Starting phenix.real_space_refine on Sat Jul 4 07:26:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.cif" model { file = "/net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a4a_11630/07_2026/7a4a_11630.map" } resolution = 3.76 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 105 5.16 5 C 6294 2.51 5 N 1743 2.21 5 O 2025 1.98 5 H 9618 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19785 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6581 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 420} Chain: "B" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6581 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 420} Chain: "C" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6581 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 420} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.17 Number of scatterers: 19785 At special positions: 0 Unit cell: (86.901, 86.901, 134.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 O 2025 8.00 N 1743 7.00 C 6294 6.00 H 9618 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 1 " - pdb=" SG CYS A 41 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 23 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 138 " distance=2.04 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 41 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 23 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 138 " distance=2.04 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 373 " - pdb=" SG CYS B 404 " distance=2.03 Simple disulfide: pdb=" SG CYS C 1 " - pdb=" SG CYS C 41 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 23 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 138 " distance=2.04 Simple disulfide: pdb=" SG CYS C 246 " - pdb=" SG CYS C 257 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS C 408 " distance=2.03 Simple disulfide: pdb=" SG CYS C 347 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 382 " distance=2.03 Simple disulfide: pdb=" SG CYS C 373 " - pdb=" SG CYS C 404 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 414 " " NAG B 501 " - " ASN B 414 " " NAG C 501 " - " ASN C 414 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 639.1 milliseconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 33 sheets defined 4.8% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.094A pdb=" N SER A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.927A pdb=" N LEU A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 4.094A pdb=" N SER B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.928A pdb=" N LEU B 289 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 4.095A pdb=" N SER C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.928A pdb=" N LEU C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 4.028A pdb=" N ILE A 5 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS A 320 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 203 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 322 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE A 201 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.645A pdb=" N CYS A 14 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 331 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS C 41 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.645A pdb=" N CYS A 14 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 331 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS C 41 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 300 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 188 removed outlier: 3.568A pdb=" N VAL A 300 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 188 removed outlier: 6.095A pdb=" N CYS A 41 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 331 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N CYS B 14 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 330 " --> pdb=" O CYS B 14 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE B 16 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 332 " --> pdb=" O ILE B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 74 removed outlier: 5.793A pdb=" N ILE A 70 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR A 161 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 72 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 217 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 85 Processing sheet with id=AA8, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA9, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.575A pdb=" N THR A 276 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 433 " --> pdb=" O CYS A 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'A' and resid 369 through 372 Processing sheet with id=AB3, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AB4, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 9 removed outlier: 4.028A pdb=" N ILE B 5 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS B 320 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B 203 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL B 322 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE B 201 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 184 through 188 removed outlier: 3.568A pdb=" N VAL B 300 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 184 through 188 removed outlier: 6.095A pdb=" N CYS B 41 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 331 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N CYS C 14 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 330 " --> pdb=" O CYS C 14 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE C 16 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS B 332 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 74 removed outlier: 5.793A pdb=" N ILE B 70 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR B 161 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 72 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 217 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 77 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AC2, first strand: chain 'B' and resid 265 through 267 removed outlier: 3.575A pdb=" N THR B 276 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 433 " --> pdb=" O CYS B 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AC4, first strand: chain 'B' and resid 369 through 372 Processing sheet with id=AC5, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AC6, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 9 removed outlier: 4.027A pdb=" N ILE C 5 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS C 320 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU C 203 " --> pdb=" O HIS C 320 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL C 322 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE C 201 " --> pdb=" O VAL C 322 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 69 through 74 removed outlier: 5.793A pdb=" N ILE C 70 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR C 161 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 72 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 217 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 77 through 85 Processing sheet with id=AD1, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AD2, first strand: chain 'C' and resid 265 through 267 removed outlier: 3.574A pdb=" N THR C 276 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 433 " --> pdb=" O CYS C 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AD4, first strand: chain 'C' and resid 369 through 372 Processing sheet with id=AD5, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AD6, first strand: chain 'C' and resid 405 through 407 366 hydrogen bonds defined for protein. 861 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: 4.92 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9618 1.03 - 1.23: 170 1.23 - 1.43: 4112 1.43 - 1.63: 5960 1.63 - 1.82: 120 Bond restraints: 19980 Sorted by residual: bond pdb=" CA ASN A 67 " pdb=" CB ASN A 67 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.75e-02 3.27e+03 3.15e+00 bond pdb=" CA ASN B 67 " pdb=" CB ASN B 67 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.75e-02 3.27e+03 3.13e+00 bond pdb=" CA ASN C 67 " pdb=" CB ASN C 67 " ideal model delta sigma weight residual 1.527 1.496 0.030 1.75e-02 3.27e+03 3.00e+00 bond pdb=" CB ILE B 207 " pdb=" CG2 ILE B 207 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CB ILE C 207 " pdb=" CG2 ILE C 207 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 19975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 34340 1.37 - 2.74: 1513 2.74 - 4.11: 120 4.11 - 5.49: 9 5.49 - 6.86: 6 Bond angle restraints: 35988 Sorted by residual: angle pdb=" N LEU A 270 " pdb=" CA LEU A 270 " pdb=" CB LEU A 270 " ideal model delta sigma weight residual 114.17 110.47 3.70 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N LEU C 270 " pdb=" CA LEU C 270 " pdb=" CB LEU C 270 " ideal model delta sigma weight residual 114.17 110.50 3.67 1.14e+00 7.69e-01 1.04e+01 angle pdb=" N LEU B 270 " pdb=" CA LEU B 270 " pdb=" CB LEU B 270 " ideal model delta sigma weight residual 114.17 110.50 3.67 1.14e+00 7.69e-01 1.04e+01 angle pdb=" C TRP B 196 " pdb=" N ASN B 197 " pdb=" CA ASN B 197 " ideal model delta sigma weight residual 122.17 117.39 4.78 1.54e+00 4.22e-01 9.64e+00 angle pdb=" C TRP A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta sigma weight residual 122.17 117.39 4.78 1.54e+00 4.22e-01 9.62e+00 ... (remaining 35983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 8627 14.74 - 29.48: 723 29.48 - 44.22: 184 44.22 - 58.96: 105 58.96 - 73.70: 15 Dihedral angle restraints: 9654 sinusoidal: 5241 harmonic: 4413 Sorted by residual: dihedral pdb=" CA GLU C 71 " pdb=" C GLU C 71 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLU B 71 " pdb=" C GLU B 71 " pdb=" N PHE B 72 " pdb=" CA PHE B 72 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLU A 71 " pdb=" C GLU A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual 180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 9651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 889 0.030 - 0.059: 506 0.059 - 0.089: 187 0.089 - 0.119: 56 0.119 - 0.149: 21 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA PRO A 190 " pdb=" N PRO A 190 " pdb=" C PRO A 190 " pdb=" CB PRO A 190 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA PRO C 190 " pdb=" N PRO C 190 " pdb=" C PRO C 190 " pdb=" CB PRO C 190 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA PRO B 190 " pdb=" N PRO B 190 " pdb=" C PRO B 190 " pdb=" CB PRO B 190 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1656 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 211 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 212 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 211 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO B 212 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO C 212 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.039 5.00e-02 4.00e+02 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1021 2.17 - 2.78: 39337 2.78 - 3.38: 49624 3.38 - 3.99: 67698 3.99 - 4.60: 104566 Nonbonded interactions: 262246 Sorted by model distance: nonbonded pdb=" O LYS A 332 " pdb=" H ILE B 16 " model vdw 1.558 2.450 nonbonded pdb=" O LYS B 332 " pdb=" H ILE C 16 " model vdw 1.573 2.450 nonbonded pdb=" HH TYR C 120 " pdb=" O PHE C 259 " model vdw 1.593 2.450 nonbonded pdb=" HH TYR B 120 " pdb=" O PHE B 259 " model vdw 1.603 2.450 nonbonded pdb=" HH TYR A 120 " pdb=" O PHE A 259 " model vdw 1.610 2.450 ... (remaining 262241 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.530 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.007 0.055 10410 Z= 0.319 Angle : 0.716 6.857 14172 Z= 0.403 Chirality : 0.043 0.149 1659 Planarity : 0.006 0.073 1821 Dihedral : 11.654 73.698 3747 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 2.96 % Allowed : 7.19 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.00 (0.16), residues: 1311 helix: -4.78 (0.19), residues: 81 sheet: -3.30 (0.17), residues: 543 loop : -4.57 (0.16), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 381 TYR 0.008 0.001 TYR C 148 PHE 0.023 0.001 PHE B 72 TRP 0.005 0.001 TRP B 196 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.32 (10362) covalent geometry : angle 0.71005 / 0.40 (14073) SS BOND : bond 0.00337 / 0.21 ( 45) SS BOND : angle 1.35042 / 0.96 ( 90) hydrogen bonds : bond 0.10512 / 6.93 ( 332) hydrogen bonds : angle 8.19522 / 5.62 ( 861) link_NAG-ASN : bond 0.00308 / 0.15 ( 3) link_NAG-ASN : angle 0.93786 / 0.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.6805 (tp30) cc_final: 0.6570 (mt-10) REVERT: A 211 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9028 (pp) REVERT: B 211 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 308 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: C 211 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8971 (pp) outliers start: 35 outliers final: 11 residues processed: 295 average time/residue: 0.1979 time to fit residues: 84.7199 Evaluate side-chains 147 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 94 HIS A 318 GLN A 389 ASN B 37 GLN B 94 HIS B 318 GLN B 389 ASN C 37 GLN C 94 HIS C 318 GLN C 389 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111433 restraints weight = 38005.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116903 restraints weight = 17427.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118304 restraints weight = 9831.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118147 restraints weight = 8563.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118339 restraints weight = 8608.700| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10410 Z= 0.160 Angle : 0.710 8.523 14172 Z= 0.376 Chirality : 0.045 0.165 1659 Planarity : 0.005 0.060 1821 Dihedral : 8.137 48.381 1413 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 3.30 % Allowed : 14.89 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.18), residues: 1311 helix: -3.98 (0.32), residues: 81 sheet: -2.80 (0.19), residues: 492 loop : -4.02 (0.17), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 381 TYR 0.008 0.001 TYR B 348 PHE 0.023 0.002 PHE B 72 TRP 0.004 0.001 TRP A 165 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (10362) covalent geometry : angle 0.68765 / 0.37 (14073) SS BOND : bond 0.00839 / 0.63 ( 45) SS BOND : angle 2.30073 / 1.53 ( 90) hydrogen bonds : bond 0.03661 / 2.41 ( 332) hydrogen bonds : angle 7.39462 / 5.06 ( 861) link_NAG-ASN : bond 0.00177 / 0.09 ( 3) link_NAG-ASN : angle 0.71514 / 0.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7049 (tp30) cc_final: 0.6770 (mt-10) REVERT: A 144 PHE cc_start: 0.7511 (m-10) cc_final: 0.6936 (m-80) REVERT: A 286 MET cc_start: 0.8228 (mtp) cc_final: 0.7934 (mtp) REVERT: B 214 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8465 (mp) outliers start: 39 outliers final: 21 residues processed: 184 average time/residue: 0.1339 time to fit residues: 41.4984 Evaluate side-chains 152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS A 333 HIS A 389 ASN B 285 HIS B 389 ASN C 235 GLN C 285 HIS C 333 HIS C 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107699 restraints weight = 38133.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111486 restraints weight = 19784.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113051 restraints weight = 11213.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113200 restraints weight = 9545.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113384 restraints weight = 9000.322| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 10410 Z= 0.216 Angle : 0.726 15.571 14172 Z= 0.383 Chirality : 0.046 0.253 1659 Planarity : 0.005 0.055 1821 Dihedral : 7.713 50.982 1407 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 3.38 % Allowed : 14.81 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.18), residues: 1311 helix: -3.46 (0.45), residues: 63 sheet: -2.36 (0.19), residues: 549 loop : -3.88 (0.17), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 381 TYR 0.017 0.002 TYR C 148 PHE 0.021 0.002 PHE A 72 TRP 0.004 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (10362) covalent geometry : angle 0.70508 / 0.37 (14073) SS BOND : bond 0.01167 / 0.91 ( 45) SS BOND : angle 2.28519 / 1.45 ( 90) hydrogen bonds : bond 0.03961 / 2.58 ( 332) hydrogen bonds : angle 6.72273 / 4.57 ( 861) link_NAG-ASN : bond 0.00170 / 0.08 ( 3) link_NAG-ASN : angle 0.89452 / 0.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.6971 (tp30) cc_final: 0.6707 (mt-10) REVERT: B 181 THR cc_start: 0.9164 (m) cc_final: 0.8951 (p) REVERT: C 181 THR cc_start: 0.9132 (m) cc_final: 0.8849 (p) REVERT: C 433 TYR cc_start: 0.7642 (t80) cc_final: 0.7332 (t80) outliers start: 40 outliers final: 30 residues processed: 174 average time/residue: 0.1339 time to fit residues: 39.4635 Evaluate side-chains 152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 9 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108515 restraints weight = 38352.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113861 restraints weight = 20064.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114518 restraints weight = 11104.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114719 restraints weight = 8975.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114734 restraints weight = 8878.741| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 10410 Z= 0.176 Angle : 0.695 14.771 14172 Z= 0.365 Chirality : 0.046 0.221 1659 Planarity : 0.004 0.054 1821 Dihedral : 7.297 48.784 1405 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 2.79 % Allowed : 15.91 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.18), residues: 1311 helix: -3.27 (0.49), residues: 63 sheet: -2.10 (0.20), residues: 516 loop : -3.71 (0.17), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 381 TYR 0.008 0.001 TYR A 161 PHE 0.020 0.001 PHE A 72 TRP 0.003 0.001 TRP A 165 HIS 0.028 0.002 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (10362) covalent geometry : angle 0.67520 / 0.36 (14073) SS BOND : bond 0.00970 / 0.73 ( 45) SS BOND : angle 2.16896 / 1.43 ( 90) hydrogen bonds : bond 0.03680 / 2.38 ( 332) hydrogen bonds : angle 6.52267 / 4.45 ( 861) link_NAG-ASN : bond 0.00164 / 0.08 ( 3) link_NAG-ASN : angle 0.71756 / 0.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8234 (mm110) REVERT: A 109 GLU cc_start: 0.7094 (tp30) cc_final: 0.6695 (mt-10) REVERT: A 181 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8843 (p) REVERT: B 181 THR cc_start: 0.9174 (m) cc_final: 0.8899 (p) REVERT: C 181 THR cc_start: 0.9112 (m) cc_final: 0.8842 (p) outliers start: 33 outliers final: 25 residues processed: 167 average time/residue: 0.1372 time to fit residues: 37.9329 Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 123 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107630 restraints weight = 38218.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111625 restraints weight = 20484.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112791 restraints weight = 11664.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113127 restraints weight = 9413.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113546 restraints weight = 8966.933| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10410 Z= 0.179 Angle : 0.691 18.757 14172 Z= 0.362 Chirality : 0.046 0.274 1659 Planarity : 0.004 0.052 1821 Dihedral : 7.135 50.628 1405 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % Rotamer: Outliers : 3.38 % Allowed : 17.26 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.19), residues: 1311 helix: -3.08 (0.52), residues: 63 sheet: -2.04 (0.20), residues: 522 loop : -3.57 (0.17), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 381 TYR 0.013 0.001 TYR C 148 PHE 0.018 0.002 PHE C 144 TRP 0.004 0.001 TRP A 165 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (10362) covalent geometry : angle 0.67079 / 0.35 (14073) SS BOND : bond 0.00875 / 0.66 ( 45) SS BOND : angle 2.20143 / 1.38 ( 90) hydrogen bonds : bond 0.03678 / 2.38 ( 332) hydrogen bonds : angle 6.43083 / 4.41 ( 861) link_NAG-ASN : bond 0.00175 / 0.08 ( 3) link_NAG-ASN : angle 0.76759 / 0.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8262 (mm110) REVERT: A 181 THR cc_start: 0.9143 (m) cc_final: 0.8935 (p) REVERT: B 38 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8103 (mm110) REVERT: B 181 THR cc_start: 0.9217 (m) cc_final: 0.9005 (p) outliers start: 40 outliers final: 29 residues processed: 172 average time/residue: 0.1344 time to fit residues: 38.4088 Evaluate side-chains 152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108656 restraints weight = 38180.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112558 restraints weight = 19363.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114232 restraints weight = 10962.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114304 restraints weight = 9329.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114481 restraints weight = 8817.731| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10410 Z= 0.152 Angle : 0.698 19.655 14172 Z= 0.363 Chirality : 0.046 0.265 1659 Planarity : 0.004 0.050 1821 Dihedral : 7.013 50.158 1405 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 3.47 % Allowed : 18.10 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.19), residues: 1311 helix: -2.86 (0.55), residues: 63 sheet: -1.77 (0.22), residues: 480 loop : -3.40 (0.17), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 381 TYR 0.014 0.001 TYR A 148 PHE 0.019 0.001 PHE C 72 TRP 0.003 0.001 TRP A 196 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (10362) covalent geometry : angle 0.67463 / 0.35 (14073) SS BOND : bond 0.00958 / 0.71 ( 45) SS BOND : angle 2.32913 / 1.46 ( 90) hydrogen bonds : bond 0.03636 / 2.34 ( 332) hydrogen bonds : angle 6.35478 / 4.35 ( 861) link_NAG-ASN : bond 0.00165 / 0.08 ( 3) link_NAG-ASN : angle 0.70413 / 0.40 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (mm110) REVERT: A 412 ILE cc_start: 0.9141 (pt) cc_final: 0.8853 (mt) REVERT: B 38 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7979 (mm110) REVERT: B 42 LEU cc_start: 0.9032 (mt) cc_final: 0.8814 (mp) REVERT: B 181 THR cc_start: 0.9251 (m) cc_final: 0.9036 (p) outliers start: 41 outliers final: 33 residues processed: 164 average time/residue: 0.1343 time to fit residues: 37.1320 Evaluate side-chains 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108052 restraints weight = 38782.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111266 restraints weight = 23483.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112978 restraints weight = 13601.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112925 restraints weight = 11044.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113024 restraints weight = 10472.255| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10410 Z= 0.186 Angle : 0.754 26.725 14172 Z= 0.391 Chirality : 0.047 0.346 1659 Planarity : 0.004 0.051 1821 Dihedral : 7.043 51.396 1405 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 3.72 % Allowed : 18.44 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.19), residues: 1311 helix: -3.30 (0.45), residues: 81 sheet: -1.72 (0.21), residues: 522 loop : -3.54 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 381 TYR 0.012 0.001 TYR C 148 PHE 0.016 0.001 PHE B 72 TRP 0.004 0.001 TRP C 165 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (10362) covalent geometry : angle 0.72589 / 0.38 (14073) SS BOND : bond 0.01035 / 0.79 ( 45) SS BOND : angle 2.65664 / 1.72 ( 90) hydrogen bonds : bond 0.03927 / 2.54 ( 332) hydrogen bonds : angle 6.30790 / 4.30 ( 861) link_NAG-ASN : bond 0.00171 / 0.08 ( 3) link_NAG-ASN : angle 0.82577 / 0.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8213 (mm110) REVERT: A 412 ILE cc_start: 0.9146 (pt) cc_final: 0.8883 (mt) REVERT: B 38 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8071 (mm110) REVERT: B 42 LEU cc_start: 0.9100 (mt) cc_final: 0.8849 (mp) outliers start: 44 outliers final: 38 residues processed: 166 average time/residue: 0.1354 time to fit residues: 37.1466 Evaluate side-chains 160 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 97 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105437 restraints weight = 38701.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108110 restraints weight = 21080.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109487 restraints weight = 12572.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109753 restraints weight = 10449.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110137 restraints weight = 9583.944| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10410 Z= 0.229 Angle : 0.747 17.264 14172 Z= 0.394 Chirality : 0.047 0.299 1659 Planarity : 0.005 0.052 1821 Dihedral : 7.129 51.585 1405 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 4.48 % Allowed : 18.19 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.20), residues: 1311 helix: -3.68 (0.36), residues: 99 sheet: -1.72 (0.21), residues: 513 loop : -3.45 (0.18), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 381 TYR 0.012 0.001 TYR A 148 PHE 0.019 0.002 PHE B 72 TRP 0.005 0.001 TRP C 165 HIS 0.012 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (10362) covalent geometry : angle 0.71709 / 0.38 (14073) SS BOND : bond 0.00852 / 0.64 ( 45) SS BOND : angle 2.72561 / 1.78 ( 90) hydrogen bonds : bond 0.04104 / 2.66 ( 332) hydrogen bonds : angle 6.32105 / 4.31 ( 861) link_NAG-ASN : bond 0.00179 / 0.09 ( 3) link_NAG-ASN : angle 1.02912 / 0.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8273 (mm110) REVERT: A 412 ILE cc_start: 0.9161 (pt) cc_final: 0.8892 (mt) REVERT: B 38 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8155 (mm110) REVERT: B 42 LEU cc_start: 0.9043 (mt) cc_final: 0.8810 (mp) outliers start: 53 outliers final: 39 residues processed: 155 average time/residue: 0.1301 time to fit residues: 33.9654 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107237 restraints weight = 37947.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112199 restraints weight = 17810.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113615 restraints weight = 10482.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113573 restraints weight = 8846.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113782 restraints weight = 8777.650| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10410 Z= 0.140 Angle : 0.705 16.243 14172 Z= 0.368 Chirality : 0.047 0.411 1659 Planarity : 0.004 0.051 1821 Dihedral : 6.659 49.584 1403 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 3.30 % Allowed : 19.46 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.20), residues: 1311 helix: -3.07 (0.48), residues: 81 sheet: -1.39 (0.22), residues: 507 loop : -3.31 (0.19), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.014 0.001 TYR C 148 PHE 0.016 0.001 PHE B 72 TRP 0.003 0.001 TRP C 196 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10362) covalent geometry : angle 0.67362 / 0.35 (14073) SS BOND : bond 0.00912 / 0.70 ( 45) SS BOND : angle 2.69163 / 1.68 ( 90) hydrogen bonds : bond 0.03704 / 2.42 ( 332) hydrogen bonds : angle 6.19149 / 4.24 ( 861) link_NAG-ASN : bond 0.00200 / 0.10 ( 3) link_NAG-ASN : angle 0.75008 / 0.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8930 (pp) REVERT: A 412 ILE cc_start: 0.9096 (pt) cc_final: 0.8873 (mt) REVERT: B 38 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7931 (mm110) REVERT: C 56 THR cc_start: 0.8754 (m) cc_final: 0.8512 (p) REVERT: C 412 ILE cc_start: 0.9007 (pt) cc_final: 0.8661 (mt) REVERT: C 433 TYR cc_start: 0.7486 (t80) cc_final: 0.7175 (t80) outliers start: 39 outliers final: 29 residues processed: 161 average time/residue: 0.1429 time to fit residues: 37.3559 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 102 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105642 restraints weight = 38790.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108321 restraints weight = 21205.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109821 restraints weight = 12988.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110402 restraints weight = 10157.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110297 restraints weight = 9739.224| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10410 Z= 0.207 Angle : 0.743 16.955 14172 Z= 0.392 Chirality : 0.048 0.394 1659 Planarity : 0.004 0.050 1821 Dihedral : 6.848 50.874 1403 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 3.05 % Allowed : 19.88 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.20), residues: 1311 helix: -3.18 (0.46), residues: 81 sheet: -1.49 (0.21), residues: 552 loop : -3.39 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 381 TYR 0.014 0.002 TYR A 161 PHE 0.018 0.002 PHE A 72 TRP 0.005 0.001 TRP C 165 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (10362) covalent geometry : angle 0.71286 / 0.38 (14073) SS BOND : bond 0.01077 / 0.80 ( 45) SS BOND : angle 2.71345 / 1.70 ( 90) hydrogen bonds : bond 0.04033 / 2.64 ( 332) hydrogen bonds : angle 6.19085 / 4.22 ( 861) link_NAG-ASN : bond 0.00163 / 0.08 ( 3) link_NAG-ASN : angle 1.02331 / 0.56 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue SER 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9021 (pp) REVERT: A 412 ILE cc_start: 0.9158 (pt) cc_final: 0.8903 (mt) REVERT: B 38 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8122 (mm110) REVERT: B 412 ILE cc_start: 0.9177 (pt) cc_final: 0.8831 (mt) REVERT: C 56 THR cc_start: 0.8817 (m) cc_final: 0.8574 (p) REVERT: C 433 TYR cc_start: 0.7483 (t80) cc_final: 0.7197 (t80) outliers start: 36 outliers final: 30 residues processed: 143 average time/residue: 0.1374 time to fit residues: 33.3458 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107476 restraints weight = 38502.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111164 restraints weight = 18872.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112334 restraints weight = 11448.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112583 restraints weight = 9375.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112899 restraints weight = 8843.901| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10410 Z= 0.156 Angle : 0.719 17.930 14172 Z= 0.376 Chirality : 0.047 0.410 1659 Planarity : 0.004 0.050 1821 Dihedral : 6.701 51.026 1403 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 3.05 % Allowed : 19.97 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.21), residues: 1311 helix: -3.04 (0.48), residues: 81 sheet: -1.37 (0.22), residues: 552 loop : -3.34 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.013 0.001 TYR B 148 PHE 0.018 0.001 PHE A 72 TRP 0.003 0.001 TRP A 165 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (10362) covalent geometry : angle 0.69012 / 0.36 (14073) SS BOND : bond 0.01029 / 0.78 ( 45) SS BOND : angle 2.61631 / 1.67 ( 90) hydrogen bonds : bond 0.03925 / 2.57 ( 332) hydrogen bonds : angle 6.17112 / 4.22 ( 861) link_NAG-ASN : bond 0.00175 / 0.08 ( 3) link_NAG-ASN : angle 0.67285 / 0.38 ( 9) =============================================================================== Job complete usr+sys time: 2941.92 seconds wall clock time: 51 minutes 6.84 seconds (3066.84 seconds total)