delta sigma weight residual 121.94 112.93 9.01 2.00e+00 2.50e-01 2.03e+01 angle pdb=" C ARG L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C SER C 140 " pdb=" N GLU C 141 " pdb=" CA GLU C 141 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C TRP C 403 " pdb=" N ASN C 404 " pdb=" CA ASN C 404 " ideal model delta sigma weight residual 121.70 128.45 -6.75 1.80e+00 3.09e-01 1.41e+01 angle pdb=" C TRP E 403 " pdb=" N ASN E 404 " pdb=" CA ASN E 404 " ideal model delta sigma weight residual 121.70 128.43 -6.73 1.80e+00 3.09e-01 1.40e+01 ... (remaining 25480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 10137 17.36 - 34.72: 793 34.72 - 52.07: 102 52.07 - 69.43: 29 69.43 - 86.79: 22 Dihedral angle restraints: 11083 sinusoidal: 4346 harmonic: 6737 Sorted by residual: dihedral pdb=" CA PRO A 221 " pdb=" C PRO A 221 " pdb=" N LEU A 222 " pdb=" CA LEU A 222 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 57.04 35.96 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA SER E 350 " pdb=" C SER E 350 " pdb=" N PRO E 351 " pdb=" CA PRO E 351 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 11080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2108 0.052 - 0.105: 469 0.105 - 0.157: 167 0.157 - 0.210: 5 0.210 - 0.262: 4 Chirality restraints: 2753 Sorted by residual: chirality pdb=" CB VAL E 201 " pdb=" CA VAL E 201 " pdb=" CG1 VAL E 201 " pdb=" CG2 VAL E 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL E 143 " pdb=" CA VAL E 143 " pdb=" CG1 VAL E 143 " pdb=" CG2 VAL E 143 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL C 201 " pdb=" CA VAL C 201 " pdb=" CG1 VAL C 201 " pdb=" CG2 VAL C 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2750 not shown) Planarity restraints: 3323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 92 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO D 93 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO D 93 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 93 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 92 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO C 93 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 92 " 0.054 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO E 93 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 93 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 93 " 0.046 5.00e-02 4.00e+02 ... (remaining 3320 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4911 2.80 - 3.33: 15958 3.33 - 3.85: 33652 3.85 - 4.38: 40162 4.38 - 4.90: 67914 Nonbonded interactions: 162597 Sorted by model distance: nonbonded pdb=" O ASP A 197 " pdb=" NZ LYS A 446 " model vdw 2.280 3.120 nonbonded pdb=" O ARG C 263 " pdb=" OG SER C 288 " model vdw 2.287 3.040 nonbonded pdb=" NH2 ARG A 258 " pdb=" OE2 GLU C 130 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASN A 146 " pdb=" OH TYR C 291 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" OD1 ASN B 146 " model vdw 2.295 3.040 ... (remaining 162592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 128.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 50.810 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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:31.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18732 Z= 0.162 Angle : 0.698 9.137 25489 Z= 0.358 Chirality : 0.050 0.262 2753 Planarity : 0.006 0.115 3323 Dihedral : 13.128 86.788 6771 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2303 helix: -1.47 (0.31), residues: 186 sheet: -0.27 (0.19), residues: 734 loop : -0.81 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 261 HIS 0.005 0.001 HIS E 367 PHE 0.027 0.002 PHE B 247 TYR 0.024 0.002 TYR B 91 ARG 0.011 0.001 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.19266 ( 252) hydrogen bonds : angle 6.98072 ( 642) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.70585 ( 4) covalent geometry : bond 0.00357 (18730) covalent geometry : angle 0.69837 (25485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 VAL cc_start: 0.0956 (m) cc_final: 0.0646 (p) REVERT: B 369 GLU cc_start: 0.2021 (mm-30) cc_final: -0.1921 (pt0) REVERT: D 64 LYS cc_start: 0.1420 (tttt) cc_final: 0.0573 (pttt) REVERT: D 97 ARG cc_start: 0.3573 (mmt-90) cc_final: 0.2603 (mpt90) REVERT: E 128 ASP cc_start: 0.0787 (t70) cc_final: 0.0139 (t0) REVERT: E 319 HIS cc_start: 0.0211 (m-70) cc_final: -0.0226 (m-70) REVERT: E 350 SER cc_start: 0.4744 (p) cc_final: 0.4365 (m) REVERT: E 389 MET cc_start: -0.1469 (ttp) cc_final: -0.2429 (mmm) REVERT: E 399 ILE cc_start: 0.1104 (mt) cc_final: 0.0790 (mt) REVERT: E 467 ARG cc_start: 0.3038 (mtt90) cc_final: 0.1501 (tpm170) REVERT: C 267 MET cc_start: 0.0810 (mmt) cc_final: 0.0392 (mpt) REVERT: C 335 ASP cc_start: 0.2494 (t0) cc_final: 0.1523 (t0) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 1.0447 time to fit residues: 169.6567 Evaluate side-chains 106 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 59 optimal weight: 0.0980 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 192 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.309361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.284241 restraints weight = 25120.451| |-----------------------------------------------------------------------------| r_work (start): 0.4981 rms_B_bonded: 2.36 r_work: 0.4926 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0356 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18732 Z= 0.110 Angle : 0.549 9.039 25489 Z= 0.278 Chirality : 0.044 0.157 2753 Planarity : 0.005 0.070 3323 Dihedral : 4.497 18.775 2527 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.89 % Allowed : 4.82 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2303 helix: -0.65 (0.34), residues: 185 sheet: -0.24 (0.19), residues: 725 loop : -0.74 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 261 HIS 0.005 0.001 HIS C 367 PHE 0.018 0.002 PHE B 73 TYR 0.022 0.001 TYR D 364 ARG 0.007 0.001 ARG C 283 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 252) hydrogen bonds : angle 5.51195 ( 642) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.60299 ( 4) covalent geometry : bond 0.00241 (18730) covalent geometry : angle 0.54922 (25485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.2602 (m-80) cc_final: 0.2325 (m-80) REVERT: B 369 GLU cc_start: 0.2268 (mm-30) cc_final: 0.0969 (tp30) REVERT: D 64 LYS cc_start: 0.2195 (tttt) cc_final: 0.1470 (pttt) REVERT: D 97 ARG cc_start: 0.3921 (mmt-90) cc_final: 0.2125 (mmt180) REVERT: D 366 ARG cc_start: 0.1818 (mmt-90) cc_final: -0.0312 (mmt180) REVERT: E 246 MET cc_start: 0.1007 (OUTLIER) cc_final: 0.0531 (mmm) REVERT: E 319 HIS cc_start: 0.0278 (m-70) cc_final: -0.0128 (m-70) REVERT: E 350 SER cc_start: 0.5535 (p) cc_final: 0.5095 (m) REVERT: E 389 MET cc_start: -0.0881 (ttp) cc_final: -0.2215 (mmt) REVERT: E 399 ILE cc_start: 0.1796 (mt) cc_final: 0.1563 (mt) REVERT: E 467 ARG cc_start: 0.2490 (mtt90) cc_final: 0.0749 (tpm170) REVERT: C 280 THR cc_start: -0.0446 (m) cc_final: -0.0866 (p) REVERT: C 282 MET cc_start: -0.0563 (pmm) cc_final: -0.1009 (ppp) REVERT: C 389 MET cc_start: -0.2063 (mmm) cc_final: -0.2621 (mmm) outliers start: 18 outliers final: 10 residues processed: 117 average time/residue: 1.1047 time to fit residues: 150.6104 Evaluate side-chains 112 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 HIS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain C residue 246 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 181 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 184 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 HIS H 77 GLN A 155 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN D 168 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN E 111 GLN E 153 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS C 308 ASN C 341 ASN ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.309192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.288209 restraints weight = 25044.210| |-----------------------------------------------------------------------------| r_work (start): 0.4996 rms_B_bonded: 2.28 r_work: 0.4934 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work (final): 0.4934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1012 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18732 Z= 0.178 Angle : 0.686 8.850 25489 Z= 0.352 Chirality : 0.047 0.213 2753 Planarity : 0.006 0.067 3323 Dihedral : 5.128 24.287 2527 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.77 % Allowed : 8.61 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2303 helix: -0.46 (0.35), residues: 186 sheet: -0.84 (0.19), residues: 700 loop : -0.98 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 448 HIS 0.012 0.002 HIS C 367 PHE 0.021 0.002 PHE C 247 TYR 0.024 0.002 TYR D 231 ARG 0.007 0.001 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 252) hydrogen bonds : angle 5.96114 ( 642) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.12608 ( 4) covalent geometry : bond 0.00397 (18730) covalent geometry : angle 0.68615 (25485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.3156 (m-80) cc_final: 0.2915 (m-80) REVERT: B 71 ARG cc_start: 0.2113 (OUTLIER) cc_final: 0.0865 (ttm110) REVERT: B 369 GLU cc_start: 0.2834 (mm-30) cc_final: 0.1519 (tp30) REVERT: B 395 MET cc_start: 0.3017 (ttt) cc_final: 0.2375 (ttp) REVERT: D 64 LYS cc_start: 0.2337 (tttt) cc_final: 0.1713 (pttt) REVERT: D 97 ARG cc_start: 0.4456 (mmt-90) cc_final: 0.2519 (mmt180) REVERT: D 356 TYR cc_start: 0.4445 (t80) cc_final: 0.2654 (t80) REVERT: D 452 LEU cc_start: 0.1770 (mt) cc_final: 0.1133 (mp) REVERT: E 41 ARG cc_start: 0.2469 (ttm-80) cc_final: 0.1380 (mtt180) REVERT: E 200 MET cc_start: 0.3853 (ptp) cc_final: 0.3103 (mpt) REVERT: E 246 MET cc_start: 0.1955 (OUTLIER) cc_final: 0.0811 (mmt) REVERT: E 282 MET cc_start: 0.2337 (OUTLIER) cc_final: 0.0851 (mmp) REVERT: E 283 ARG cc_start: 0.3458 (OUTLIER) cc_final: 0.1722 (tpp-160) REVERT: E 319 HIS cc_start: 0.0564 (m-70) cc_final: 0.0068 (m-70) REVERT: E 350 SER cc_start: 0.5458 (p) cc_final: 0.4932 (m) REVERT: E 399 ILE cc_start: 0.1408 (mt) cc_final: 0.1116 (mt) REVERT: E 450 VAL cc_start: 0.5086 (m) cc_final: 0.4692 (t) REVERT: E 467 ARG cc_start: 0.3234 (mtt90) cc_final: 0.0040 (tpp80) REVERT: C 200 MET cc_start: 0.0521 (mmt) cc_final: 0.0254 (mmm) REVERT: C 255 LEU cc_start: 0.3248 (OUTLIER) cc_final: 0.1297 (pp) REVERT: C 282 MET cc_start: -0.0545 (pmm) cc_final: -0.4054 (ttp) REVERT: C 308 ASN cc_start: 0.0024 (OUTLIER) cc_final: -0.1073 (m-40) REVERT: C 389 MET cc_start: -0.2110 (mmm) cc_final: -0.2556 (tmm) outliers start: 36 outliers final: 20 residues processed: 129 average time/residue: 1.0963 time to fit residues: 164.8888 Evaluate side-chains 125 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 94 HIS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 82 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 224 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS D 47 ASN D 155 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 168 HIS E 259 HIS E 321 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.309972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.292032 restraints weight = 25200.127| |-----------------------------------------------------------------------------| r_work (start): 0.5053 rms_B_bonded: 1.93 r_work: 0.4999 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4895 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1626 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18732 Z= 0.235 Angle : 0.840 12.641 25489 Z= 0.437 Chirality : 0.052 0.305 2753 Planarity : 0.006 0.070 3323 Dihedral : 6.238 28.677 2527 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.15 % Allowed : 11.36 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2303 helix: -0.67 (0.35), residues: 182 sheet: -1.24 (0.19), residues: 635 loop : -1.35 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 169 HIS 0.011 0.003 HIS L 39 PHE 0.039 0.003 PHE C 307 TYR 0.034 0.003 TYR A 49 ARG 0.009 0.001 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 252) hydrogen bonds : angle 7.12241 ( 642) SS BOND : bond 0.00678 ( 2) SS BOND : angle 1.63998 ( 4) covalent geometry : bond 0.00526 (18730) covalent geometry : angle 0.83945 (25485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 108 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3707 (pmm) cc_final: 0.2444 (mpp) REVERT: A 282 MET cc_start: 0.0717 (OUTLIER) cc_final: -0.3016 (mtp) REVERT: B 50 PHE cc_start: 0.2114 (OUTLIER) cc_final: 0.1739 (p90) REVERT: B 283 ARG cc_start: 0.0001 (OUTLIER) cc_final: -0.0567 (ptp90) REVERT: B 369 GLU cc_start: 0.3544 (mm-30) cc_final: 0.3037 (tp30) REVERT: D 64 LYS cc_start: 0.3419 (tttt) cc_final: 0.2515 (pttt) REVERT: D 130 GLU cc_start: 0.3608 (OUTLIER) cc_final: 0.3135 (pp20) REVERT: E 41 ARG cc_start: 0.2547 (ttm-80) cc_final: 0.1925 (ptm160) REVERT: E 50 PHE cc_start: 0.0534 (OUTLIER) cc_final: -0.0256 (p90) REVERT: E 125 LYS cc_start: -0.0486 (OUTLIER) cc_final: -0.1606 (ptmm) REVERT: E 200 MET cc_start: 0.4235 (ptp) cc_final: 0.3167 (mpp) REVERT: E 282 MET cc_start: 0.2295 (tmt) cc_final: 0.0200 (mmp) REVERT: E 283 ARG cc_start: 0.3640 (OUTLIER) cc_final: 0.2133 (tpp-160) REVERT: E 319 HIS cc_start: 0.1497 (m-70) cc_final: 0.0816 (m-70) REVERT: E 467 ARG cc_start: 0.3316 (mtt90) cc_final: 0.0081 (tpt-90) REVERT: C 282 MET cc_start: -0.0706 (pmm) cc_final: -0.3911 (tmt) REVERT: C 389 MET cc_start: -0.2235 (mmm) cc_final: -0.2811 (tmm) outliers start: 64 outliers final: 29 residues processed: 152 average time/residue: 1.0141 time to fit residues: 179.1530 Evaluate side-chains 132 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 242 TYR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 382 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 13 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 93 optimal weight: 0.0020 chunk 171 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS A 254 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.309868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.290196 restraints weight = 25268.352| |-----------------------------------------------------------------------------| r_work (start): 0.5019 rms_B_bonded: 2.03 r_work: 0.4968 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4864 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1382 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18732 Z= 0.114 Angle : 0.579 8.606 25489 Z= 0.295 Chirality : 0.044 0.168 2753 Planarity : 0.004 0.046 3323 Dihedral : 5.091 23.461 2527 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.07 % Allowed : 13.28 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2303 helix: -0.84 (0.33), residues: 206 sheet: -1.23 (0.20), residues: 632 loop : -1.12 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 261 HIS 0.004 0.001 HIS E 120 PHE 0.015 0.002 PHE E 73 TYR 0.018 0.001 TYR D 442 ARG 0.006 0.000 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 252) hydrogen bonds : angle 5.90654 ( 642) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.59556 ( 4) covalent geometry : bond 0.00259 (18730) covalent geometry : angle 0.57890 (25485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 VAL cc_start: 0.2993 (p) cc_final: 0.2667 (p) REVERT: A 267 MET cc_start: 0.3252 (pmm) cc_final: 0.2322 (ptp) REVERT: A 282 MET cc_start: 0.0860 (tmt) cc_final: -0.3047 (mmm) REVERT: A 371 TYR cc_start: 0.3117 (m-80) cc_final: 0.1968 (m-80) REVERT: B 369 GLU cc_start: 0.2959 (mm-30) cc_final: 0.2553 (tp30) REVERT: B 389 MET cc_start: 0.0385 (ttt) cc_final: -0.0796 (pp-130) REVERT: E 153 GLN cc_start: 0.2604 (OUTLIER) cc_final: 0.1911 (mt0) REVERT: E 184 ASP cc_start: 0.1193 (m-30) cc_final: 0.0760 (t0) REVERT: E 200 MET cc_start: 0.3900 (ptp) cc_final: 0.3533 (mpp) REVERT: E 282 MET cc_start: 0.2170 (tmt) cc_final: 0.0145 (mmp) REVERT: E 319 HIS cc_start: 0.1347 (m-70) cc_final: 0.0686 (m-70) REVERT: E 350 SER cc_start: 0.5614 (p) cc_final: 0.5077 (m) REVERT: E 467 ARG cc_start: 0.3157 (mtt90) cc_final: 0.0006 (tpp80) REVERT: C 255 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.3026 (pp) REVERT: C 282 MET cc_start: -0.1245 (pmm) cc_final: -0.4263 (tmt) REVERT: C 389 MET cc_start: -0.2223 (mmm) cc_final: -0.2796 (tmm) outliers start: 42 outliers final: 20 residues processed: 126 average time/residue: 1.1025 time to fit residues: 164.1158 Evaluate side-chains 114 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 336 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 30 optimal weight: 0.0470 chunk 114 optimal weight: 7.9990 chunk 218 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS L 32 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS A 254 GLN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 HIS ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.310586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.295145 restraints weight = 25602.393| |-----------------------------------------------------------------------------| r_work (start): 0.5055 rms_B_bonded: 1.82 r_work: 0.5009 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4914 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2120 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 18732 Z= 0.305 Angle : 0.986 14.171 25489 Z= 0.517 Chirality : 0.056 0.389 2753 Planarity : 0.007 0.083 3323 Dihedral : 7.237 35.104 2527 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 29.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.77 % Favored : 91.06 % Rotamer: Outliers : 3.54 % Allowed : 13.97 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2303 helix: -0.83 (0.36), residues: 179 sheet: -1.64 (0.20), residues: 586 loop : -1.74 (0.14), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 169 HIS 0.018 0.004 HIS A 133 PHE 0.042 0.004 PHE B 307 TYR 0.040 0.004 TYR B 68 ARG 0.012 0.002 ARG E 109 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 252) hydrogen bonds : angle 7.80876 ( 642) SS BOND : bond 0.01145 ( 2) SS BOND : angle 2.49553 ( 4) covalent geometry : bond 0.00694 (18730) covalent geometry : angle 0.98579 (25485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 106 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.3333 (mmt180) cc_final: 0.3101 (mmt180) REVERT: A 267 MET cc_start: 0.4053 (pmm) cc_final: 0.3262 (ptp) REVERT: A 282 MET cc_start: 0.0646 (tmt) cc_final: -0.2884 (mmt) REVERT: A 395 MET cc_start: 0.0327 (ttt) cc_final: -0.1024 (ttp) REVERT: B 50 PHE cc_start: 0.2642 (OUTLIER) cc_final: 0.2130 (p90) REVERT: B 51 ARG cc_start: 0.2912 (ttt90) cc_final: 0.2441 (ttp-170) REVERT: B 330 PHE cc_start: 0.4334 (m-80) cc_final: 0.3741 (m-80) REVERT: B 389 MET cc_start: 0.1046 (ttt) cc_final: -0.0499 (pp-130) REVERT: D 325 TRP cc_start: 0.4917 (m100) cc_final: 0.4515 (m100) REVERT: D 366 ARG cc_start: 0.3328 (mmt-90) cc_final: 0.0748 (ttm110) REVERT: E 50 PHE cc_start: 0.1465 (OUTLIER) cc_final: 0.0892 (p90) REVERT: E 125 LYS cc_start: -0.0276 (OUTLIER) cc_final: -0.1316 (ptmm) REVERT: E 200 MET cc_start: 0.4827 (ptp) cc_final: 0.4588 (mpp) REVERT: E 247 PHE cc_start: 0.3401 (OUTLIER) cc_final: 0.3161 (p90) REVERT: E 282 MET cc_start: 0.2388 (tmt) cc_final: 0.0524 (mmp) REVERT: E 319 HIS cc_start: 0.1808 (m-70) cc_final: 0.1347 (m-70) REVERT: E 360 LYS cc_start: 0.0533 (OUTLIER) cc_final: 0.0275 (mttt) REVERT: E 464 PRO cc_start: 0.5526 (Cg_endo) cc_final: 0.5315 (Cg_exo) REVERT: E 467 ARG cc_start: 0.3723 (mtt90) cc_final: 0.0388 (tpp80) REVERT: C 282 MET cc_start: -0.0278 (pmm) cc_final: -0.4100 (tmt) REVERT: C 344 ILE cc_start: 0.2906 (mp) cc_final: 0.2591 (mp) outliers start: 72 outliers final: 40 residues processed: 164 average time/residue: 0.9451 time to fit residues: 182.3209 Evaluate side-chains 139 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 375 PHE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 223 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 HIS E 317 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN C 305 GLN ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5165 r_free = 0.5165 target = 0.311437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.295814 restraints weight = 25278.804| |-----------------------------------------------------------------------------| r_work (start): 0.5056 rms_B_bonded: 1.75 r_work: 0.5007 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4911 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1794 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18732 Z= 0.133 Angle : 0.639 9.635 25489 Z= 0.328 Chirality : 0.046 0.395 2753 Planarity : 0.005 0.065 3323 Dihedral : 5.799 29.389 2527 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.36 % Allowed : 15.49 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.16), residues: 2303 helix: -0.57 (0.37), residues: 185 sheet: -1.56 (0.19), residues: 632 loop : -1.38 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 261 HIS 0.007 0.001 HIS A 133 PHE 0.021 0.002 PHE D 122 TYR 0.027 0.002 TYR A 70 ARG 0.004 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 252) hydrogen bonds : angle 6.50331 ( 642) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.97330 ( 4) covalent geometry : bond 0.00305 (18730) covalent geometry : angle 0.63881 (25485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3833 (pmm) cc_final: 0.1717 (mpp) REVERT: A 282 MET cc_start: 0.0310 (tmt) cc_final: -0.2721 (mmt) REVERT: A 371 TYR cc_start: 0.3203 (m-80) cc_final: 0.2211 (m-80) REVERT: B 330 PHE cc_start: 0.3747 (m-80) cc_final: 0.3109 (m-80) REVERT: B 369 GLU cc_start: 0.3513 (tp30) cc_final: 0.2989 (mm-30) REVERT: B 389 MET cc_start: 0.0970 (ttt) cc_final: -0.0479 (pp-130) REVERT: D 44 THR cc_start: 0.3328 (OUTLIER) cc_final: 0.3112 (p) REVERT: D 129 THR cc_start: 0.2255 (OUTLIER) cc_final: 0.1653 (p) REVERT: D 395 MET cc_start: 0.0032 (ptm) cc_final: -0.2671 (tmm) REVERT: D 442 TYR cc_start: 0.4787 (m-80) cc_final: 0.3953 (m-10) REVERT: E 41 ARG cc_start: 0.4526 (mmm160) cc_final: 0.3773 (mtp85) REVERT: E 247 PHE cc_start: 0.3033 (OUTLIER) cc_final: 0.2640 (p90) REVERT: E 282 MET cc_start: 0.2140 (tmt) cc_final: 0.0328 (mmp) REVERT: E 319 HIS cc_start: 0.1387 (m-70) cc_final: 0.1045 (m-70) REVERT: E 464 PRO cc_start: 0.5684 (Cg_endo) cc_final: 0.5455 (Cg_exo) REVERT: E 467 ARG cc_start: 0.3459 (mtt90) cc_final: 0.0554 (tpp80) REVERT: C 35 TYR cc_start: 0.2769 (OUTLIER) cc_final: 0.1448 (t80) REVERT: C 282 MET cc_start: -0.0838 (pmm) cc_final: -0.3956 (tmt) REVERT: C 389 MET cc_start: -0.1850 (OUTLIER) cc_final: -0.2568 (mmm) REVERT: C 395 MET cc_start: -0.0536 (ptt) cc_final: -0.3636 (tpt) outliers start: 48 outliers final: 29 residues processed: 133 average time/residue: 1.0371 time to fit residues: 161.2222 Evaluate side-chains 127 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 375 PHE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 389 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 HIS ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 HIS ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.310942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.295242 restraints weight = 25156.833| |-----------------------------------------------------------------------------| r_work (start): 0.5050 rms_B_bonded: 1.79 r_work: 0.5001 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4908 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1817 moved from start: 0.7376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18732 Z= 0.127 Angle : 0.622 9.138 25489 Z= 0.316 Chirality : 0.045 0.233 2753 Planarity : 0.005 0.058 3323 Dihedral : 5.436 27.260 2527 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.66 % Allowed : 15.84 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2303 helix: -0.21 (0.38), residues: 185 sheet: -1.43 (0.20), residues: 602 loop : -1.39 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 261 HIS 0.005 0.001 HIS E 120 PHE 0.016 0.002 PHE C 256 TYR 0.020 0.002 TYR A 123 ARG 0.007 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 252) hydrogen bonds : angle 6.22476 ( 642) SS BOND : bond 0.00516 ( 2) SS BOND : angle 1.02366 ( 4) covalent geometry : bond 0.00290 (18730) covalent geometry : angle 0.62206 (25485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 40 LEU cc_start: 0.1181 (mt) cc_final: 0.0885 (mt) REVERT: A 267 MET cc_start: 0.3927 (pmm) cc_final: 0.1889 (mpp) REVERT: A 282 MET cc_start: 0.0270 (tmt) cc_final: -0.2486 (mmt) REVERT: A 371 TYR cc_start: 0.3381 (m-80) cc_final: 0.2267 (m-80) REVERT: B 330 PHE cc_start: 0.3692 (m-80) cc_final: 0.2958 (m-80) REVERT: B 389 MET cc_start: 0.1174 (ttt) cc_final: -0.0332 (pp-130) REVERT: D 129 THR cc_start: 0.2366 (OUTLIER) cc_final: 0.1797 (p) REVERT: D 395 MET cc_start: 0.0430 (ptm) cc_final: -0.1766 (tmm) REVERT: E 41 ARG cc_start: 0.4564 (mmm160) cc_final: 0.2532 (mtp85) REVERT: E 282 MET cc_start: 0.2255 (tmt) cc_final: 0.0393 (mmp) REVERT: E 319 HIS cc_start: 0.1333 (m-70) cc_final: 0.1045 (m-70) REVERT: E 464 PRO cc_start: 0.5680 (Cg_endo) cc_final: 0.5430 (Cg_exo) REVERT: E 467 ARG cc_start: 0.3416 (mtt90) cc_final: 0.0142 (ttm170) REVERT: C 35 TYR cc_start: 0.2553 (OUTLIER) cc_final: 0.1415 (t80) REVERT: C 282 MET cc_start: -0.0838 (pmm) cc_final: -0.3939 (tmt) REVERT: C 389 MET cc_start: -0.1776 (mmm) cc_final: -0.2567 (mmm) REVERT: C 395 MET cc_start: -0.0763 (ptt) cc_final: -0.3733 (tpt) outliers start: 54 outliers final: 34 residues processed: 137 average time/residue: 0.9803 time to fit residues: 158.1499 Evaluate side-chains 129 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 375 PHE Chi-restraints excluded: chain E residue 448 TRP Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 13 optimal weight: 0.1980 chunk 167 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 190 optimal weight: 0.0170 chunk 144 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 HIS ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.313157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.295603 restraints weight = 25094.889| |-----------------------------------------------------------------------------| r_work (start): 0.5047 rms_B_bonded: 1.97 r_work: 0.4998 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4897 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1665 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18732 Z= 0.101 Angle : 0.571 9.985 25489 Z= 0.286 Chirality : 0.044 0.190 2753 Planarity : 0.004 0.050 3323 Dihedral : 5.027 23.664 2527 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.92 % Allowed : 16.43 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2303 helix: -0.02 (0.38), residues: 185 sheet: -1.38 (0.20), residues: 610 loop : -1.25 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 261 HIS 0.004 0.001 HIS B 168 PHE 0.016 0.001 PHE C 256 TYR 0.018 0.001 TYR B 371 ARG 0.004 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 252) hydrogen bonds : angle 5.89348 ( 642) SS BOND : bond 0.00419 ( 2) SS BOND : angle 0.70545 ( 4) covalent geometry : bond 0.00233 (18730) covalent geometry : angle 0.57133 (25485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.6451 (p0) cc_final: 0.6171 (p0) REVERT: A 267 MET cc_start: 0.3608 (pmm) cc_final: 0.1485 (mpp) REVERT: A 282 MET cc_start: -0.0272 (tmt) cc_final: -0.2772 (mmt) REVERT: A 371 TYR cc_start: 0.3120 (m-80) cc_final: 0.2172 (m-80) REVERT: B 330 PHE cc_start: 0.3377 (m-80) cc_final: 0.2616 (m-80) REVERT: B 369 GLU cc_start: 0.3794 (tp30) cc_final: 0.3237 (mm-30) REVERT: B 389 MET cc_start: 0.1040 (ttt) cc_final: -0.0508 (pp-130) REVERT: D 79 ASP cc_start: 0.1432 (OUTLIER) cc_final: -0.0507 (p0) REVERT: D 129 THR cc_start: 0.2328 (OUTLIER) cc_final: 0.1743 (p) REVERT: D 395 MET cc_start: 0.0303 (ptm) cc_final: -0.1972 (ttp) REVERT: E 41 ARG cc_start: 0.4374 (mmm160) cc_final: 0.3711 (mmm160) REVERT: E 282 MET cc_start: 0.2000 (tmt) cc_final: 0.0159 (mmp) REVERT: E 319 HIS cc_start: 0.1370 (m-70) cc_final: 0.1025 (m-70) REVERT: E 467 ARG cc_start: 0.2877 (mtt90) cc_final: 0.0282 (tpp80) REVERT: C 282 MET cc_start: -0.0831 (pmm) cc_final: -0.3919 (tmt) REVERT: C 389 MET cc_start: -0.2147 (mmm) cc_final: -0.2721 (mmm) outliers start: 39 outliers final: 28 residues processed: 122 average time/residue: 1.0535 time to fit residues: 150.2395 Evaluate side-chains 118 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 375 PHE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 0.1980 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 66 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 207 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 HIS ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.313197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.295990 restraints weight = 24975.395| |-----------------------------------------------------------------------------| r_work (start): 0.5045 rms_B_bonded: 1.94 r_work: 0.4996 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4896 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1772 moved from start: 0.7613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18732 Z= 0.118 Angle : 0.594 8.585 25489 Z= 0.299 Chirality : 0.044 0.222 2753 Planarity : 0.004 0.051 3323 Dihedral : 5.078 24.223 2527 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.72 % Allowed : 16.82 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2303 helix: 0.07 (0.38), residues: 185 sheet: -1.38 (0.20), residues: 603 loop : -1.24 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 261 HIS 0.005 0.001 HIS E 259 PHE 0.012 0.002 PHE B 361 TYR 0.019 0.002 TYR B 371 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 252) hydrogen bonds : angle 5.90935 ( 642) SS BOND : bond 0.00564 ( 2) SS BOND : angle 0.99888 ( 4) covalent geometry : bond 0.00270 (18730) covalent geometry : angle 0.59366 (25485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASP cc_start: 0.6572 (p0) cc_final: 0.6307 (p0) REVERT: A 267 MET cc_start: 0.3573 (pmm) cc_final: 0.1622 (mpp) REVERT: A 282 MET cc_start: -0.0307 (tmt) cc_final: -0.2733 (mmt) REVERT: A 371 TYR cc_start: 0.3421 (m-80) cc_final: 0.2266 (m-80) REVERT: B 200 MET cc_start: 0.3463 (ttm) cc_final: 0.1105 (ptm) REVERT: B 330 PHE cc_start: 0.3773 (m-80) cc_final: 0.2950 (m-80) REVERT: B 369 GLU cc_start: 0.3623 (tp30) cc_final: 0.3229 (tp30) REVERT: B 389 MET cc_start: 0.1108 (ttt) cc_final: -0.0541 (pp-130) REVERT: D 79 ASP cc_start: 0.1750 (OUTLIER) cc_final: -0.0802 (p0) REVERT: D 129 THR cc_start: 0.2498 (OUTLIER) cc_final: 0.2258 (t) REVERT: D 395 MET cc_start: 0.0357 (ptm) cc_final: -0.1933 (tmm) REVERT: E 282 MET cc_start: 0.2042 (tmt) cc_final: 0.0164 (mmp) REVERT: E 319 HIS cc_start: 0.1474 (m-70) cc_final: 0.1104 (m-70) REVERT: C 35 TYR cc_start: 0.2621 (OUTLIER) cc_final: 0.1506 (t80) REVERT: C 282 MET cc_start: -0.0710 (pmm) cc_final: -0.4227 (tmt) REVERT: C 389 MET cc_start: -0.2157 (mmm) cc_final: -0.2717 (mmm) REVERT: C 395 MET cc_start: -0.1047 (ptt) cc_final: -0.3937 (tpt) outliers start: 35 outliers final: 27 residues processed: 119 average time/residue: 1.0726 time to fit residues: 148.6477 Evaluate side-chains 118 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 256 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 375 PHE Chi-restraints excluded: chain E residue 448 TRP Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 89 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 HIS ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 92 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5187 r_free = 0.5187 target = 0.313469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.296466 restraints weight = 24952.353| |-----------------------------------------------------------------------------| r_work (start): 0.5056 rms_B_bonded: 1.93 r_work: 0.5007 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4908 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1795 moved from start: 0.7928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18732 Z= 0.116 Angle : 0.596 8.878 25489 Z= 0.299 Chirality : 0.044 0.216 2753 Planarity : 0.004 0.052 3323 Dihedral : 5.048 23.767 2527 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.87 % Allowed : 16.87 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2303 helix: 0.19 (0.38), residues: 187 sheet: -1.34 (0.20), residues: 626 loop : -1.20 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 261 HIS 0.005 0.001 HIS D 326 PHE 0.012 0.001 PHE B 361 TYR 0.018 0.002 TYR A 123 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 252) hydrogen bonds : angle 5.79575 ( 642) SS BOND : bond 0.00569 ( 2) SS BOND : angle 0.95334 ( 4) covalent geometry : bond 0.00269 (18730) covalent geometry : angle 0.59544 (25485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11313.84 seconds wall clock time: 196 minutes 23.04 seconds (11783.04 seconds total)