Starting phenix.real_space_refine on Sun Apr 5 23:48:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfq_27411/04_2026/8dfq_27411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfq_27411/04_2026/8dfq_27411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfq_27411/04_2026/8dfq_27411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfq_27411/04_2026/8dfq_27411.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfq_27411/04_2026/8dfq_27411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfq_27411/04_2026/8dfq_27411.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 35 5.16 5 C 4947 2.51 5 N 1310 2.21 5 O 1427 1.98 5 H 6514 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14233 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 5414 Classifications: {'peptide': 438} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 4, 'ASP:plan': 20, 'ARG:plan': 8, 'GLU:plan': 27, 'ASN:plan1': 14, 'GLN:plan1': 8, 'PHE:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 352 Chain: "B" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 5269 Classifications: {'peptide': 436} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 580 Unresolved non-hydrogen angles: 724 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 23, 'ARG:plan': 7, 'GLU:plan': 27, 'ASN:plan1': 14, 'GLN:plan1': 8, 'PHE:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 336 Chain: "C" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1707 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1745 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 62 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: "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 Time building chain proxies: 2.68, per 1000 atoms: 0.19 Number of scatterers: 14233 At special positions: 0 Unit cell: (77.9185, 133.17, 184.171, 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 35 16.00 O 1427 8.00 N 1310 7.00 C 4947 6.00 H 6514 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=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 186 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 491 " distance=2.05 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 491 " distance=2.06 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=2.01 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-ASN " NAG A1001 " - " ASN A 293 " " NAG E 1 " - " ASN A 300 " " NAG F 1 " - " ASN B 293 " " NAG G 1 " - " ASN B 300 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 551.9 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 25 sheets defined 17.6% alpha, 43.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 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 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 removed outlier: 3.579A pdb=" N HIS B 180 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.963A pdb=" N VAL C 12 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.538A pdb=" N ASN C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 63 removed outlier: 3.996A pdb=" N SER C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.960A pdb=" N PHE C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 9 through 12 removed outlier: 3.939A pdb=" N VAL D 12 " --> pdb=" O THR D 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 13 through 21 removed outlier: 4.340A pdb=" N LYS D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 61 removed outlier: 4.289A pdb=" N TRP D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 94 removed outlier: 3.626A pdb=" N ILE D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 127 removed outlier: 4.091A pdb=" N PHE D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 4.037A 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: 3.580A pdb=" N LEU A 57 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.298A pdb=" N LEU A 46 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG A 112 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 48 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 94 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 removed outlier: 7.013A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 150 removed outlier: 4.601A pdb=" N TYR A 146 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER A 187 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 148 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS A 185 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLY A 150 " --> pdb=" O CYS A 183 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N CYS A 183 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 150 removed outlier: 4.601A pdb=" N TYR A 146 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER A 187 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 148 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS A 185 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLY A 150 " --> pdb=" O CYS A 183 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N CYS A 183 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 182 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.741A pdb=" N VAL A 213 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 224 removed outlier: 6.763A pdb=" N TYR A 221 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL A 308 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 223 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AB1, first strand: chain 'A' and resid 322 through 326 removed outlier: 6.593A pdb=" N VAL A 323 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASN A 410 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 325 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LYS A 412 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 322 through 326 removed outlier: 6.593A pdb=" N VAL A 323 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASN A 410 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 325 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LYS A 412 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS A 412 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE A 433 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 437 through 441 removed outlier: 20.417A pdb=" N LYS A 499 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 17.459A pdb=" N SER B 501 " --> pdb=" O LYS A 499 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N SER A 501 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N TYR B 503 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR A 503 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ASN B 505 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN A 505 " --> pdb=" O ASN B 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.581A pdb=" N LEU B 57 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.328A pdb=" N LEU B 46 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG B 112 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 48 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.915A pdb=" N GLY B 126 " --> pdb=" O ARG B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB8, first strand: chain 'B' and resid 144 through 150 removed outlier: 5.556A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 144 through 150 removed outlier: 5.556A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AC2, first strand: chain 'B' and resid 221 through 224 removed outlier: 6.605A pdb=" N TYR B 221 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL B 308 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU B 223 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 326 removed outlier: 6.158A pdb=" N VAL B 323 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN B 410 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 325 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 414 through 420 removed outlier: 4.089A pdb=" N LEU B 426 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 28 through 31 396 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6512 1.04 - 1.25: 1146 1.25 - 1.45: 2280 1.45 - 1.65: 4425 1.65 - 1.86: 44 Bond restraints: 14407 Sorted by residual: bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.466 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.48e+01 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 3.43e+01 bond pdb=" C7 NAG E 2 " pdb=" N2 NAG E 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.37e+01 ... (remaining 14402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 25440 3.16 - 6.32: 256 6.32 - 9.48: 16 9.48 - 12.64: 5 12.64 - 15.80: 1 Bond angle restraints: 25718 Sorted by residual: angle pdb=" C3 NAG G 1 " pdb=" C2 NAG G 1 " pdb=" N2 NAG G 1 " ideal model delta sigma weight residual 110.74 126.54 -15.80 3.00e+00 1.11e-01 2.77e+01 angle pdb=" CA TRP B 246 " pdb=" CB TRP B 246 " pdb=" CG TRP B 246 " ideal model delta sigma weight residual 113.60 121.35 -7.75 1.90e+00 2.77e-01 1.67e+01 angle pdb=" CA CYS B 428 " pdb=" CB CYS B 428 " pdb=" SG CYS B 428 " ideal model delta sigma weight residual 114.40 123.13 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CA TRP A 246 " pdb=" CB TRP A 246 " pdb=" CG TRP A 246 " ideal model delta sigma weight residual 113.60 120.60 -7.00 1.90e+00 2.77e-01 1.36e+01 angle pdb=" C1 NAG G 1 " pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " ideal model delta sigma weight residual 109.80 98.91 10.89 3.00e+00 1.11e-01 1.32e+01 ... (remaining 25713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 6488 16.37 - 32.74: 502 32.74 - 49.11: 121 49.11 - 65.48: 139 65.48 - 81.85: 33 Dihedral angle restraints: 7283 sinusoidal: 3476 harmonic: 3807 Sorted by residual: dihedral pdb=" CB CYS B 151 " pdb=" SG CYS B 151 " pdb=" SG CYS B 183 " pdb=" CB CYS B 183 " ideal model delta sinusoidal sigma weight residual -86.00 -166.42 80.42 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CA GLU B 198 " pdb=" C GLU B 198 " pdb=" N LYS B 199 " pdb=" CA LYS B 199 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA CYS B 183 " pdb=" C CYS B 183 " pdb=" N LEU B 184 " pdb=" CA LEU B 184 " ideal model delta harmonic sigma weight residual -180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 7280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1270 0.118 - 0.235: 78 0.235 - 0.353: 1 0.353 - 0.470: 1 0.470 - 0.588: 1 Chirality restraints: 1351 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 -1.90 -0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 300 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ILE A 172 " pdb=" N ILE A 172 " pdb=" C ILE A 172 " pdb=" CB ILE A 172 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1348 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 129 " 0.001 2.00e-02 2.50e+03 7.71e-02 1.78e+02 pdb=" CG PHE D 129 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE D 129 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE D 129 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE D 129 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 PHE D 129 " -0.123 2.00e-02 2.50e+03 pdb=" CZ PHE D 129 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 PHE D 129 " 0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE D 129 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE D 129 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE D 129 " 0.138 2.00e-02 2.50e+03 pdb=" HZ PHE D 129 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 271 " 0.264 9.50e-02 1.11e+02 9.84e-02 5.18e+01 pdb=" NE ARG B 271 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 271 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 271 " 0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG B 271 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG B 271 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 271 " -0.060 2.00e-02 2.50e+03 pdb="HH21 ARG B 271 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG B 271 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 248 " 0.030 9.50e-02 1.11e+02 3.26e-02 2.17e+01 pdb=" NE ARG B 248 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 248 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 248 " 0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG B 248 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG B 248 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 248 " -0.048 2.00e-02 2.50e+03 pdb="HH21 ARG B 248 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 248 " 0.047 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 1611 2.28 - 2.86: 28945 2.86 - 3.44: 31290 3.44 - 4.02: 42408 4.02 - 4.60: 63187 Nonbonded interactions: 167441 Sorted by model distance: nonbonded pdb=" O ALA B 219 " pdb=" HG1 THR B 303 " model vdw 1.696 2.450 nonbonded pdb=" O ALA A 219 " pdb=" HG1 THR A 303 " model vdw 1.729 2.450 nonbonded pdb=" H GLU B 344 " pdb=" O SER B 395 " model vdw 1.770 2.450 nonbonded pdb=" O LYS B 116 " pdb=" HG1 THR B 139 " model vdw 1.783 2.450 nonbonded pdb=" O GLY B 62 " pdb=" H LYS B 100 " model vdw 1.788 2.450 ... (remaining 167436 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 36 through 46 or (resid 47 through 50 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 51 through 55 \ or (resid 56 through 57 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 58 through 66 or (resid 67 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 68 through 69 \ or (resid 70 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 71 through 79 or (resid 80 through 81 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 82 through 91 o \ r (resid 92 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 93 through 106 or (resid 107 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 108 through 130 or (resid \ 131 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 132 through 142 or (resid 143 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 172 or \ (resid 173 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 174 through 184 or (resid 185 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 186 through 221 or (resid 222 through 225 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 226 through 235 or \ (resid 236 through 237 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 238 through 244 or (resid 245 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 246 or (resi \ d 247 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 248 through 252 or (resid 253 through 258 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 259 through 313 or \ (resid 314 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 315 or (resid 316 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 317 through 321 or (resid 322 throug \ h 325 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 326 through 331 or (resid 332 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 333 through 346 or (resid 347 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 348 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 355 or (resi \ d 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 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 400 through 414 or \ (resid 415 through 416 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 417 through 437 or (resid 438 through 441 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or (resid \ 471 through 473 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 474 through 478 or (resid 479 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 486 through 496 or \ (resid 497 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 498 through 507)) selection = (chain 'B' and (resid 36 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 66 through 74 \ or (resid 75 through 81 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 82 through 93 or (resid 94 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 95 through 111 \ or (resid 112 through 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 116 or (resid 117 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 118 throu \ gh 139 or (resid 140 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 141 through 148 or (resid 149 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 150 through 189 \ or (resid 190 through 191 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 192 through 194 or (resid 195 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 196 throu \ gh 198 or (resid 199 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 200 through 323 or (resid 324 through 325 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 326 \ through 344 or (resid 345 through 347 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 348 through 379 or (resid 380 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 381 or (resid 382 through 383 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 384 through 409 or (resid 410 through 41 \ 2 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 413 through 425 or (resid 426 through 427 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 428 or (resid 429 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 430 through 493 or (resid 494 through 497 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 498 through 507)) } ncs_group { reference = (chain 'C' 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 57 or (resid 58 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 59 through 77 or (resid 78 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 79 through 130)) selection = (chain 'D' and (resid 3 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 through 20 or (resid 21 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 22 through 35 or (resid 36 through 39 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 40 through 95 or resid 105 th \ rough 130)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 13.680 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 7912 Z= 0.379 Angle : 1.163 16.984 10905 Z= 0.642 Chirality : 0.061 0.588 1351 Planarity : 0.008 0.085 1378 Dihedral : 13.047 81.846 2553 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.15 % Allowed : 2.11 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.23), residues: 1094 helix: -0.57 (0.39), residues: 126 sheet: 0.35 (0.23), residues: 440 loop : -1.59 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.004 ARG B 271 TYR 0.028 0.007 TYR B 350 PHE 0.108 0.006 PHE D 129 TRP 0.040 0.007 TRP B 66 HIS 0.009 0.003 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00719 ( 7893) covalent geometry : angle 1.12069 (10860) SS BOND : bond 0.01358 ( 12) SS BOND : angle 2.57388 ( 24) hydrogen bonds : bond 0.19865 ( 390) hydrogen bonds : angle 8.84635 ( 993) link_BETA1-4 : bond 0.00720 ( 3) link_BETA1-4 : angle 4.02643 ( 9) link_NAG-ASN : bond 0.00971 ( 4) link_NAG-ASN : angle 8.15458 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 31 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8213 (ttp) cc_final: 0.8002 (ttm) REVERT: B 170 ILE cc_start: 0.7807 (mt) cc_final: 0.7432 (tt) REVERT: B 289 MET cc_start: 0.8034 (ttp) cc_final: 0.7738 (ttt) REVERT: D 36 MET cc_start: 0.9322 (ppp) cc_final: 0.8689 (ppp) REVERT: D 85 ASP cc_start: 0.9212 (m-30) cc_final: 0.8948 (t0) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.2464 time to fit residues: 9.9748 Evaluate side-chains 22 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043786 restraints weight = 176843.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045045 restraints weight = 82802.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045857 restraints weight = 48322.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046404 restraints weight = 32986.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046784 restraints weight = 25058.160| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7912 Z= 0.162 Angle : 0.725 12.243 10905 Z= 0.380 Chirality : 0.046 0.174 1351 Planarity : 0.005 0.044 1378 Dihedral : 9.245 58.680 1317 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.45 % Allowed : 3.63 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1094 helix: 0.48 (0.41), residues: 134 sheet: 0.37 (0.24), residues: 430 loop : -0.99 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 135 TYR 0.017 0.002 TYR A 146 PHE 0.017 0.002 PHE B 63 TRP 0.018 0.002 TRP B 66 HIS 0.003 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7893) covalent geometry : angle 0.69494 (10860) SS BOND : bond 0.00551 ( 12) SS BOND : angle 1.66394 ( 24) hydrogen bonds : bond 0.05864 ( 390) hydrogen bonds : angle 6.32016 ( 993) link_BETA1-4 : bond 0.00800 ( 3) link_BETA1-4 : angle 3.08408 ( 9) link_NAG-ASN : bond 0.00262 ( 4) link_NAG-ASN : angle 5.23233 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 28 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7779 (tp) REVERT: B 170 ILE cc_start: 0.8478 (mt) cc_final: 0.7947 (tt) REVERT: D 36 MET cc_start: 0.9193 (ppp) cc_final: 0.8282 (ppp) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.1029 time to fit residues: 5.1291 Evaluate side-chains 27 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042855 restraints weight = 176295.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044102 restraints weight = 81761.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.044778 restraints weight = 47800.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045398 restraints weight = 34667.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.045796 restraints weight = 25758.061| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7912 Z= 0.179 Angle : 0.646 9.982 10905 Z= 0.337 Chirality : 0.045 0.252 1351 Planarity : 0.004 0.046 1378 Dihedral : 7.983 56.308 1317 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.30 % Allowed : 6.04 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1094 helix: 1.07 (0.44), residues: 134 sheet: 0.10 (0.23), residues: 459 loop : -0.94 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 7 TYR 0.013 0.001 TYR A 146 PHE 0.018 0.001 PHE B 63 TRP 0.015 0.002 TRP B 66 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7893) covalent geometry : angle 0.62496 (10860) SS BOND : bond 0.00575 ( 12) SS BOND : angle 1.53961 ( 24) hydrogen bonds : bond 0.05251 ( 390) hydrogen bonds : angle 5.82563 ( 993) link_BETA1-4 : bond 0.00713 ( 3) link_BETA1-4 : angle 2.42930 ( 9) link_NAG-ASN : bond 0.00557 ( 4) link_NAG-ASN : angle 4.00385 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 26 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.9083 (ppp) cc_final: 0.8255 (ppp) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.1026 time to fit residues: 4.6800 Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.050576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042737 restraints weight = 174504.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.043997 restraints weight = 79993.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044810 restraints weight = 46478.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045342 restraints weight = 31830.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045741 restraints weight = 24454.109| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7912 Z= 0.160 Angle : 0.596 7.229 10905 Z= 0.311 Chirality : 0.045 0.242 1351 Planarity : 0.004 0.039 1378 Dihedral : 7.470 54.957 1317 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.60 % Allowed : 5.74 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.25), residues: 1094 helix: 1.43 (0.45), residues: 134 sheet: 0.04 (0.23), residues: 466 loop : -0.92 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.012 0.001 TYR A 269 PHE 0.010 0.001 PHE C 116 TRP 0.020 0.002 TRP A 440 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7893) covalent geometry : angle 0.57590 (10860) SS BOND : bond 0.00455 ( 12) SS BOND : angle 1.48217 ( 24) hydrogen bonds : bond 0.04360 ( 390) hydrogen bonds : angle 5.55254 ( 993) link_BETA1-4 : bond 0.00636 ( 3) link_BETA1-4 : angle 2.48494 ( 9) link_NAG-ASN : bond 0.00392 ( 4) link_NAG-ASN : angle 3.61976 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 26 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7936 (tp) REVERT: D 36 MET cc_start: 0.9087 (ppp) cc_final: 0.8219 (ppp) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.0958 time to fit residues: 4.3629 Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.042483 restraints weight = 175340.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043735 restraints weight = 80854.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044554 restraints weight = 46954.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045096 restraints weight = 31950.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045490 restraints weight = 24450.470| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7912 Z= 0.147 Angle : 0.580 7.625 10905 Z= 0.301 Chirality : 0.044 0.255 1351 Planarity : 0.004 0.037 1378 Dihedral : 7.160 54.414 1317 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.45 % Allowed : 6.19 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1094 helix: 1.72 (0.47), residues: 133 sheet: 0.07 (0.23), residues: 461 loop : -0.93 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 7 TYR 0.010 0.001 TYR A 146 PHE 0.013 0.001 PHE B 63 TRP 0.012 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7893) covalent geometry : angle 0.56083 (10860) SS BOND : bond 0.00553 ( 12) SS BOND : angle 1.45006 ( 24) hydrogen bonds : bond 0.04277 ( 390) hydrogen bonds : angle 5.38270 ( 993) link_BETA1-4 : bond 0.00687 ( 3) link_BETA1-4 : angle 2.38486 ( 9) link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 3.50739 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.9151 (ppp) cc_final: 0.8245 (ppp) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.0878 time to fit residues: 3.8374 Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 41 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042222 restraints weight = 175926.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043458 restraints weight = 80965.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044255 restraints weight = 47346.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.044814 restraints weight = 32543.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045169 restraints weight = 24685.045| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7912 Z= 0.148 Angle : 0.568 8.548 10905 Z= 0.293 Chirality : 0.044 0.260 1351 Planarity : 0.004 0.038 1378 Dihedral : 6.924 52.653 1317 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.76 % Allowed : 6.19 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1094 helix: 1.78 (0.46), residues: 133 sheet: 0.07 (0.23), residues: 465 loop : -0.97 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.011 0.001 TYR A 269 PHE 0.010 0.001 PHE C 116 TRP 0.012 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7893) covalent geometry : angle 0.54896 (10860) SS BOND : bond 0.00489 ( 12) SS BOND : angle 1.48636 ( 24) hydrogen bonds : bond 0.04086 ( 390) hydrogen bonds : angle 5.28900 ( 993) link_BETA1-4 : bond 0.00654 ( 3) link_BETA1-4 : angle 2.34175 ( 9) link_NAG-ASN : bond 0.00398 ( 4) link_NAG-ASN : angle 3.47896 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 27 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7991 (tp) REVERT: D 36 MET cc_start: 0.9195 (ppp) cc_final: 0.8134 (ppp) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.1036 time to fit residues: 4.8898 Evaluate side-chains 26 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 83 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041709 restraints weight = 177711.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.042925 restraints weight = 81547.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043735 restraints weight = 47792.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044278 restraints weight = 32683.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.044609 restraints weight = 24927.149| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7912 Z= 0.174 Angle : 0.582 8.201 10905 Z= 0.304 Chirality : 0.044 0.266 1351 Planarity : 0.004 0.040 1378 Dihedral : 6.882 52.147 1317 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.60 % Allowed : 7.10 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1094 helix: 1.71 (0.46), residues: 133 sheet: -0.02 (0.23), residues: 474 loop : -1.04 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 7 TYR 0.010 0.001 TYR A 269 PHE 0.012 0.001 PHE B 63 TRP 0.010 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7893) covalent geometry : angle 0.56586 (10860) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.09388 ( 24) hydrogen bonds : bond 0.04374 ( 390) hydrogen bonds : angle 5.47203 ( 993) link_BETA1-4 : bond 0.00654 ( 3) link_BETA1-4 : angle 2.24635 ( 9) link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 3.51217 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7989 (tp) REVERT: D 36 MET cc_start: 0.9233 (ppp) cc_final: 0.8237 (ppp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0994 time to fit residues: 4.4101 Evaluate side-chains 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041985 restraints weight = 174618.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.043221 restraints weight = 79081.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044019 restraints weight = 45786.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.044524 restraints weight = 31301.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.044902 restraints weight = 24172.687| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7912 Z= 0.138 Angle : 0.556 8.168 10905 Z= 0.288 Chirality : 0.044 0.251 1351 Planarity : 0.004 0.038 1378 Dihedral : 6.633 51.682 1317 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.60 % Allowed : 6.80 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 1094 helix: 1.94 (0.47), residues: 133 sheet: -0.10 (0.23), residues: 488 loop : -0.87 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.008 0.001 TYR D 26 PHE 0.010 0.001 PHE C 116 TRP 0.013 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7893) covalent geometry : angle 0.53675 (10860) SS BOND : bond 0.00460 ( 12) SS BOND : angle 1.56418 ( 24) hydrogen bonds : bond 0.03969 ( 390) hydrogen bonds : angle 5.25526 ( 993) link_BETA1-4 : bond 0.00721 ( 3) link_BETA1-4 : angle 2.34251 ( 9) link_NAG-ASN : bond 0.00355 ( 4) link_NAG-ASN : angle 3.40976 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7957 (tp) REVERT: D 36 MET cc_start: 0.9207 (ppp) cc_final: 0.8220 (ppp) outliers start: 4 outliers final: 3 residues processed: 23 average time/residue: 0.0997 time to fit residues: 4.2733 Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042053 restraints weight = 175866.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.043288 restraints weight = 80219.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044087 restraints weight = 46585.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044591 restraints weight = 31872.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044892 restraints weight = 24604.835| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7912 Z= 0.132 Angle : 0.544 8.971 10905 Z= 0.280 Chirality : 0.044 0.244 1351 Planarity : 0.004 0.036 1378 Dihedral : 6.444 51.695 1317 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.60 % Allowed : 7.10 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1094 helix: 2.10 (0.47), residues: 133 sheet: -0.06 (0.23), residues: 502 loop : -0.83 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 7 TYR 0.008 0.001 TYR D 26 PHE 0.009 0.001 PHE C 116 TRP 0.012 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7893) covalent geometry : angle 0.52821 (10860) SS BOND : bond 0.00459 ( 12) SS BOND : angle 0.71422 ( 24) hydrogen bonds : bond 0.03764 ( 390) hydrogen bonds : angle 5.18028 ( 993) link_BETA1-4 : bond 0.00640 ( 3) link_BETA1-4 : angle 2.32251 ( 9) link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 3.31040 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7973 (tp) REVERT: A 289 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7647 (ptm) REVERT: D 36 MET cc_start: 0.9173 (ppp) cc_final: 0.8231 (ppp) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.1001 time to fit residues: 4.0975 Evaluate side-chains 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042118 restraints weight = 175018.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043367 restraints weight = 79935.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044198 restraints weight = 46198.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044627 restraints weight = 31236.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045048 restraints weight = 24624.310| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7912 Z= 0.122 Angle : 0.542 8.021 10905 Z= 0.277 Chirality : 0.044 0.240 1351 Planarity : 0.004 0.033 1378 Dihedral : 6.379 51.618 1317 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.60 % Allowed : 7.25 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1094 helix: 2.19 (0.47), residues: 133 sheet: -0.05 (0.24), residues: 488 loop : -0.82 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 7 TYR 0.008 0.001 TYR D 26 PHE 0.009 0.001 PHE C 116 TRP 0.014 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7893) covalent geometry : angle 0.52605 (10860) SS BOND : bond 0.00433 ( 12) SS BOND : angle 0.82220 ( 24) hydrogen bonds : bond 0.03691 ( 390) hydrogen bonds : angle 5.12606 ( 993) link_BETA1-4 : bond 0.00684 ( 3) link_BETA1-4 : angle 2.34400 ( 9) link_NAG-ASN : bond 0.00278 ( 4) link_NAG-ASN : angle 3.28473 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue VAL 64 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 ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue THR 98 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 116 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 149 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 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue VAL 195 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue LYS 209 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 LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue THR 380 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue VAL 429 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue TYR 441 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 ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue TYR 494 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue ILE 39 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue VAL 50 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue THR 59 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 67 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue ILE 83 is missing expected H atoms. Skipping. Residue THR 84 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 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 ILE 107 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 143 is missing expected H atoms. Skipping. Residue THR 144 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 173 is missing expected H atoms. Skipping. Residue LYS 176 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 236 is missing expected H atoms. Skipping. Residue THR 245 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LEU 255 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 ILE 319 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue VAL 323 is missing expected H atoms. Skipping. Residue VAL 325 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 364 is missing expected H atoms. Skipping. Residue LEU 379 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue VAL 399 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue LEU 416 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue THR 437 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue TYR 441 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 VAL 473 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue THR 488 is missing expected H atoms. Skipping. Residue VAL 489 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue VAL 497 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue THR 500 is missing expected H atoms. Skipping. Residue VAL 8 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue VAL 38 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Evaluate side-chains 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7963 (tp) REVERT: A 289 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7645 (ptm) REVERT: D 36 MET cc_start: 0.9176 (ppp) cc_final: 0.8258 (ppp) outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.1000 time to fit residues: 4.4545 Evaluate side-chains 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain B residue 428 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 84 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042613 restraints weight = 176519.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043859 restraints weight = 79786.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044680 restraints weight = 46461.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045222 restraints weight = 31751.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.045589 restraints weight = 24197.172| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7912 Z= 0.096 Angle : 0.519 8.003 10905 Z= 0.264 Chirality : 0.044 0.219 1351 Planarity : 0.004 0.034 1378 Dihedral : 6.035 51.625 1317 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.30 % Allowed : 7.40 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.27), residues: 1094 helix: 2.46 (0.48), residues: 134 sheet: -0.03 (0.24), residues: 497 loop : -0.68 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.007 0.001 TYR A 146 PHE 0.009 0.001 PHE B 63 TRP 0.015 0.001 TRP B 66 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 7893) covalent geometry : angle 0.50345 (10860) SS BOND : bond 0.00380 ( 12) SS BOND : angle 0.77119 ( 24) hydrogen bonds : bond 0.03173 ( 390) hydrogen bonds : angle 4.88493 ( 993) link_BETA1-4 : bond 0.00623 ( 3) link_BETA1-4 : angle 2.49072 ( 9) link_NAG-ASN : bond 0.00152 ( 4) link_NAG-ASN : angle 3.15273 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.32 seconds wall clock time: 38 minutes 27.65 seconds (2307.65 seconds total)