Starting phenix.real_space_refine on Thu Mar 5 04:41:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a4a_11630/03_2026/7a4a_11630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a4a_11630/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7a4a_11630/03_2026/7a4a_11630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a4a_11630/03_2026/7a4a_11630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a4a_11630/03_2026/7a4a_11630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a4a_11630/03_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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.41, 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: 1.26 Conformation dependent library (CDL) restraints added in 585.7 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: 0.54 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: 4.41 Time building geometry restraints manager: 1.96 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: 8684 14.74 - 29.48: 723 29.48 - 44.22: 184 44.22 - 58.96: 111 58.96 - 73.70: 15 Dihedral angle restraints: 9717 sinusoidal: 5304 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 9714 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: 0.03 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: 0.710 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 11.730 73.698 3810 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 covalent geometry : bond 0.00747 (10362) covalent geometry : angle 0.71005 (14073) SS BOND : bond 0.00337 ( 45) SS BOND : angle 1.35042 ( 90) hydrogen bonds : bond 0.10512 ( 332) hydrogen bonds : angle 8.19522 ( 861) link_NAG-ASN : bond 0.00308 ( 3) link_NAG-ASN : angle 0.93786 ( 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 : 0.411 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: 0.1985 time to fit residues: 83.7335 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 : 0.444 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.156918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111455 restraints weight = 38005.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117074 restraints weight = 17465.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118439 restraints weight = 9769.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118259 restraints weight = 8487.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118410 restraints weight = 8536.226| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10410 Z= 0.154 Angle : 0.717 8.987 14172 Z= 0.379 Chirality : 0.045 0.166 1659 Planarity : 0.005 0.060 1821 Dihedral : 8.246 48.394 1476 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 3.13 % Allowed : 15.23 % Favored : 81.64 % 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 (0.17), residues: 1311 helix: -3.97 (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 0.009 0.001 TYR B 348 PHE 0.023 0.002 PHE B 72 TRP 0.003 0.001 TRP A 196 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00361 (10362) covalent geometry : angle 0.68925 (14073) SS BOND : bond 0.00980 ( 45) SS BOND : angle 2.56161 ( 90) hydrogen bonds : bond 0.03689 ( 332) hydrogen bonds : angle 7.38170 ( 861) link_NAG-ASN : bond 0.00125 ( 3) link_NAG-ASN : angle 0.73538 ( 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 190 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.353 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: 0.7044 (tp30) cc_final: 0.6769 (mt-10) REVERT: A 144 PHE cc_start: 0.7516 (m-10) cc_final: 0.6935 (m-80) REVERT: A 286 MET cc_start: 0.8212 (mtp) cc_final: 0.7911 (mtp) REVERT: B 214 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8484 (mp) outliers start: 37 outliers final: 20 residues processed: 184 average time/residue: 0.1292 time to fit residues: 40.1444 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS A 333 HIS A 389 ASN B 285 HIS B 389 ASN C 333 HIS C 389 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109240 restraints weight = 37798.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115352 restraints weight = 17145.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116350 restraints weight = 9519.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116217 restraints weight = 8344.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116434 restraints weight = 8459.096| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 10410 Z= 0.166 Angle : 0.700 15.254 14172 Z= 0.368 Chirality : 0.046 0.242 1659 Planarity : 0.004 0.052 1821 Dihedral : 7.449 52.162 1470 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 2.71 % Allowed : 15.14 % Favored : 82.15 % 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: -4.63 (0.19), residues: 1311 helix: -3.29 (0.48), residues: 63 sheet: -2.29 (0.19), residues: 549 loop : -3.82 (0.17), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 381 TYR 0.014 0.001 TYR C 148 PHE 0.019 0.001 PHE A 72 TRP 0.004 0.001 TRP A 165 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00406 (10362) covalent geometry : angle 0.68043 (14073) SS BOND : bond 0.01030 ( 45) SS BOND : angle 2.16939 ( 90) hydrogen bonds : bond 0.03785 ( 332) hydrogen bonds : angle 6.74868 ( 861) link_NAG-ASN : bond 0.00145 ( 3) link_NAG-ASN : angle 0.76113 ( 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 180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.405 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 144 PHE cc_start: 0.7524 (m-10) cc_final: 0.7092 (m-80) REVERT: B 181 THR cc_start: 0.9121 (m) cc_final: 0.8827 (p) REVERT: C 181 THR cc_start: 0.9091 (m) cc_final: 0.8786 (p) outliers start: 32 outliers final: 27 residues processed: 176 average time/residue: 0.1369 time to fit residues: 40.2783 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 A residue 405 THR 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 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 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: 3.9990 chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 53 optimal weight: 0.0040 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS C 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107398 restraints weight = 38232.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113261 restraints weight = 17565.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114241 restraints weight = 9726.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114132 restraints weight = 8562.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114322 restraints weight = 8512.612| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10410 Z= 0.180 Angle : 0.695 14.894 14172 Z= 0.364 Chirality : 0.046 0.221 1659 Planarity : 0.004 0.053 1821 Dihedral : 7.095 48.583 1468 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.39 (0.19), residues: 1311 helix: -3.17 (0.51), residues: 63 sheet: -2.16 (0.21), residues: 489 loop : -3.56 (0.17), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 381 TYR 0.008 0.001 TYR C 433 PHE 0.019 0.002 PHE A 72 TRP 0.004 0.001 TRP A 165 HIS 0.020 0.002 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00441 (10362) covalent geometry : angle 0.67480 (14073) SS BOND : bond 0.00770 ( 45) SS BOND : angle 2.17537 ( 90) hydrogen bonds : bond 0.03667 ( 332) hydrogen bonds : angle 6.53712 ( 861) link_NAG-ASN : bond 0.00161 ( 3) link_NAG-ASN : angle 0.89155 ( 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 168 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.383 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 18 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7823 (pp20) REVERT: A 38 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8245 (mm110) REVERT: A 181 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8788 (p) REVERT: A 389 ASN cc_start: 0.7339 (m110) cc_final: 0.7115 (m-40) REVERT: B 181 THR cc_start: 0.9137 (m) cc_final: 0.8882 (p) REVERT: C 181 THR cc_start: 0.9125 (m) cc_final: 0.8850 (p) outliers start: 34 outliers final: 27 residues processed: 164 average time/residue: 0.1289 time to fit residues: 35.9023 Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 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 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 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: 1.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN C 99 HIS C 235 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108040 restraints weight = 38080.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110880 restraints weight = 21038.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112868 restraints weight = 12985.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113108 restraints weight = 10191.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113176 restraints weight = 9345.669| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10410 Z= 0.185 Angle : 0.695 21.365 14172 Z= 0.363 Chirality : 0.046 0.255 1659 Planarity : 0.004 0.052 1821 Dihedral : 7.019 50.352 1468 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 3.13 % Allowed : 17.17 % Favored : 79.70 % 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: -4.28 (0.19), residues: 1311 helix: -3.05 (0.52), residues: 63 sheet: -2.02 (0.20), residues: 516 loop : -3.57 (0.17), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.013 0.001 TYR C 148 PHE 0.021 0.002 PHE C 72 TRP 0.005 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00439 (10362) covalent geometry : angle 0.67387 (14073) SS BOND : bond 0.00912 ( 45) SS BOND : angle 2.20646 ( 90) hydrogen bonds : bond 0.03648 ( 332) hydrogen bonds : angle 6.44029 ( 861) link_NAG-ASN : bond 0.00188 ( 3) link_NAG-ASN : angle 0.94057 ( 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 170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.418 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 18 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7781 (pp20) REVERT: A 38 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8251 (mm110) REVERT: A 181 THR cc_start: 0.9137 (m) cc_final: 0.8927 (p) REVERT: B 38 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8119 (mm110) REVERT: B 42 LEU cc_start: 0.9053 (mt) cc_final: 0.8808 (mp) outliers start: 37 outliers final: 28 residues processed: 166 average time/residue: 0.1313 time to fit residues: 36.9512 Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 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 350 CYS 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 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 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 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: 0.9990 chunk 80 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107161 restraints weight = 38140.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112780 restraints weight = 17833.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114054 restraints weight = 10056.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113874 restraints weight = 8716.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114150 restraints weight = 8676.110| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3998 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= 0.151 Angle : 0.694 19.013 14172 Z= 0.362 Chirality : 0.046 0.291 1659 Planarity : 0.004 0.051 1821 Dihedral : 6.890 50.094 1468 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 3.47 % Allowed : 18.19 % Favored : 78.34 % 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: -4.13 (0.19), residues: 1311 helix: -3.28 (0.44), residues: 81 sheet: -1.77 (0.20), residues: 546 loop : -3.61 (0.18), residues: 684 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 0.017 0.001 PHE C 72 TRP 0.003 0.001 TRP A 165 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00361 (10362) covalent geometry : angle 0.67011 (14073) SS BOND : bond 0.00926 ( 45) SS BOND : angle 2.35511 ( 90) hydrogen bonds : bond 0.03603 ( 332) hydrogen bonds : angle 6.33072 ( 861) link_NAG-ASN : bond 0.00191 ( 3) link_NAG-ASN : angle 0.78727 ( 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 176 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.405 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: A 18 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7873 (pp20) REVERT: A 38 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8188 (mm110) REVERT: A 412 ILE cc_start: 0.9137 (pt) cc_final: 0.8861 (mt) REVERT: B 38 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7974 (mm110) REVERT: B 42 LEU cc_start: 0.9016 (mt) cc_final: 0.8806 (mp) outliers start: 41 outliers final: 33 residues processed: 168 average time/residue: 0.1346 time to fit residues: 37.1820 Evaluate side-chains 152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 275 CYS Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 350 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 193 THR 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 70 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: 3.9990 chunk 20 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110602 restraints weight = 38403.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113393 restraints weight = 21524.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114979 restraints weight = 13048.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115349 restraints weight = 10913.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115374 restraints weight = 10723.144| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10410 Z= 0.135 Angle : 0.682 18.636 14172 Z= 0.356 Chirality : 0.046 0.236 1659 Planarity : 0.004 0.049 1821 Dihedral : 6.730 49.936 1468 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 3.13 % Allowed : 18.87 % Favored : 78.00 % 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: -3.84 (0.19), residues: 1311 helix: -3.12 (0.46), residues: 81 sheet: -1.49 (0.22), residues: 465 loop : -3.34 (0.17), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 187 TYR 0.013 0.001 TYR C 148 PHE 0.014 0.001 PHE C 72 TRP 0.003 0.001 TRP A 165 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00330 (10362) covalent geometry : angle 0.65742 (14073) SS BOND : bond 0.00781 ( 45) SS BOND : angle 2.36992 ( 90) hydrogen bonds : bond 0.03657 ( 332) hydrogen bonds : angle 6.24909 ( 861) link_NAG-ASN : bond 0.00196 ( 3) link_NAG-ASN : angle 0.74185 ( 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 162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.602 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: A 18 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (pp20) REVERT: A 412 ILE cc_start: 0.9085 (pt) cc_final: 0.8860 (mt) REVERT: B 38 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7814 (mm110) REVERT: B 42 LEU cc_start: 0.9074 (mt) cc_final: 0.8859 (mp) outliers start: 37 outliers final: 31 residues processed: 153 average time/residue: 0.1452 time to fit residues: 36.2666 Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 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 350 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 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 79 ILE Chi-restraints excluded: chain C residue 99 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3791 r_free = 0.3791 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106065 restraints weight = 38704.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110363 restraints weight = 19665.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111843 restraints weight = 10988.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111910 restraints weight = 9513.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111901 restraints weight = 9541.968| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10410 Z= 0.215 Angle : 0.776 30.859 14172 Z= 0.404 Chirality : 0.048 0.427 1659 Planarity : 0.004 0.051 1821 Dihedral : 6.949 53.406 1468 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 3.72 % Allowed : 18.36 % Favored : 77.92 % 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: -3.93 (0.20), residues: 1311 helix: -3.57 (0.37), residues: 99 sheet: -1.52 (0.21), residues: 531 loop : -3.46 (0.19), residues: 681 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 0.018 0.002 PHE B 72 TRP 0.006 0.001 TRP C 165 HIS 0.015 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00501 (10362) covalent geometry : angle 0.74877 (14073) SS BOND : bond 0.01045 ( 45) SS BOND : angle 2.66263 ( 90) hydrogen bonds : bond 0.04067 ( 332) hydrogen bonds : angle 6.24729 ( 861) link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 1.17636 ( 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 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 0.467 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 18 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: A 412 ILE cc_start: 0.9136 (pt) cc_final: 0.8858 (mt) REVERT: B 38 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8128 (mm110) REVERT: B 42 LEU cc_start: 0.9027 (mt) cc_final: 0.8803 (mp) REVERT: C 56 THR cc_start: 0.8866 (m) cc_final: 0.8609 (p) outliers start: 44 outliers final: 35 residues processed: 150 average time/residue: 0.1305 time to fit residues: 33.1637 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 9 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3824 r_free = 0.3824 target = 0.152780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.107696 restraints weight = 37980.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113166 restraints weight = 17437.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114216 restraints weight = 10434.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114215 restraints weight = 8828.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114527 restraints weight = 8656.906| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10410 Z= 0.136 Angle : 0.707 17.381 14172 Z= 0.368 Chirality : 0.047 0.356 1659 Planarity : 0.004 0.050 1821 Dihedral : 6.749 50.288 1468 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 2.88 % Allowed : 19.54 % Favored : 77.58 % 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: -3.66 (0.20), residues: 1311 helix: -3.01 (0.48), residues: 81 sheet: -1.24 (0.23), residues: 465 loop : -3.30 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.012 0.001 TYR B 148 PHE 0.016 0.001 PHE B 72 TRP 0.003 0.001 TRP A 196 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00320 (10362) covalent geometry : angle 0.67814 (14073) SS BOND : bond 0.00899 ( 45) SS BOND : angle 2.57935 ( 90) hydrogen bonds : bond 0.03788 ( 332) hydrogen bonds : angle 6.16643 ( 861) link_NAG-ASN : bond 0.00195 ( 3) link_NAG-ASN : angle 0.75989 ( 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 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.385 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 412 ILE cc_start: 0.9090 (pt) cc_final: 0.8844 (mt) REVERT: B 38 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8018 (mm110) REVERT: B 412 ILE cc_start: 0.9123 (pt) cc_final: 0.8776 (mt) REVERT: C 56 THR cc_start: 0.8800 (m) cc_final: 0.8540 (p) outliers start: 34 outliers final: 30 residues processed: 149 average time/residue: 0.1423 time to fit residues: 35.2385 Evaluate side-chains 149 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 264 CYS Chi-restraints excluded: chain A residue 275 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 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 360 CYS Chi-restraints excluded: chain B residue 367 VAL 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 68 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3823 r_free = 0.3823 target = 0.152741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107775 restraints weight = 38480.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113184 restraints weight = 17733.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114444 restraints weight = 10455.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114393 restraints weight = 8858.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114549 restraints weight = 8790.741| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10410 Z= 0.148 Angle : 0.713 20.711 14172 Z= 0.372 Chirality : 0.047 0.418 1659 Planarity : 0.004 0.049 1821 Dihedral : 6.584 51.151 1468 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.62 % Allowed : 19.88 % Favored : 77.50 % 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: -3.55 (0.21), residues: 1311 helix: -2.91 (0.48), residues: 81 sheet: -1.34 (0.22), residues: 552 loop : -3.25 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.017 0.001 TYR A 148 PHE 0.014 0.001 PHE B 72 TRP 0.003 0.001 TRP A 196 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00351 (10362) covalent geometry : angle 0.68197 (14073) SS BOND : bond 0.00975 ( 45) SS BOND : angle 2.69666 ( 90) hydrogen bonds : bond 0.03804 ( 332) hydrogen bonds : angle 6.07685 ( 861) link_NAG-ASN : bond 0.00198 ( 3) link_NAG-ASN : angle 0.84789 ( 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 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.546 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 412 ILE cc_start: 0.9080 (pt) cc_final: 0.8846 (mt) REVERT: B 38 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7980 (mm110) REVERT: B 412 ILE cc_start: 0.9113 (pt) cc_final: 0.8763 (mt) outliers start: 31 outliers final: 29 residues processed: 150 average time/residue: 0.1365 time to fit residues: 34.6980 Evaluate side-chains 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 264 CYS Chi-restraints excluded: chain A residue 275 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 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 360 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 72 PHE 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: 3.9990 chunk 120 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106296 restraints weight = 38493.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110558 restraints weight = 18003.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111893 restraints weight = 10850.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111934 restraints weight = 9463.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112074 restraints weight = 9194.829| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10410 Z= 0.169 Angle : 0.701 17.143 14172 Z= 0.369 Chirality : 0.046 0.340 1659 Planarity : 0.004 0.048 1821 Dihedral : 6.669 50.300 1468 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 2.88 % Allowed : 20.14 % 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: -3.54 (0.21), residues: 1311 helix: -2.90 (0.48), residues: 81 sheet: -1.31 (0.22), residues: 552 loop : -3.27 (0.19), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 381 TYR 0.013 0.001 TYR C 148 PHE 0.016 0.002 PHE B 72 TRP 0.005 0.001 TRP C 165 HIS 0.004 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00396 (10362) covalent geometry : angle 0.67383 (14073) SS BOND : bond 0.00771 ( 45) SS BOND : angle 2.51663 ( 90) hydrogen bonds : bond 0.03918 ( 332) hydrogen bonds : angle 6.04414 ( 861) link_NAG-ASN : bond 0.00179 ( 3) link_NAG-ASN : angle 0.97029 ( 9) =============================================================================== Job complete usr+sys time: 2958.88 seconds wall clock time: 51 minutes 32.91 seconds (3092.91 seconds total)