Starting phenix.real_space_refine on Wed Mar 4 20:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfp_27410/03_2026/8dfp_27410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfp_27410/03_2026/8dfp_27410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dfp_27410/03_2026/8dfp_27410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfp_27410/03_2026/8dfp_27410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dfp_27410/03_2026/8dfp_27410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfp_27410/03_2026/8dfp_27410.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 37 5.16 5 C 5407 2.51 5 N 1389 2.21 5 O 1588 1.98 5 H 7703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 16124 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6145 Classifications: {'peptide': 438} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 5, 'ASP:plan': 16, 'GLU:plan': 19, 'GLN:plan1': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 6141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6141 Classifications: {'peptide': 440} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 419} Chain breaks: 2 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'ARG:plan': 5, 'GLU:plan': 20, 'GLN:plan1': 4, 'ASN:plan1': 7, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1852 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1846 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Time building chain proxies: 2.95, per 1000 atoms: 0.18 Number of scatterers: 16124 At special positions: 0 Unit cell: (75.376, 130.562, 183.056, 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 37 16.00 O 1588 8.00 N 1389 7.00 C 5407 6.00 H 7703 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 186 " distance=2.05 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 491 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 89 " distance=2.04 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1001 " - " ASN A 283 " " NAG B1001 " - " ASN B 283 " " NAG E 1 " - " ASN A 300 " " NAG F 1 " - " ASN A 293 " " NAG G 1 " - " ASN B 293 " " NAG H 1 " - " ASN B 300 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 599.0 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 18.1% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.851A pdb=" N GLY A 387 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.145A pdb=" N GLY B 387 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 12 removed outlier: 3.841A pdb=" N VAL C 12 " --> pdb=" O THR C 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 12' Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.485A pdb=" N LYS C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 62 removed outlier: 4.327A pdb=" N TRP C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 94 removed outlier: 3.584A pdb=" N GLU C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.912A pdb=" N PHE C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 removed outlier: 3.629A pdb=" N VAL D 12 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 40 through 63 removed outlier: 3.968A pdb=" N TRP D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 94 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.747A pdb=" N PHE D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.803A pdb=" N SER A 38 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.866A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 182 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 189 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 145 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.866A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 182 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.527A pdb=" N ALA A 273 " --> pdb=" O CYS A 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 224 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AB1, first strand: chain 'A' and resid 411 through 420 removed outlier: 5.378A pdb=" N LYS A 412 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 433 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 429 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 418 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 427 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 437 through 441 removed outlier: 18.234A pdb=" N LYS A 499 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 15.368A pdb=" N SER B 501 " --> pdb=" O LYS A 499 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N SER A 501 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N TYR B 503 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 503 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TYR B 505 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR A 505 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN B 507 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN A 507 " --> pdb=" O ASN B 507 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 488 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 443 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.637A pdb=" N SER B 38 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.608A pdb=" N LEU B 46 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG B 112 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 48 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 77 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB7, first strand: chain 'B' and resid 144 through 150 removed outlier: 5.701A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 144 through 150 removed outlier: 5.701A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AC1, first strand: chain 'B' and resid 220 through 224 removed outlier: 7.791A pdb=" N TRP B 246 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 253 " --> pdb=" O TRP B 246 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 248 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 326 removed outlier: 6.294A pdb=" N VAL B 323 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 410 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 325 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 412 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 345 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TRP B 348 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 326 removed outlier: 6.294A pdb=" N VAL B 323 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 410 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 325 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 412 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE B 433 " --> pdb=" O PRO B 413 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 415 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 431 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 417 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'D' and resid 28 through 31 409 hydrogen bonds defined for protein. 1050 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: 3.54 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 7701 1.01 - 1.22: 12 1.22 - 1.42: 3585 1.42 - 1.63: 4969 1.63 - 1.83: 48 Bond restraints: 16315 Sorted by residual: bond pdb=" C7 NAG A1001 " pdb=" N2 NAG A1001 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C7 NAG E 2 " pdb=" N2 NAG E 2 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 16310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 28876 2.87 - 5.74: 378 5.74 - 8.61: 13 8.61 - 11.48: 12 11.48 - 14.35: 1 Bond angle restraints: 29280 Sorted by residual: angle pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " ideal model delta sigma weight residual 110.24 95.89 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 118.68 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb="HH11 ARG A 122 " pdb=" NH1 ARG A 122 " pdb="HH12 ARG A 122 " ideal model delta sigma weight residual 120.00 108.66 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 110.79 121.36 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N LYS C 62 " pdb=" CA LYS C 62 " pdb=" C LYS C 62 " ideal model delta sigma weight residual 112.38 116.60 -4.22 1.22e+00 6.72e-01 1.20e+01 ... (remaining 29275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 7194 16.47 - 32.94: 523 32.94 - 49.40: 161 49.40 - 65.87: 164 65.87 - 82.34: 29 Dihedral angle restraints: 8071 sinusoidal: 4168 harmonic: 3903 Sorted by residual: dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sinusoidal sigma weight residual -86.00 -166.09 80.09 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CA PHE A 118 " pdb=" C PHE A 118 " pdb=" N LEU A 119 " pdb=" CA LEU A 119 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA THR B 59 " pdb=" C THR B 59 " pdb=" N ASP B 60 " pdb=" CA ASP B 60 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 8068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1398 0.154 - 0.308: 38 0.308 - 0.462: 0 0.462 - 0.616: 2 0.616 - 0.770: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" C2 NAG G 1 " pdb=" C1 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" N2 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.49 -1.72 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.93 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -1.91 -0.58 2.00e-01 2.50e+01 8.35e+00 ... (remaining 1436 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 122 " 0.052 9.50e-02 1.11e+02 8.19e-02 1.44e+02 pdb=" NE ARG A 122 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 122 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 122 " 0.133 2.00e-02 2.50e+03 pdb=" NH2 ARG A 122 " 0.108 2.00e-02 2.50e+03 pdb="HH11 ARG A 122 " 0.017 2.00e-02 2.50e+03 pdb="HH12 ARG A 122 " -0.144 2.00e-02 2.50e+03 pdb="HH21 ARG A 122 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 122 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 248 " 0.361 9.50e-02 1.11e+02 1.39e-01 1.26e+02 pdb=" NE ARG B 248 " 0.075 2.00e-02 2.50e+03 pdb=" CZ ARG B 248 " -0.072 2.00e-02 2.50e+03 pdb=" NH1 ARG B 248 " -0.106 2.00e-02 2.50e+03 pdb=" NH2 ARG B 248 " -0.085 2.00e-02 2.50e+03 pdb="HH11 ARG B 248 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 248 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG B 248 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 248 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 372 " 0.256 9.50e-02 1.11e+02 9.76e-02 5.74e+01 pdb=" NE ARG A 372 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 372 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 372 " -0.083 2.00e-02 2.50e+03 pdb=" NH2 ARG A 372 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 372 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 372 " 0.072 2.00e-02 2.50e+03 pdb="HH21 ARG A 372 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 372 " 0.041 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1422 2.26 - 2.84: 35029 2.84 - 3.43: 39397 3.43 - 4.01: 56418 4.01 - 4.60: 84579 Nonbonded interactions: 216845 Sorted by model distance: nonbonded pdb=" OD1 ASP B 159 " pdb=" HH TYR B 179 " model vdw 1.670 2.450 nonbonded pdb=" HG SER D 53 " pdb=" OD1 ASP D 84 " model vdw 1.674 2.450 nonbonded pdb=" O CYS A 491 " pdb=" HG SER A 501 " model vdw 1.692 2.450 nonbonded pdb=" OD1 ASP C 25 " pdb=" HH TYR D 26 " model vdw 1.724 2.450 nonbonded pdb="HD21 ASN A 293 " pdb=" O7 NAG F 1 " model vdw 1.738 2.450 ... (remaining 216840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 46 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 128 through 143 or (resid 144 through 145 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 146 through 164 or \ (resid 165 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 166 through 217 or (resid 218 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 219 through 227 or (resid \ 228 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 229 through 248 or (resid 249 through 250 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 251 through 265 or \ (resid 266 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 267 through 351 or (resid 352 through 353 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 354 through 3 \ 69 or (resid 370 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 371 through 375 or (resid 376 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 377 through 478 or \ resid 488 through 507 or (resid 508 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 1001)) selection = (chain 'B' and (resid 35 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 92 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 114 through 120 or (resid 121 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 122 through 128 or (resid 129 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 130 through 153 or (resid 154 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 155 through 188 or (resid 189 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 190 through 226 or (resid 227 through 228 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 229 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 319 through 328 or (resid 329 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 330 through 355 or (resid 356 through \ 358 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 359 through 438 or (resid 439 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 440 through 441 or resid 471 th \ rough 478 or resid 488 through 498 or (resid 499 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 500 through 1001)) } ncs_group { reference = (chain 'C' and (resid 3 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 93 through 95 or resid 10 \ 5 through 130)) selection = (chain 'D' and (resid 3 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 7 through 60 or (resid 61 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 62 through 87 or (resid 88 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 89 through 130)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.170 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.008 0.117 8634 Z= 0.409 Angle : 1.151 14.345 11844 Z= 0.629 Chirality : 0.071 0.770 1439 Planarity : 0.010 0.118 1478 Dihedral : 12.920 82.341 3049 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1098 helix: -1.24 (0.37), residues: 121 sheet: 0.55 (0.23), residues: 453 loop : -1.53 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.009 ARG B 122 TYR 0.073 0.010 TYR B 291 PHE 0.027 0.004 PHE D 126 TRP 0.043 0.008 TRP A 82 HIS 0.010 0.004 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00796 ( 8612) covalent geometry : angle 1.12769 (11790) SS BOND : bond 0.00938 ( 12) SS BOND : angle 1.38142 ( 24) hydrogen bonds : bond 0.15501 ( 402) hydrogen bonds : angle 7.86872 ( 1050) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 3.72054 ( 12) link_NAG-ASN : bond 0.00601 ( 6) link_NAG-ASN : angle 5.14742 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ILE cc_start: 0.8051 (mt) cc_final: 0.7793 (mp) REVERT: A 289 MET cc_start: 0.8862 (ttp) cc_final: 0.8441 (ttp) REVERT: B 171 MET cc_start: 0.8638 (ttm) cc_final: 0.8404 (ttt) REVERT: B 336 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8312 (mt-10) REVERT: C 84 ASP cc_start: 0.8760 (m-30) cc_final: 0.8286 (m-30) REVERT: D 88 GLU cc_start: 0.8464 (tt0) cc_final: 0.8242 (tp30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1660 time to fit residues: 15.8183 Evaluate side-chains 45 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 272 GLN C 51 GLN C 65 ASN D 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.073258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060646 restraints weight = 76977.628| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.06 r_work: 0.3084 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8634 Z= 0.186 Angle : 0.722 8.823 11844 Z= 0.376 Chirality : 0.049 0.252 1439 Planarity : 0.004 0.036 1478 Dihedral : 8.259 57.409 1398 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.24 % Allowed : 4.49 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1098 helix: 0.41 (0.39), residues: 124 sheet: 0.92 (0.24), residues: 439 loop : -0.92 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 112 TYR 0.021 0.002 TYR A 146 PHE 0.018 0.002 PHE C 116 TRP 0.013 0.002 TRP A 66 HIS 0.005 0.002 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8612) covalent geometry : angle 0.70576 (11790) SS BOND : bond 0.00685 ( 12) SS BOND : angle 1.39334 ( 24) hydrogen bonds : bond 0.04861 ( 402) hydrogen bonds : angle 6.08971 ( 1050) link_BETA1-4 : bond 0.00219 ( 4) link_BETA1-4 : angle 3.06040 ( 12) link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 2.79903 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.8350 (ttm) cc_final: 0.7987 (ttt) REVERT: C 114 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8750 (mt-10) REVERT: C 124 ASP cc_start: 0.8685 (m-30) cc_final: 0.8422 (m-30) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1110 time to fit residues: 9.4951 Evaluate side-chains 40 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.072164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059556 restraints weight = 78294.814| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.08 r_work: 0.3061 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8634 Z= 0.204 Angle : 0.636 10.695 11844 Z= 0.335 Chirality : 0.046 0.211 1439 Planarity : 0.004 0.035 1478 Dihedral : 6.906 55.956 1398 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.47 % Allowed : 4.14 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1098 helix: 1.31 (0.42), residues: 124 sheet: 0.60 (0.24), residues: 448 loop : -0.69 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 181 TYR 0.014 0.002 TYR A 146 PHE 0.019 0.001 PHE C 116 TRP 0.010 0.001 TRP A 66 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8612) covalent geometry : angle 0.62279 (11790) SS BOND : bond 0.00798 ( 12) SS BOND : angle 1.05968 ( 24) hydrogen bonds : bond 0.04166 ( 402) hydrogen bonds : angle 5.58577 ( 1050) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 2.63458 ( 12) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 2.36101 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: B 171 MET cc_start: 0.8498 (ttm) cc_final: 0.8274 (tpp) REVERT: C 124 ASP cc_start: 0.8667 (m-30) cc_final: 0.8255 (m-30) outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 0.1096 time to fit residues: 8.4619 Evaluate side-chains 43 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 17 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058489 restraints weight = 77995.018| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.23 r_work: 0.3010 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8634 Z= 0.153 Angle : 0.559 5.268 11844 Z= 0.293 Chirality : 0.045 0.210 1439 Planarity : 0.003 0.034 1478 Dihedral : 6.100 53.879 1398 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.71 % Allowed : 4.85 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1098 helix: 1.97 (0.44), residues: 124 sheet: 0.54 (0.24), residues: 437 loop : -0.50 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.011 0.001 TYR A 146 PHE 0.014 0.001 PHE C 116 TRP 0.009 0.001 TRP A 66 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8612) covalent geometry : angle 0.54714 (11790) SS BOND : bond 0.00565 ( 12) SS BOND : angle 0.97954 ( 24) hydrogen bonds : bond 0.03589 ( 402) hydrogen bonds : angle 5.22942 ( 1050) link_BETA1-4 : bond 0.00211 ( 4) link_BETA1-4 : angle 2.21398 ( 12) link_NAG-ASN : bond 0.00165 ( 6) link_NAG-ASN : angle 2.15268 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8685 (m-30) cc_final: 0.8180 (m-30) REVERT: D 27 MET cc_start: 0.9363 (mmt) cc_final: 0.9117 (mmm) REVERT: D 114 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8466 (mp0) REVERT: D 123 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9246 (mm) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1086 time to fit residues: 8.6222 Evaluate side-chains 46 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057427 restraints weight = 78327.682| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.17 r_work: 0.2990 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8634 Z= 0.211 Angle : 0.563 5.272 11844 Z= 0.297 Chirality : 0.044 0.193 1439 Planarity : 0.004 0.036 1478 Dihedral : 5.901 54.949 1398 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.18 % Allowed : 4.85 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1098 helix: 2.20 (0.45), residues: 124 sheet: 0.29 (0.24), residues: 443 loop : -0.37 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.012 0.001 TYR A 95 PHE 0.016 0.001 PHE C 116 TRP 0.008 0.001 TRP A 246 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8612) covalent geometry : angle 0.55093 (11790) SS BOND : bond 0.00597 ( 12) SS BOND : angle 0.93196 ( 24) hydrogen bonds : bond 0.03625 ( 402) hydrogen bonds : angle 5.16297 ( 1050) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 2.34767 ( 12) link_NAG-ASN : bond 0.00459 ( 6) link_NAG-ASN : angle 2.27234 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8771 (m-30) cc_final: 0.8197 (m-30) REVERT: D 36 MET cc_start: 0.8829 (ptm) cc_final: 0.8479 (ptm) REVERT: D 123 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9195 (mm) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.1106 time to fit residues: 9.2915 Evaluate side-chains 43 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.070705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058034 restraints weight = 77610.702| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.18 r_work: 0.3003 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8634 Z= 0.151 Angle : 0.523 5.075 11844 Z= 0.276 Chirality : 0.044 0.200 1439 Planarity : 0.003 0.036 1478 Dihedral : 5.623 52.817 1398 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.83 % Allowed : 5.32 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1098 helix: 2.33 (0.45), residues: 124 sheet: 0.29 (0.24), residues: 445 loop : -0.29 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.009 0.001 TYR A 95 PHE 0.013 0.001 PHE C 116 TRP 0.008 0.001 TRP A 66 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8612) covalent geometry : angle 0.51330 (11790) SS BOND : bond 0.00488 ( 12) SS BOND : angle 0.78979 ( 24) hydrogen bonds : bond 0.03359 ( 402) hydrogen bonds : angle 5.01363 ( 1050) link_BETA1-4 : bond 0.00216 ( 4) link_BETA1-4 : angle 2.04991 ( 12) link_NAG-ASN : bond 0.00163 ( 6) link_NAG-ASN : angle 2.01893 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8709 (m-30) cc_final: 0.8109 (m-30) REVERT: D 36 MET cc_start: 0.8818 (ptm) cc_final: 0.8471 (ptm) REVERT: D 114 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8448 (mp0) REVERT: D 123 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9184 (mm) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.1164 time to fit residues: 8.9709 Evaluate side-chains 46 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 96 optimal weight: 0.0070 chunk 91 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.070720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058017 restraints weight = 77667.728| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.19 r_work: 0.3006 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8634 Z= 0.146 Angle : 0.510 5.070 11844 Z= 0.268 Chirality : 0.044 0.189 1439 Planarity : 0.003 0.037 1478 Dihedral : 5.442 52.045 1398 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.83 % Allowed : 5.44 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1098 helix: 2.48 (0.46), residues: 124 sheet: 0.32 (0.24), residues: 446 loop : -0.20 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.009 0.001 TYR A 95 PHE 0.013 0.001 PHE C 116 TRP 0.008 0.001 TRP A 66 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8612) covalent geometry : angle 0.49981 (11790) SS BOND : bond 0.00455 ( 12) SS BOND : angle 0.78860 ( 24) hydrogen bonds : bond 0.03239 ( 402) hydrogen bonds : angle 4.89657 ( 1050) link_BETA1-4 : bond 0.00219 ( 4) link_BETA1-4 : angle 1.99600 ( 12) link_NAG-ASN : bond 0.00240 ( 6) link_NAG-ASN : angle 1.98015 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8721 (m-30) cc_final: 0.8125 (m-30) REVERT: D 36 MET cc_start: 0.8805 (ptm) cc_final: 0.8445 (ptm) REVERT: D 114 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8308 (mp0) REVERT: D 123 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9183 (mm) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1145 time to fit residues: 8.8500 Evaluate side-chains 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.070338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057694 restraints weight = 78133.010| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.17 r_work: 0.2998 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8634 Z= 0.171 Angle : 0.516 5.081 11844 Z= 0.272 Chirality : 0.044 0.183 1439 Planarity : 0.004 0.038 1478 Dihedral : 5.472 52.152 1398 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.95 % Allowed : 5.44 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1098 helix: 2.39 (0.46), residues: 124 sheet: 0.28 (0.24), residues: 445 loop : -0.18 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.010 0.001 TYR A 95 PHE 0.016 0.001 PHE C 116 TRP 0.007 0.001 TRP B 246 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8612) covalent geometry : angle 0.50646 (11790) SS BOND : bond 0.00459 ( 12) SS BOND : angle 0.74257 ( 24) hydrogen bonds : bond 0.03249 ( 402) hydrogen bonds : angle 4.87361 ( 1050) link_BETA1-4 : bond 0.00251 ( 4) link_BETA1-4 : angle 1.97175 ( 12) link_NAG-ASN : bond 0.00238 ( 6) link_NAG-ASN : angle 1.96307 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8729 (m-30) cc_final: 0.8120 (m-30) REVERT: D 114 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8440 (mp0) REVERT: D 123 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9189 (mm) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 0.1158 time to fit residues: 9.2182 Evaluate side-chains 46 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.070420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057794 restraints weight = 78195.791| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.18 r_work: 0.2996 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8634 Z= 0.164 Angle : 0.517 6.572 11844 Z= 0.272 Chirality : 0.043 0.179 1439 Planarity : 0.004 0.038 1478 Dihedral : 5.437 52.048 1398 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.95 % Allowed : 5.79 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1098 helix: 2.45 (0.46), residues: 124 sheet: 0.20 (0.24), residues: 446 loop : -0.17 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.008 0.001 TYR A 95 PHE 0.015 0.001 PHE C 116 TRP 0.008 0.001 TRP A 66 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8612) covalent geometry : angle 0.50198 (11790) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.82735 ( 24) hydrogen bonds : bond 0.03210 ( 402) hydrogen bonds : angle 4.86793 ( 1050) link_BETA1-4 : bond 0.00249 ( 4) link_BETA1-4 : angle 1.93551 ( 12) link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 1.95107 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8731 (m-30) cc_final: 0.8068 (m-30) REVERT: D 61 ASP cc_start: 0.8698 (t0) cc_final: 0.8469 (t0) REVERT: D 123 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9204 (mm) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.1205 time to fit residues: 9.7898 Evaluate side-chains 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.070879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058277 restraints weight = 77757.433| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.17 r_work: 0.3009 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8634 Z= 0.127 Angle : 0.500 7.639 11844 Z= 0.263 Chirality : 0.043 0.180 1439 Planarity : 0.003 0.038 1478 Dihedral : 5.276 50.154 1398 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.95 % Allowed : 6.03 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1098 helix: 2.50 (0.45), residues: 127 sheet: 0.23 (0.24), residues: 445 loop : -0.13 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.008 0.001 TYR A 95 PHE 0.012 0.001 PHE C 116 TRP 0.010 0.001 TRP A 66 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8612) covalent geometry : angle 0.48488 (11790) SS BOND : bond 0.00452 ( 12) SS BOND : angle 1.93957 ( 24) hydrogen bonds : bond 0.03098 ( 402) hydrogen bonds : angle 4.77478 ( 1050) link_BETA1-4 : bond 0.00202 ( 4) link_BETA1-4 : angle 1.79424 ( 12) link_NAG-ASN : bond 0.00137 ( 6) link_NAG-ASN : angle 1.86051 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 124 ASP cc_start: 0.8725 (m-30) cc_final: 0.8047 (m-30) REVERT: D 61 ASP cc_start: 0.8688 (t0) cc_final: 0.8470 (t0) REVERT: D 114 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8363 (mp0) REVERT: D 123 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9199 (mm) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1146 time to fit residues: 9.7578 Evaluate side-chains 49 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain D residue 123 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.070271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057698 restraints weight = 78044.227| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.17 r_work: 0.2991 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8634 Z= 0.198 Angle : 0.523 6.226 11844 Z= 0.275 Chirality : 0.043 0.173 1439 Planarity : 0.004 0.038 1478 Dihedral : 5.426 51.877 1398 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.83 % Allowed : 6.15 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1098 helix: 2.47 (0.46), residues: 124 sheet: 0.19 (0.23), residues: 450 loop : -0.20 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 181 TYR 0.009 0.001 TYR B 441 PHE 0.017 0.001 PHE C 116 TRP 0.008 0.001 TRP A 66 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8612) covalent geometry : angle 0.51008 (11790) SS BOND : bond 0.00452 ( 12) SS BOND : angle 1.62878 ( 24) hydrogen bonds : bond 0.03217 ( 402) hydrogen bonds : angle 4.83753 ( 1050) link_BETA1-4 : bond 0.00284 ( 4) link_BETA1-4 : angle 1.91357 ( 12) link_NAG-ASN : bond 0.00317 ( 6) link_NAG-ASN : angle 1.97268 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3339.64 seconds wall clock time: 57 minutes 17.31 seconds (3437.31 seconds total)