Starting phenix.real_space_refine on Sat Jun 14 16:05:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfp_27410/06_2025/8dfp_27410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfp_27410/06_2025/8dfp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfp_27410/06_2025/8dfp_27410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfp_27410/06_2025/8dfp_27410.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfp_27410/06_2025/8dfp_27410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfp_27410/06_2025/8dfp_27410.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 16, 'GLU:plan': 19, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 5} 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: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} 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: 9.85, per 1000 atoms: 0.61 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: 4.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.66 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: 6.78 Time building geometry restraints manager: 5.22 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 508 or resid \ 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: 6.270 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: 0.310 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 39.710 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.043 0.008 TRP A 82 HIS 0.010 0.004 HIS A 185 PHE 0.027 0.004 PHE D 126 TYR 0.073 0.010 TYR B 291 ARG 0.060 0.009 ARG B 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 6) link_NAG-ASN : angle 5.14742 ( 18) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 3.72054 ( 12) hydrogen bonds : bond 0.15501 ( 402) hydrogen bonds : angle 7.86872 ( 1050) SS BOND : bond 0.00938 ( 12) SS BOND : angle 1.38142 ( 24) covalent geometry : bond 0.00796 ( 8612) covalent geometry : angle 1.12769 (11790) *********************** 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 : 1.355 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: 0.8311 (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: 0.3699 time to fit residues: 35.5017 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 : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.0060 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.073244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060622 restraints weight = 76785.252| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.07 r_work: 0.3082 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1391 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 : 0.725 8.737 11844 Z= 0.377 Chirality : 0.049 0.250 1439 Planarity : 0.004 0.037 1478 Dihedral : 8.336 57.285 1398 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.12 % Allowed : 4.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1098 helix: 0.36 (0.39), residues: 124 sheet: 0.93 (0.24), residues: 439 loop : -0.93 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 66 HIS 0.005 0.001 HIS A 185 PHE 0.016 0.002 PHE C 116 TYR 0.021 0.002 TYR A 146 ARG 0.009 0.001 ARG A 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 6) link_NAG-ASN : angle 2.80613 ( 18) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 3.08927 ( 12) hydrogen bonds : bond 0.04881 ( 402) hydrogen bonds : angle 6.11991 ( 1050) SS BOND : bond 0.00779 ( 12) SS BOND : angle 1.36840 ( 24) covalent geometry : bond 0.00400 ( 8612) covalent geometry : angle 0.70845 (11790) *********************** 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 48 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8684 (m-30) cc_final: 0.8423 (m-30) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.2890 time to fit residues: 22.6228 Evaluate side-chains 41 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.071875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059109 restraints weight = 76987.913| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.21 r_work: 0.3028 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2017 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= 0.141 Angle : 0.596 5.686 11844 Z= 0.314 Chirality : 0.046 0.212 1439 Planarity : 0.004 0.034 1478 Dihedral : 6.641 54.192 1398 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.47 % Allowed : 4.02 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1098 helix: 1.51 (0.43), residues: 124 sheet: 0.68 (0.24), residues: 449 loop : -0.54 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.003 0.001 HIS A 263 PHE 0.016 0.001 PHE C 116 TYR 0.012 0.001 TYR C 32 ARG 0.003 0.001 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00117 ( 6) link_NAG-ASN : angle 2.20207 ( 18) link_BETA1-4 : bond 0.00193 ( 4) link_BETA1-4 : angle 2.44261 ( 12) hydrogen bonds : bond 0.03977 ( 402) hydrogen bonds : angle 5.47864 ( 1050) SS BOND : bond 0.00674 ( 12) SS BOND : angle 1.40247 ( 24) covalent geometry : bond 0.00306 ( 8612) covalent geometry : angle 0.58297 (11790) *********************** 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 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8756 (m-30) cc_final: 0.8344 (m-30) REVERT: D 27 MET cc_start: 0.9310 (mmt) cc_final: 0.9072 (mmm) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.2661 time to fit residues: 20.4550 Evaluate side-chains 43 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.071032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058376 restraints weight = 77106.236| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.17 r_work: 0.3010 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8634 Z= 0.176 Angle : 0.566 5.742 11844 Z= 0.297 Chirality : 0.044 0.197 1439 Planarity : 0.003 0.034 1478 Dihedral : 6.022 54.305 1398 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.95 % Allowed : 4.14 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1098 helix: 2.02 (0.44), residues: 124 sheet: 0.48 (0.24), residues: 445 loop : -0.47 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.003 0.001 HIS C 42 PHE 0.016 0.001 PHE C 116 TYR 0.012 0.001 TYR A 95 ARG 0.004 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 2.25010 ( 18) link_BETA1-4 : bond 0.00441 ( 4) link_BETA1-4 : angle 2.25765 ( 12) hydrogen bonds : bond 0.03592 ( 402) hydrogen bonds : angle 5.19608 ( 1050) SS BOND : bond 0.00296 ( 12) SS BOND : angle 1.32495 ( 24) covalent geometry : bond 0.00392 ( 8612) covalent geometry : angle 0.55254 (11790) *********************** 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 49 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 124 ASP cc_start: 0.8701 (m-30) cc_final: 0.8165 (m-30) REVERT: D 27 MET cc_start: 0.9360 (mmt) cc_final: 0.9119 (mmm) REVERT: D 123 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9235 (mm) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.2626 time to fit residues: 21.6210 Evaluate side-chains 44 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 GLU 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 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 91 optimal weight: 0.1980 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058112 restraints weight = 78470.436| |-----------------------------------------------------------------------------| 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: 0.8237 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8634 Z= 0.172 Angle : 0.547 6.959 11844 Z= 0.288 Chirality : 0.044 0.205 1439 Planarity : 0.003 0.035 1478 Dihedral : 5.759 53.449 1398 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.83 % Allowed : 4.85 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1098 helix: 2.21 (0.45), residues: 124 sheet: 0.34 (0.24), residues: 444 loop : -0.29 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.004 0.001 HIS A 263 PHE 0.015 0.001 PHE C 116 TYR 0.010 0.001 TYR A 95 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 6) link_NAG-ASN : angle 2.07192 ( 18) link_BETA1-4 : bond 0.00237 ( 4) link_BETA1-4 : angle 2.17518 ( 12) hydrogen bonds : bond 0.03511 ( 402) hydrogen bonds : angle 5.08059 ( 1050) SS BOND : bond 0.00589 ( 12) SS BOND : angle 1.59289 ( 24) covalent geometry : bond 0.00384 ( 8612) covalent geometry : angle 0.53320 (11790) *********************** 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 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8726 (m-30) cc_final: 0.8173 (m-30) REVERT: D 27 MET cc_start: 0.9376 (mmt) cc_final: 0.9122 (mmm) REVERT: D 36 MET cc_start: 0.8806 (ptm) cc_final: 0.8455 (ptm) REVERT: D 114 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8501 (mp0) REVERT: D 123 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9200 (mm) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.2569 time to fit residues: 20.1942 Evaluate side-chains 44 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 106 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.070472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057836 restraints weight = 78109.292| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.15 r_work: 0.2996 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8634 Z= 0.192 Angle : 0.547 6.538 11844 Z= 0.287 Chirality : 0.044 0.197 1439 Planarity : 0.004 0.037 1478 Dihedral : 5.708 54.070 1398 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.59 % Allowed : 5.32 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1098 helix: 2.27 (0.45), residues: 124 sheet: 0.29 (0.24), residues: 444 loop : -0.29 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 246 HIS 0.003 0.001 HIS A 263 PHE 0.015 0.001 PHE C 116 TYR 0.010 0.001 TYR A 95 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 2.12882 ( 18) link_BETA1-4 : bond 0.00190 ( 4) link_BETA1-4 : angle 2.18914 ( 12) hydrogen bonds : bond 0.03452 ( 402) hydrogen bonds : angle 5.06510 ( 1050) SS BOND : bond 0.00330 ( 12) SS BOND : angle 1.52292 ( 24) covalent geometry : bond 0.00430 ( 8612) covalent geometry : angle 0.53247 (11790) *********************** 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 45 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8716 (m-30) cc_final: 0.8134 (m-30) REVERT: D 114 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8355 (mp0) REVERT: D 123 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9162 (mm) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.2640 time to fit residues: 20.0509 Evaluate side-chains 44 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 overall best weight: 0.2758 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.071367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058690 restraints weight = 77877.497| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.18 r_work: 0.3017 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8634 Z= 0.110 Angle : 0.503 4.978 11844 Z= 0.265 Chirality : 0.044 0.199 1439 Planarity : 0.003 0.036 1478 Dihedral : 5.394 51.033 1398 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.71 % Allowed : 5.20 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1098 helix: 2.50 (0.46), residues: 124 sheet: 0.39 (0.24), residues: 443 loop : -0.18 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.002 0.001 HIS A 263 PHE 0.011 0.001 PHE C 116 TYR 0.007 0.001 TYR A 505 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 6) link_NAG-ASN : angle 1.91785 ( 18) link_BETA1-4 : bond 0.00224 ( 4) link_BETA1-4 : angle 1.92162 ( 12) hydrogen bonds : bond 0.03217 ( 402) hydrogen bonds : angle 4.87495 ( 1050) SS BOND : bond 0.00233 ( 12) SS BOND : angle 1.16644 ( 24) covalent geometry : bond 0.00252 ( 8612) covalent geometry : angle 0.49237 (11790) *********************** 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 49 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 124 ASP cc_start: 0.8700 (m-30) cc_final: 0.8090 (m-30) REVERT: D 36 MET cc_start: 0.8782 (ptm) cc_final: 0.8421 (ptm) REVERT: D 114 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8444 (mp0) REVERT: D 123 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9179 (mm) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.2707 time to fit residues: 21.9970 Evaluate side-chains 48 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 96 optimal weight: 0.0670 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.070634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058088 restraints weight = 78194.701| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.16 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: 0.8237 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8634 Z= 0.168 Angle : 0.524 6.492 11844 Z= 0.275 Chirality : 0.043 0.186 1439 Planarity : 0.003 0.037 1478 Dihedral : 5.449 51.980 1398 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.83 % Allowed : 5.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1098 helix: 2.45 (0.46), residues: 124 sheet: 0.30 (0.24), residues: 443 loop : -0.20 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 246 HIS 0.003 0.001 HIS A 263 PHE 0.014 0.001 PHE C 116 TYR 0.008 0.001 TYR B 441 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 2.01424 ( 18) link_BETA1-4 : bond 0.00305 ( 4) link_BETA1-4 : angle 1.99195 ( 12) hydrogen bonds : bond 0.03250 ( 402) hydrogen bonds : angle 4.88990 ( 1050) SS BOND : bond 0.00311 ( 12) SS BOND : angle 1.88788 ( 24) covalent geometry : bond 0.00377 ( 8612) covalent geometry : angle 0.50814 (11790) *********************** 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: 7 poor density : 41 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8707 (m-30) cc_final: 0.8095 (m-30) REVERT: D 36 MET cc_start: 0.8810 (ptm) cc_final: 0.8439 (ptm) REVERT: D 123 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9178 (mm) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.2568 time to fit residues: 20.5515 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 : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 100 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.071178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058604 restraints weight = 77375.646| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.16 r_work: 0.3015 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8634 Z= 0.117 Angle : 0.502 5.588 11844 Z= 0.263 Chirality : 0.044 0.188 1439 Planarity : 0.003 0.037 1478 Dihedral : 5.295 50.505 1398 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.47 % Allowed : 5.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1098 helix: 2.55 (0.46), residues: 124 sheet: 0.30 (0.24), residues: 449 loop : -0.13 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.002 0.001 HIS A 263 PHE 0.012 0.001 PHE C 116 TYR 0.008 0.001 TYR A 95 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 6) link_NAG-ASN : angle 1.88319 ( 18) link_BETA1-4 : bond 0.00123 ( 4) link_BETA1-4 : angle 1.85285 ( 12) hydrogen bonds : bond 0.03143 ( 402) hydrogen bonds : angle 4.78081 ( 1050) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.57889 ( 24) covalent geometry : bond 0.00262 ( 8612) covalent geometry : angle 0.48889 (11790) *********************** 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 48 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 124 ASP cc_start: 0.8707 (m-30) cc_final: 0.8085 (m-30) REVERT: D 36 MET cc_start: 0.8766 (ptm) cc_final: 0.8388 (ptm) REVERT: D 114 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8453 (mp0) REVERT: D 123 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9179 (mm) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.2743 time to fit residues: 22.0175 Evaluate side-chains 47 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 108 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.070244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057621 restraints weight = 78656.412| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.18 r_work: 0.2994 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8634 Z= 0.198 Angle : 0.538 8.860 11844 Z= 0.281 Chirality : 0.043 0.180 1439 Planarity : 0.004 0.037 1478 Dihedral : 5.453 52.347 1398 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.47 % Allowed : 5.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1098 helix: 2.45 (0.46), residues: 124 sheet: 0.23 (0.23), residues: 452 loop : -0.17 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 66 HIS 0.007 0.001 HIS A 185 PHE 0.018 0.001 PHE C 116 TYR 0.011 0.001 TYR A 95 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 6) link_NAG-ASN : angle 2.01266 ( 18) link_BETA1-4 : bond 0.00398 ( 4) link_BETA1-4 : angle 2.00025 ( 12) hydrogen bonds : bond 0.03272 ( 402) hydrogen bonds : angle 4.85749 ( 1050) SS BOND : bond 0.00307 ( 12) SS BOND : angle 1.49314 ( 24) covalent geometry : bond 0.00445 ( 8612) covalent geometry : angle 0.52499 (11790) ********************** 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 42 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 ASP cc_start: 0.8728 (m-30) cc_final: 0.8112 (m-30) REVERT: D 114 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8474 (mp0) REVERT: D 123 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9183 (mm) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.2542 time to fit residues: 18.5825 Evaluate side-chains 42 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 18 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.070447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057836 restraints weight = 78037.433| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.16 r_work: 0.2999 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8634 Z= 0.159 Angle : 0.527 12.658 11844 Z= 0.274 Chirality : 0.044 0.180 1439 Planarity : 0.004 0.037 1478 Dihedral : 5.371 51.450 1398 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.59 % Allowed : 5.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1098 helix: 2.45 (0.45), residues: 127 sheet: 0.27 (0.23), residues: 449 loop : -0.11 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.006 0.001 HIS A 185 PHE 0.014 0.001 PHE C 116 TYR 0.009 0.001 TYR A 95 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 6) link_NAG-ASN : angle 1.88981 ( 18) link_BETA1-4 : bond 0.00137 ( 4) link_BETA1-4 : angle 1.87883 ( 12) hydrogen bonds : bond 0.03204 ( 402) hydrogen bonds : angle 4.80143 ( 1050) SS BOND : bond 0.00298 ( 12) SS BOND : angle 1.42374 ( 24) covalent geometry : bond 0.00360 ( 8612) covalent geometry : angle 0.51602 (11790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6928.05 seconds wall clock time: 118 minutes 27.26 seconds (7107.26 seconds total)