Starting phenix.real_space_refine on Thu Sep 18 15:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yei_39196/09_2025/8yei_39196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yei_39196/09_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_39196/09_2025/8yei_39196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yei_39196/09_2025/8yei_39196.map" model { file = "/net/cci-nas-00/data/ceres_data/8yei_39196/09_2025/8yei_39196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yei_39196/09_2025/8yei_39196.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.26, per 1000 atoms: 0.23 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: 1.43 Conformation dependent library (CDL) restraints added in 766.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 2.99 Time building geometry restraints manager: 1.94 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.360 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG E 109 TYR 0.024 0.002 TYR B 91 PHE 0.027 0.002 PHE B 247 TRP 0.025 0.002 TRP B 261 HIS 0.005 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00357 (18730) covalent geometry : angle 0.69837 (25485) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.70585 ( 4) hydrogen bonds : bond 0.19266 ( 252) hydrogen bonds : angle 6.98072 ( 642) *********************** 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 : 0.581 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: 0.4686 time to fit residues: 75.8049 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 : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 111 GLN E 153 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 259 HIS C 393 HIS ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.309792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.287072 restraints weight = 25330.499| |-----------------------------------------------------------------------------| r_work (start): 0.4997 rms_B_bonded: 2.17 r_work: 0.4945 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4839 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0815 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18732 Z= 0.195 Angle : 0.704 9.081 25489 Z= 0.364 Chirality : 0.048 0.277 2753 Planarity : 0.006 0.074 3323 Dihedral : 5.104 24.349 2527 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.03 % Allowed : 6.69 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.16), residues: 2303 helix: -0.92 (0.33), residues: 192 sheet: -0.55 (0.18), residues: 749 loop : -0.96 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 366 TYR 0.047 0.002 TYR D 364 PHE 0.026 0.003 PHE C 247 TRP 0.016 0.002 TRP H 34 HIS 0.012 0.002 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00428 (18730) covalent geometry : angle 0.70439 (25485) SS BOND : bond 0.00224 ( 2) SS BOND : angle 0.87517 ( 4) hydrogen bonds : bond 0.04042 ( 252) hydrogen bonds : angle 6.03963 ( 642) *********************** 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 132 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 VAL cc_start: 0.2369 (t) cc_final: 0.2167 (t) REVERT: B 205 TYR cc_start: 0.5623 (m-80) cc_final: 0.4243 (m-10) REVERT: B 369 GLU cc_start: 0.2584 (mm-30) cc_final: 0.1128 (tp30) REVERT: D 64 LYS cc_start: 0.2428 (tttt) cc_final: 0.1878 (pttt) REVERT: D 97 ARG cc_start: 0.4253 (mmt-90) cc_final: 0.2590 (mmt180) REVERT: D 237 MET cc_start: 0.1093 (mpp) cc_final: -0.1062 (tmt) REVERT: D 356 TYR cc_start: 0.4250 (t80) cc_final: 0.2894 (t80) REVERT: E 44 THR cc_start: 0.0249 (p) cc_final: -0.0871 (t) REVERT: E 237 MET cc_start: 0.0533 (ttp) cc_final: -0.0316 (ttt) REVERT: E 283 ARG cc_start: 0.2961 (OUTLIER) cc_final: 0.1589 (tpp-160) REVERT: E 319 HIS cc_start: 0.1020 (m-70) cc_final: 0.0340 (m-70) REVERT: E 350 SER cc_start: 0.5436 (p) cc_final: 0.4955 (m) REVERT: E 389 MET cc_start: -0.0458 (ttp) cc_final: -0.2068 (mmt) REVERT: E 399 ILE cc_start: 0.1295 (mt) cc_final: 0.1011 (mt) REVERT: E 450 VAL cc_start: 0.4992 (m) cc_final: 0.4577 (t) REVERT: E 467 ARG cc_start: 0.2515 (mtt90) cc_final: -0.0492 (ttm-80) REVERT: C 335 ASP cc_start: 0.4988 (t0) cc_final: 0.3332 (t0) REVERT: C 389 MET cc_start: -0.2584 (mmm) cc_final: -0.2937 (mmm) outliers start: 21 outliers final: 15 residues processed: 121 average time/residue: 0.4405 time to fit residues: 62.5412 Evaluate side-chains 115 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 B residue 283 ARG Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain E residue 52 VAL 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 E residue 333 VAL Chi-restraints excluded: chain E residue 395 MET Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 HIS A 155 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN A 327 ASN ** 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 308 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 168 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.309066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.287942 restraints weight = 25365.475| |-----------------------------------------------------------------------------| r_work (start): 0.4997 rms_B_bonded: 2.11 r_work: 0.4944 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4839 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1221 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18732 Z= 0.173 Angle : 0.682 9.700 25489 Z= 0.350 Chirality : 0.048 0.255 2753 Planarity : 0.005 0.056 3323 Dihedral : 5.302 22.535 2527 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.07 % Allowed : 10.13 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.16), residues: 2303 helix: -0.59 (0.35), residues: 189 sheet: -1.00 (0.19), residues: 676 loop : -1.01 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 74 TYR 0.020 0.002 TYR A 49 PHE 0.023 0.003 PHE D 247 TRP 0.015 0.002 TRP D 403 HIS 0.009 0.002 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00389 (18730) covalent geometry : angle 0.68237 (25485) SS BOND : bond 0.00438 ( 2) SS BOND : angle 1.01889 ( 4) hydrogen bonds : bond 0.04129 ( 252) hydrogen bonds : angle 6.21747 ( 642) *********************** 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 152 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3261 (pmm) cc_final: 0.2831 (ptp) REVERT: A 317 GLN cc_start: 0.3654 (pp30) cc_final: 0.1463 (tp-100) REVERT: A 371 TYR cc_start: 0.3304 (m-80) cc_final: 0.2080 (m-80) REVERT: A 377 PHE cc_start: 0.2623 (m-80) cc_final: 0.2155 (m-80) REVERT: B 146 ASN cc_start: 0.2318 (OUTLIER) cc_final: 0.2018 (t0) REVERT: B 283 ARG cc_start: 0.0004 (OUTLIER) cc_final: -0.0574 (ptp90) REVERT: B 369 GLU cc_start: 0.3181 (mm-30) cc_final: 0.2518 (tp30) REVERT: B 375 PHE cc_start: 0.1739 (OUTLIER) cc_final: 0.1303 (m-80) REVERT: B 395 MET cc_start: 0.3138 (ttt) cc_final: 0.2085 (ttp) REVERT: D 64 LYS cc_start: 0.2814 (tttt) cc_final: 0.2387 (ptmt) REVERT: D 237 MET cc_start: 0.1009 (mpp) cc_final: -0.0799 (tmt) REVERT: E 41 ARG cc_start: 0.2320 (ttm-80) cc_final: 0.1108 (mtt90) REVERT: E 200 MET cc_start: 0.3789 (ptp) cc_final: 0.3403 (mpp) REVERT: E 283 ARG cc_start: 0.3379 (OUTLIER) cc_final: 0.1907 (tpp-160) REVERT: E 319 HIS cc_start: 0.1095 (m-70) cc_final: 0.0405 (m-70) REVERT: E 350 SER cc_start: 0.5378 (p) cc_final: 0.4815 (m) REVERT: E 399 ILE cc_start: 0.1514 (mt) cc_final: 0.1166 (mt) REVERT: E 467 ARG cc_start: 0.2986 (mtt90) cc_final: -0.0065 (tpp80) REVERT: C 200 MET cc_start: 0.0298 (mmt) cc_final: 0.0077 (mmm) REVERT: C 255 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.1788 (pp) REVERT: C 308 ASN cc_start: 0.0356 (OUTLIER) cc_final: -0.0892 (m-40) REVERT: C 389 MET cc_start: -0.2330 (mmm) cc_final: -0.2657 (tmm) outliers start: 42 outliers final: 22 residues processed: 139 average time/residue: 0.4709 time to fit residues: 75.5292 Evaluate side-chains 123 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 299 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 283 ARG 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 245 SER Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 202 ASP 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 120 HIS Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 THR 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 56 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 0.0370 chunk 170 optimal weight: 2.9990 overall best weight: 1.6462 ------------------------------------------------------------------------------- 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN D 47 ASN D 124 ASN D 155 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN E 192 ASN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 396 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.310016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.290934 restraints weight = 25394.672| |-----------------------------------------------------------------------------| r_work (start): 0.5020 rms_B_bonded: 1.99 r_work: 0.4967 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4864 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1472 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18732 Z= 0.170 Angle : 0.685 18.014 25489 Z= 0.350 Chirality : 0.048 0.326 2753 Planarity : 0.005 0.055 3323 Dihedral : 5.424 24.369 2527 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.61 % Allowed : 12.49 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.16), residues: 2303 helix: -0.95 (0.33), residues: 206 sheet: -1.27 (0.19), residues: 656 loop : -1.12 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 71 TYR 0.029 0.002 TYR A 49 PHE 0.022 0.002 PHE B 361 TRP 0.023 0.002 TRP B 448 HIS 0.010 0.002 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00391 (18730) covalent geometry : angle 0.68467 (25485) SS BOND : bond 0.00507 ( 2) SS BOND : angle 1.21975 ( 4) hydrogen bonds : bond 0.03645 ( 252) hydrogen bonds : angle 6.34009 ( 642) *********************** 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 150 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 97 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3485 (pmm) cc_final: 0.2493 (ptp) REVERT: A 282 MET cc_start: 0.1231 (tmt) cc_final: -0.2839 (mmt) REVERT: A 371 TYR cc_start: 0.3595 (m-80) cc_final: 0.2217 (m-80) REVERT: A 377 PHE cc_start: 0.3319 (m-80) cc_final: 0.2489 (m-80) REVERT: B 50 PHE cc_start: 0.1872 (OUTLIER) cc_final: 0.1588 (p90) REVERT: B 369 GLU cc_start: 0.3426 (mm-30) cc_final: 0.2885 (tp30) REVERT: B 375 PHE cc_start: 0.2079 (OUTLIER) cc_final: 0.1700 (m-80) REVERT: B 389 MET cc_start: 0.0489 (ttt) cc_final: -0.0623 (pp-130) REVERT: D 97 ARG cc_start: 0.4724 (mmp80) cc_final: 0.4098 (mmp80) REVERT: D 130 GLU cc_start: 0.3338 (OUTLIER) cc_final: 0.2971 (pp20) REVERT: E 41 ARG cc_start: 0.2491 (ttm-80) cc_final: 0.1668 (mtm-85) REVERT: E 50 PHE cc_start: 0.0331 (OUTLIER) cc_final: -0.0140 (p90) REVERT: E 153 GLN cc_start: 0.2945 (OUTLIER) cc_final: 0.2147 (mt0) REVERT: E 200 MET cc_start: 0.4056 (ptp) cc_final: 0.3369 (mpp) REVERT: E 283 ARG cc_start: 0.3579 (OUTLIER) cc_final: 0.1900 (tpp-160) REVERT: E 319 HIS cc_start: 0.1243 (m-70) cc_final: 0.0391 (m-70) REVERT: E 350 SER cc_start: 0.5652 (p) cc_final: 0.5089 (m) REVERT: E 399 ILE cc_start: 0.1369 (mt) cc_final: 0.0973 (mt) REVERT: E 467 ARG cc_start: 0.3149 (mtt90) cc_final: 0.0011 (tpp80) REVERT: C 255 LEU cc_start: 0.3818 (OUTLIER) cc_final: 0.3241 (pp) REVERT: C 308 ASN cc_start: 0.0316 (OUTLIER) cc_final: -0.0172 (m110) REVERT: C 389 MET cc_start: -0.2228 (mmm) cc_final: -0.2732 (mmm) outliers start: 53 outliers final: 22 residues processed: 137 average time/residue: 0.4192 time to fit residues: 67.0022 Evaluate side-chains 121 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 HIS 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 329 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 275 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 345 CYS 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 267 MET 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 153 GLN Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 283 ARG Chi-restraints excluded: chain E residue 333 VAL 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 255 LEU Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 341 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 226 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 135 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 190 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 153 GLN ** 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 ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.309563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.290671 restraints weight = 25093.894| |-----------------------------------------------------------------------------| r_work (start): 0.5028 rms_B_bonded: 2.10 r_work: 0.4969 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4865 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1268 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18732 Z= 0.100 Angle : 0.545 7.950 25489 Z= 0.276 Chirality : 0.044 0.153 2753 Planarity : 0.004 0.044 3323 Dihedral : 4.725 17.976 2527 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.92 % Allowed : 13.97 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.17), residues: 2303 helix: -0.62 (0.34), residues: 206 sheet: -1.23 (0.19), residues: 677 loop : -0.91 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.015 0.001 TYR D 442 PHE 0.014 0.001 PHE C 256 TRP 0.010 0.001 TRP D 169 HIS 0.005 0.001 HIS D 367 Details of bonding type rmsd covalent geometry : bond 0.00224 (18730) covalent geometry : angle 0.54517 (25485) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.54970 ( 4) hydrogen bonds : bond 0.03066 ( 252) hydrogen bonds : angle 5.58436 ( 642) *********************** 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 136 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 VAL cc_start: 0.2676 (p) cc_final: 0.2348 (p) REVERT: A 267 MET cc_start: 0.3090 (pmm) cc_final: 0.2160 (ptp) REVERT: A 282 MET cc_start: 0.0944 (tmt) cc_final: -0.2886 (mmt) REVERT: A 371 TYR cc_start: 0.3254 (m-80) cc_final: 0.2191 (m-80) REVERT: A 377 PHE cc_start: 0.2958 (m-80) cc_final: 0.2216 (m-80) REVERT: B 369 GLU cc_start: 0.2710 (mm-30) cc_final: 0.2257 (mm-30) REVERT: B 375 PHE cc_start: 0.2010 (OUTLIER) cc_final: 0.1688 (m-80) REVERT: B 389 MET cc_start: 0.0352 (ttt) cc_final: -0.0675 (pp-130) REVERT: D 97 ARG cc_start: 0.4620 (mmp80) cc_final: 0.3985 (mmp80) REVERT: D 129 THR cc_start: 0.1784 (OUTLIER) cc_final: 0.1331 (p) REVERT: D 130 GLU cc_start: 0.2981 (OUTLIER) cc_final: 0.2530 (pp20) REVERT: E 41 ARG cc_start: 0.2398 (ttm-80) cc_final: 0.1696 (mtm-85) REVERT: E 319 HIS cc_start: 0.1308 (m-70) cc_final: 0.0576 (m-70) REVERT: E 350 SER cc_start: 0.5632 (p) cc_final: 0.5089 (m) REVERT: E 399 ILE cc_start: 0.1386 (mt) cc_final: 0.1059 (mt) REVERT: E 467 ARG cc_start: 0.2928 (mtt90) cc_final: -0.0003 (tpt170) REVERT: C 255 LEU cc_start: 0.3320 (OUTLIER) cc_final: 0.2783 (pp) REVERT: C 308 ASN cc_start: -0.0119 (OUTLIER) cc_final: -0.1011 (m-40) REVERT: C 389 MET cc_start: -0.2310 (mmm) cc_final: -0.2671 (tmm) outliers start: 39 outliers final: 20 residues processed: 122 average time/residue: 0.4248 time to fit residues: 60.7759 Evaluate side-chains 118 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 329 LEU 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 375 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 247 PHE 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 255 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 308 ASN 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 197 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 108 optimal weight: 0.0000 chunk 222 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 32 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 314 HIS D 155 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN D 341 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 HIS ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** C 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.309870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.293292 restraints weight = 25207.811| |-----------------------------------------------------------------------------| r_work (start): 0.5040 rms_B_bonded: 1.89 r_work: 0.4992 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4893 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1816 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 18732 Z= 0.207 Angle : 0.757 9.699 25489 Z= 0.394 Chirality : 0.049 0.228 2753 Planarity : 0.006 0.061 3323 Dihedral : 5.933 27.429 2527 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.44 % Allowed : 13.43 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.16), residues: 2303 helix: -0.56 (0.35), residues: 191 sheet: -1.29 (0.20), residues: 599 loop : -1.40 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 71 TYR 0.031 0.003 TYR H 104 PHE 0.027 0.003 PHE A 330 TRP 0.023 0.002 TRP B 169 HIS 0.012 0.002 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00472 (18730) covalent geometry : angle 0.75697 (25485) SS BOND : bond 0.00820 ( 2) SS BOND : angle 1.94566 ( 4) hydrogen bonds : bond 0.03992 ( 252) hydrogen bonds : angle 6.67881 ( 642) *********************** 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 171 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 101 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3755 (pmm) cc_final: 0.1623 (mpp) REVERT: A 282 MET cc_start: 0.0410 (tmt) cc_final: -0.3384 (mmt) REVERT: A 371 TYR cc_start: 0.3775 (m-80) cc_final: 0.2394 (m-80) REVERT: A 395 MET cc_start: -0.0106 (ttp) cc_final: -0.1458 (ttp) REVERT: B 330 PHE cc_start: 0.3794 (m-80) cc_final: 0.3049 (m-80) REVERT: B 369 GLU cc_start: 0.3384 (mm-30) cc_final: 0.2619 (mm-30) REVERT: B 389 MET cc_start: 0.0795 (ttt) cc_final: -0.0562 (pp-130) REVERT: D 366 ARG cc_start: 0.3080 (mmt-90) cc_final: 0.0697 (ttm-80) REVERT: E 41 ARG cc_start: 0.3254 (ttm-80) cc_final: 0.2318 (mtp180) REVERT: E 50 PHE cc_start: 0.0722 (OUTLIER) cc_final: 0.0073 (p90) REVERT: E 99 VAL cc_start: -0.2555 (OUTLIER) cc_final: -0.2902 (t) REVERT: E 125 LYS cc_start: -0.0482 (OUTLIER) cc_final: -0.1619 (ptmm) REVERT: E 247 PHE cc_start: 0.3112 (OUTLIER) cc_final: 0.2580 (p90) REVERT: E 319 HIS cc_start: 0.1777 (m-70) cc_final: 0.1180 (m-70) REVERT: E 350 SER cc_start: 0.5292 (OUTLIER) cc_final: 0.4716 (m) REVERT: E 467 ARG cc_start: 0.3479 (mtt90) cc_final: -0.0004 (tpt-90) REVERT: C 255 LEU cc_start: 0.4153 (OUTLIER) cc_final: 0.3542 (pp) REVERT: C 282 MET cc_start: -0.1124 (OUTLIER) cc_final: -0.1542 (ptm) REVERT: C 389 MET cc_start: -0.1980 (mmm) cc_final: -0.2626 (mmm) outliers start: 70 outliers final: 35 residues processed: 154 average time/residue: 0.3860 time to fit residues: 69.9300 Evaluate side-chains 133 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 133 HIS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 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 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 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 442 TYR 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 210 PHE 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 350 SER Chi-restraints excluded: chain E residue 375 PHE 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 246 MET Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 282 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 32 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 168 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 355 GLN B 462 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS D 367 HIS ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** 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 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.310104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.292757 restraints weight = 25101.978| |-----------------------------------------------------------------------------| r_work (start): 0.5040 rms_B_bonded: 1.90 r_work: 0.4991 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4895 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1639 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18732 Z= 0.120 Angle : 0.601 9.532 25489 Z= 0.306 Chirality : 0.045 0.183 2753 Planarity : 0.004 0.054 3323 Dihedral : 5.225 22.576 2527 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 14.61 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.17), residues: 2303 helix: -0.50 (0.35), residues: 205 sheet: -1.26 (0.20), residues: 617 loop : -1.16 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 338 TYR 0.020 0.002 TYR D 442 PHE 0.015 0.002 PHE E 73 TRP 0.012 0.001 TRP D 169 HIS 0.010 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00273 (18730) covalent geometry : angle 0.60051 (25485) SS BOND : bond 0.00433 ( 2) SS BOND : angle 0.89082 ( 4) hydrogen bonds : bond 0.03353 ( 252) hydrogen bonds : angle 5.91071 ( 642) *********************** 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 141 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 90 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3501 (pmm) cc_final: 0.1456 (mpp) REVERT: A 282 MET cc_start: 0.0656 (tmt) cc_final: -0.3072 (mmt) REVERT: A 371 TYR cc_start: 0.3218 (m-80) cc_final: 0.2110 (m-80) REVERT: A 395 MET cc_start: -0.0233 (ttp) cc_final: -0.1640 (ttp) REVERT: B 246 MET cc_start: 0.3285 (mtp) cc_final: 0.3057 (mtp) REVERT: B 330 PHE cc_start: 0.3394 (m-80) cc_final: 0.2690 (m-80) REVERT: B 369 GLU cc_start: 0.3237 (mm-30) cc_final: 0.2855 (mm-30) REVERT: B 389 MET cc_start: 0.0940 (ttt) cc_final: -0.0497 (pp-130) REVERT: D 129 THR cc_start: 0.2090 (OUTLIER) cc_final: 0.1512 (p) REVERT: D 366 ARG cc_start: 0.3082 (mmt-90) cc_final: 0.0603 (ttm110) REVERT: E 319 HIS cc_start: 0.1558 (m-70) cc_final: 0.1104 (m-70) REVERT: E 350 SER cc_start: 0.5373 (OUTLIER) cc_final: 0.4771 (m) REVERT: E 464 PRO cc_start: 0.5285 (Cg_endo) cc_final: 0.5051 (Cg_exo) REVERT: E 467 ARG cc_start: 0.3255 (mtt90) cc_final: 0.0272 (tpp80) REVERT: C 255 LEU cc_start: 0.3668 (OUTLIER) cc_final: 0.3344 (pp) REVERT: C 389 MET cc_start: -0.1928 (mmm) cc_final: -0.2544 (mmm) outliers start: 51 outliers final: 39 residues processed: 127 average time/residue: 0.4184 time to fit residues: 62.3451 Evaluate side-chains 127 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 133 HIS Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 MET 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 450 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain D residue 44 THR 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 210 PHE Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 395 MET 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 237 MET Chi-restraints excluded: chain E residue 247 PHE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 375 PHE Chi-restraints excluded: chain E residue 399 ILE 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 235 LEU Chi-restraints excluded: chain C residue 255 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 185 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 199 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 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 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 = 0.5155 r_free = 0.5155 target = 0.309640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.291933 restraints weight = 25054.182| |-----------------------------------------------------------------------------| r_work (start): 0.5031 rms_B_bonded: 1.93 r_work: 0.4982 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4884 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1570 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18732 Z= 0.104 Angle : 0.561 8.943 25489 Z= 0.281 Chirality : 0.044 0.215 2753 Planarity : 0.004 0.046 3323 Dihedral : 4.846 21.335 2527 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.51 % Allowed : 14.85 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.17), residues: 2303 helix: -0.24 (0.37), residues: 199 sheet: -1.24 (0.20), residues: 634 loop : -1.07 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.016 0.001 TYR H 104 PHE 0.012 0.001 PHE D 122 TRP 0.015 0.001 TRP D 169 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00238 (18730) covalent geometry : angle 0.56129 (25485) SS BOND : bond 0.00412 ( 2) SS BOND : angle 0.72671 ( 4) hydrogen bonds : bond 0.03096 ( 252) hydrogen bonds : angle 5.53621 ( 642) *********************** 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 137 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 86 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3257 (pmm) cc_final: 0.1229 (mpp) REVERT: A 282 MET cc_start: 0.0420 (tmt) cc_final: -0.3050 (mmt) REVERT: A 371 TYR cc_start: 0.3065 (m-80) cc_final: 0.2108 (m-80) REVERT: A 395 MET cc_start: -0.0631 (ttp) cc_final: -0.1987 (ttp) REVERT: B 330 PHE cc_start: 0.3329 (m-80) cc_final: 0.2587 (m-80) REVERT: B 369 GLU cc_start: 0.2907 (mm-30) cc_final: 0.2565 (tp30) REVERT: B 389 MET cc_start: 0.0856 (ttt) cc_final: -0.0485 (pp-130) REVERT: D 129 THR cc_start: 0.2001 (OUTLIER) cc_final: 0.1453 (p) REVERT: D 366 ARG cc_start: 0.2726 (mmt-90) cc_final: 0.0568 (ttm-80) REVERT: E 319 HIS cc_start: 0.1397 (m-70) cc_final: 0.0941 (m-70) REVERT: E 467 ARG cc_start: 0.3076 (mtt90) cc_final: 0.0101 (tpp80) REVERT: C 255 LEU cc_start: 0.3509 (OUTLIER) cc_final: 0.3277 (pp) REVERT: C 389 MET cc_start: -0.1902 (mmm) cc_final: -0.2504 (mmm) REVERT: C 395 MET cc_start: -0.0917 (ptm) cc_final: -0.4554 (tpt) outliers start: 51 outliers final: 39 residues processed: 125 average time/residue: 0.3726 time to fit residues: 55.6253 Evaluate side-chains 125 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 64 SER 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 185 CYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 246 MET 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 450 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 44 THR 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 210 PHE Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 237 MET 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 375 PHE 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 216 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 324 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 62 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 178 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN 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 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 GLN ** C 36 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.309708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.293853 restraints weight = 25263.277| |-----------------------------------------------------------------------------| r_work (start): 0.5045 rms_B_bonded: 1.86 r_work: 0.4998 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4902 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1916 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18732 Z= 0.179 Angle : 0.708 10.064 25489 Z= 0.363 Chirality : 0.048 0.266 2753 Planarity : 0.005 0.055 3323 Dihedral : 5.654 25.804 2527 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.10 % Allowed : 14.31 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.17), residues: 2303 helix: -0.08 (0.38), residues: 183 sheet: -1.38 (0.21), residues: 583 loop : -1.38 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 109 TYR 0.033 0.002 TYR D 442 PHE 0.023 0.002 PHE B 50 TRP 0.023 0.002 TRP E 261 HIS 0.011 0.002 HIS C 367 Details of bonding type rmsd covalent geometry : bond 0.00409 (18730) covalent geometry : angle 0.70794 (25485) SS BOND : bond 0.00793 ( 2) SS BOND : angle 1.78744 ( 4) hydrogen bonds : bond 0.03762 ( 252) hydrogen bonds : angle 6.33499 ( 642) *********************** 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 157 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 40 LEU cc_start: 0.1319 (mt) cc_final: 0.1037 (mt) REVERT: A 267 MET cc_start: 0.3849 (pmm) cc_final: 0.1959 (mpp) REVERT: A 282 MET cc_start: 0.0083 (tmt) cc_final: -0.3220 (mmt) REVERT: A 371 TYR cc_start: 0.3419 (m-80) cc_final: 0.2259 (m-80) REVERT: B 330 PHE cc_start: 0.4007 (m-80) cc_final: 0.3082 (m-80) REVERT: B 371 TYR cc_start: 0.2620 (m-80) cc_final: 0.2355 (m-80) REVERT: B 389 MET cc_start: 0.0852 (ttt) cc_final: -0.0488 (pp-130) REVERT: D 44 THR cc_start: 0.2941 (OUTLIER) cc_final: 0.2590 (p) REVERT: D 366 ARG cc_start: 0.3203 (mmt-90) cc_final: 0.0708 (ttm110) REVERT: D 395 MET cc_start: 0.0125 (OUTLIER) cc_final: -0.2527 (tmt) REVERT: D 442 TYR cc_start: 0.4370 (m-80) cc_final: 0.3679 (m-10) REVERT: E 50 PHE cc_start: 0.1074 (OUTLIER) cc_final: 0.0600 (p90) REVERT: E 125 LYS cc_start: -0.0420 (OUTLIER) cc_final: -0.1196 (ptmm) REVERT: E 247 PHE cc_start: 0.3106 (OUTLIER) cc_final: 0.2368 (p90) REVERT: E 319 HIS cc_start: 0.1609 (m-70) cc_final: 0.1212 (m-70) REVERT: E 360 LYS cc_start: 0.0370 (OUTLIER) cc_final: 0.0011 (mmtm) REVERT: E 467 ARG cc_start: 0.3554 (mtt90) cc_final: 0.0228 (tpt-90) REVERT: C 389 MET cc_start: -0.1792 (OUTLIER) cc_final: -0.2564 (mmm) outliers start: 63 outliers final: 42 residues processed: 142 average time/residue: 0.3773 time to fit residues: 63.3352 Evaluate side-chains 138 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 89 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 MET 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 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 B residue 442 TYR Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 115 VAL 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 210 PHE Chi-restraints excluded: chain D residue 395 MET 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 237 MET 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 360 LYS Chi-restraints excluded: chain E residue 375 PHE 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 216 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 389 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 6 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- 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** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 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 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 = 0.5157 r_free = 0.5157 target = 0.310069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.294031 restraints weight = 25107.736| |-----------------------------------------------------------------------------| r_work (start): 0.5048 rms_B_bonded: 1.85 r_work: 0.5000 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4904 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1806 moved from start: 0.7503 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 : 0.606 10.361 25489 Z= 0.306 Chirality : 0.045 0.229 2753 Planarity : 0.004 0.050 3323 Dihedral : 5.250 24.706 2527 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.31 % Allowed : 15.45 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.17), residues: 2303 helix: 0.01 (0.38), residues: 183 sheet: -1.35 (0.20), residues: 602 loop : -1.27 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 109 TYR 0.026 0.002 TYR D 442 PHE 0.013 0.002 PHE E 73 TRP 0.015 0.001 TRP D 169 HIS 0.006 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00291 (18730) covalent geometry : angle 0.60603 (25485) SS BOND : bond 0.00543 ( 2) SS BOND : angle 1.02491 ( 4) hydrogen bonds : bond 0.03327 ( 252) hydrogen bonds : angle 5.96593 ( 642) ********************** 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 133 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.3539 (pmm) cc_final: 0.1720 (mpp) REVERT: A 282 MET cc_start: 0.0179 (tmt) cc_final: -0.3082 (mmt) REVERT: A 371 TYR cc_start: 0.3225 (m-80) cc_final: 0.2226 (m-80) REVERT: B 330 PHE cc_start: 0.3697 (m-80) cc_final: 0.2907 (m-80) REVERT: B 389 MET cc_start: 0.0709 (ttt) cc_final: -0.0634 (pp-130) REVERT: D 129 THR cc_start: 0.2193 (OUTLIER) cc_final: 0.1614 (p) REVERT: D 366 ARG cc_start: 0.3019 (mmt-90) cc_final: 0.0680 (ttm110) REVERT: D 395 MET cc_start: -0.0136 (OUTLIER) cc_final: -0.2424 (tmm) REVERT: E 247 PHE cc_start: 0.3153 (OUTLIER) cc_final: 0.2331 (p90) REVERT: E 282 MET cc_start: 0.2477 (tmt) cc_final: 0.1800 (tmm) REVERT: E 319 HIS cc_start: 0.1418 (m-70) cc_final: 0.1093 (m-70) REVERT: E 467 ARG cc_start: 0.3430 (mtt90) cc_final: 0.0238 (tpt-90) REVERT: C 389 MET cc_start: -0.1576 (OUTLIER) cc_final: -0.2307 (mmm) REVERT: C 395 MET cc_start: -0.0579 (ptm) cc_final: -0.4655 (tpt) outliers start: 47 outliers final: 35 residues processed: 122 average time/residue: 0.4127 time to fit residues: 59.5321 Evaluate side-chains 125 residues out of total 2033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 154 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 332 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain D residue 44 THR 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 210 PHE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 237 MET 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 C residue 115 VAL Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 389 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 171 optimal weight: 0.0270 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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** D 138 ASN ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.310034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.293687 restraints weight = 25118.177| |-----------------------------------------------------------------------------| r_work (start): 0.5046 rms_B_bonded: 1.85 r_work: 0.4997 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4900 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1718 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18732 Z= 0.107 Angle : 0.569 10.652 25489 Z= 0.283 Chirality : 0.044 0.216 2753 Planarity : 0.004 0.048 3323 Dihedral : 4.866 23.414 2527 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.21 % Allowed : 15.69 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.17), residues: 2303 helix: 0.28 (0.38), residues: 183 sheet: -1.14 (0.21), residues: 569 loop : -1.18 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 338 TYR 0.016 0.001 TYR H 104 PHE 0.011 0.001 PHE H 78 TRP 0.014 0.001 TRP D 169 HIS 0.007 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00245 (18730) covalent geometry : angle 0.56880 (25485) SS BOND : bond 0.00481 ( 2) SS BOND : angle 0.78161 ( 4) hydrogen bonds : bond 0.03002 ( 252) hydrogen bonds : angle 5.56250 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.28 seconds wall clock time: 89 minutes 57.59 seconds (5397.59 seconds total)