Starting phenix.real_space_refine on Thu Jun 12 23:15:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfq_27411/06_2025/8dfq_27411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfq_27411/06_2025/8dfq_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_27411/06_2025/8dfq_27411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfq_27411/06_2025/8dfq_27411.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfq_27411/06_2025/8dfq_27411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfq_27411/06_2025/8dfq_27411.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 14, 'ASP:plan': 20, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 23, 'PHE:plan': 4, 'GLU:plan': 27, 'ARG:plan': 7} 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: {'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5} 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: {'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6} 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: 9.38, per 1000 atoms: 0.66 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: 3.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.46 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: 5.44 Time building geometry restraints manager: 4.43 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: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.800 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.007 TRP B 66 HIS 0.009 0.003 HIS A 180 PHE 0.108 0.006 PHE D 129 TYR 0.028 0.007 TYR B 350 ARG 0.020 0.004 ARG B 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 4) link_NAG-ASN : angle 8.15458 ( 12) link_BETA1-4 : bond 0.00720 ( 3) link_BETA1-4 : angle 4.02643 ( 9) hydrogen bonds : bond 0.19865 ( 390) hydrogen bonds : angle 8.84635 ( 993) SS BOND : bond 0.01358 ( 12) SS BOND : angle 2.57388 ( 24) covalent geometry : bond 0.00719 ( 7893) covalent geometry : angle 1.12069 (10860) *********************** 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 : 1.119 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: 0.4881 time to fit residues: 20.4625 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 : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.051401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.043563 restraints weight = 176453.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044806 restraints weight = 83266.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045612 restraints weight = 48864.328| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7912 Z= 0.179 Angle : 0.730 12.384 10905 Z= 0.384 Chirality : 0.046 0.205 1351 Planarity : 0.005 0.044 1378 Dihedral : 9.252 59.073 1317 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1094 helix: 0.45 (0.41), residues: 134 sheet: 0.26 (0.24), residues: 443 loop : -0.99 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 66 HIS 0.003 0.001 HIS A 180 PHE 0.019 0.002 PHE B 63 TYR 0.018 0.002 TYR A 146 ARG 0.004 0.001 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 5.13467 ( 12) link_BETA1-4 : bond 0.00875 ( 3) link_BETA1-4 : angle 2.94560 ( 9) hydrogen bonds : bond 0.06029 ( 390) hydrogen bonds : angle 6.35115 ( 993) SS BOND : bond 0.00573 ( 12) SS BOND : angle 1.71322 ( 24) covalent geometry : bond 0.00367 ( 7893) covalent geometry : angle 0.70117 (10860) *********************** 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 27 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 289 MET cc_start: 0.7751 (ttp) cc_final: 0.7445 (ttm) REVERT: D 36 MET cc_start: 0.9207 (ppp) cc_final: 0.8314 (ppp) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.2652 time to fit residues: 13.1579 Evaluate side-chains 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 1 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.051025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043177 restraints weight = 174349.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044431 restraints weight = 81234.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045270 restraints weight = 47416.699| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2222 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= 0.151 Angle : 0.617 8.157 10905 Z= 0.324 Chirality : 0.045 0.238 1351 Planarity : 0.004 0.044 1378 Dihedral : 7.894 57.541 1317 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.30 % Allowed : 5.59 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1094 helix: 1.27 (0.45), residues: 134 sheet: 0.10 (0.23), residues: 452 loop : -0.92 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 66 HIS 0.003 0.001 HIS A 185 PHE 0.017 0.001 PHE B 63 TYR 0.012 0.001 TYR A 146 ARG 0.004 0.000 ARG D 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 4) link_NAG-ASN : angle 3.98989 ( 12) link_BETA1-4 : bond 0.00912 ( 3) link_BETA1-4 : angle 2.54055 ( 9) hydrogen bonds : bond 0.05052 ( 390) hydrogen bonds : angle 5.68619 ( 993) SS BOND : bond 0.00696 ( 12) SS BOND : angle 1.54976 ( 24) covalent geometry : bond 0.00321 ( 7893) covalent geometry : angle 0.59502 (10860) *********************** 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 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.9110 (ppp) cc_final: 0.8237 (ppp) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.2944 time to fit residues: 12.8307 Evaluate side-chains 23 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.051159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043283 restraints weight = 175170.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.044545 restraints weight = 81703.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045381 restraints weight = 47623.117| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2638 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= 0.125 Angle : 0.579 7.710 10905 Z= 0.300 Chirality : 0.044 0.233 1351 Planarity : 0.004 0.038 1378 Dihedral : 7.387 56.649 1317 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.45 % Allowed : 5.59 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1094 helix: 1.74 (0.46), residues: 134 sheet: 0.07 (0.23), residues: 465 loop : -0.79 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 440 HIS 0.004 0.001 HIS A 185 PHE 0.009 0.001 PHE B 63 TYR 0.011 0.001 TYR A 146 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 4) link_NAG-ASN : angle 3.63924 ( 12) link_BETA1-4 : bond 0.00700 ( 3) link_BETA1-4 : angle 2.59618 ( 9) hydrogen bonds : bond 0.04056 ( 390) hydrogen bonds : angle 5.39176 ( 993) SS BOND : bond 0.00412 ( 12) SS BOND : angle 1.38070 ( 24) covalent geometry : bond 0.00271 ( 7893) covalent geometry : angle 0.55857 (10860) *********************** 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: 3 poor density : 23 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7880 (tp) REVERT: D 36 MET cc_start: 0.9046 (ppp) cc_final: 0.8111 (ppp) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.2228 time to fit residues: 10.6426 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 : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU 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 79 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.050359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042538 restraints weight = 174066.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.043790 restraints weight = 79743.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044593 restraints weight = 46391.201| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2963 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= 0.165 Angle : 0.584 8.090 10905 Z= 0.303 Chirality : 0.044 0.261 1351 Planarity : 0.004 0.039 1378 Dihedral : 7.158 54.519 1317 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.60 % Allowed : 5.59 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1094 helix: 1.67 (0.46), residues: 133 sheet: -0.01 (0.23), residues: 462 loop : -0.88 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 PHE 0.012 0.001 PHE B 63 TYR 0.010 0.001 TYR A 146 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 4) link_NAG-ASN : angle 3.58845 ( 12) link_BETA1-4 : bond 0.00628 ( 3) link_BETA1-4 : angle 2.33902 ( 9) hydrogen bonds : bond 0.04396 ( 390) hydrogen bonds : angle 5.37530 ( 993) SS BOND : bond 0.00546 ( 12) SS BOND : angle 1.48938 ( 24) covalent geometry : bond 0.00362 ( 7893) covalent geometry : angle 0.56433 (10860) *********************** 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 26 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.9151 (ppp) cc_final: 0.8041 (ppp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.2322 time to fit residues: 10.4864 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 : 1.255 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.050346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042513 restraints weight = 176574.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.043772 restraints weight = 81093.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044584 restraints weight = 46980.230| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3185 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= 0.137 Angle : 0.562 8.044 10905 Z= 0.290 Chirality : 0.044 0.255 1351 Planarity : 0.004 0.037 1378 Dihedral : 6.918 53.351 1317 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.60 % Allowed : 6.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1094 helix: 1.90 (0.47), residues: 133 sheet: 0.03 (0.23), residues: 466 loop : -0.86 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 PHE 0.009 0.001 PHE C 116 TYR 0.012 0.001 TYR A 269 ARG 0.001 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 4) link_NAG-ASN : angle 3.50783 ( 12) link_BETA1-4 : bond 0.00749 ( 3) link_BETA1-4 : angle 2.37452 ( 9) hydrogen bonds : bond 0.03997 ( 390) hydrogen bonds : angle 5.22880 ( 993) SS BOND : bond 0.00606 ( 12) SS BOND : angle 1.41154 ( 24) covalent geometry : bond 0.00299 ( 7893) covalent geometry : angle 0.54241 (10860) *********************** 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 26 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.9162 (ppp) cc_final: 0.8054 (ppp) outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.2232 time to fit residues: 10.4507 Evaluate side-chains 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.049987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042199 restraints weight = 178006.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043431 restraints weight = 81266.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044244 restraints weight = 47433.710| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3368 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= 0.146 Angle : 0.565 7.978 10905 Z= 0.293 Chirality : 0.044 0.255 1351 Planarity : 0.004 0.036 1378 Dihedral : 6.771 52.644 1317 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.60 % Allowed : 6.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1094 helix: 1.87 (0.46), residues: 133 sheet: 0.00 (0.23), residues: 465 loop : -0.89 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 PHE 0.012 0.001 PHE B 63 TYR 0.009 0.001 TYR A 269 ARG 0.002 0.000 ARG D 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 4) link_NAG-ASN : angle 3.44460 ( 12) link_BETA1-4 : bond 0.00650 ( 3) link_BETA1-4 : angle 2.34077 ( 9) hydrogen bonds : bond 0.04051 ( 390) hydrogen bonds : angle 5.30915 ( 993) SS BOND : bond 0.00451 ( 12) SS BOND : angle 1.29372 ( 24) covalent geometry : bond 0.00318 ( 7893) covalent geometry : angle 0.54738 (10860) *********************** 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 : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7954 (tp) REVERT: D 36 MET cc_start: 0.9178 (ppp) cc_final: 0.8101 (ppp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.2226 time to fit residues: 9.9902 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 : 1.121 ------------------------------------------------------------------------------- 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 51 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.049459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041718 restraints weight = 176956.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.042947 restraints weight = 80869.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043734 restraints weight = 46984.909| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3585 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= 0.170 Angle : 0.574 8.299 10905 Z= 0.297 Chirality : 0.044 0.263 1351 Planarity : 0.004 0.035 1378 Dihedral : 6.756 51.636 1317 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.60 % Allowed : 6.50 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1094 helix: 1.83 (0.46), residues: 133 sheet: -0.11 (0.23), residues: 493 loop : -0.90 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 PHE 0.011 0.001 PHE A 118 TYR 0.011 0.001 TYR D 26 ARG 0.002 0.000 ARG D 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 4) link_NAG-ASN : angle 3.51204 ( 12) link_BETA1-4 : bond 0.00623 ( 3) link_BETA1-4 : angle 2.23623 ( 9) hydrogen bonds : bond 0.04279 ( 390) hydrogen bonds : angle 5.34537 ( 993) SS BOND : bond 0.00524 ( 12) SS BOND : angle 1.48206 ( 24) covalent geometry : bond 0.00374 ( 7893) covalent geometry : angle 0.55538 (10860) *********************** 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 : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7959 (tp) REVERT: A 289 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7581 (ptm) REVERT: D 36 MET cc_start: 0.9224 (ppp) cc_final: 0.8268 (ppp) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.2434 time to fit residues: 10.5095 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 : 1.126 ------------------------------------------------------------------------------- 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 77 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 57 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.049993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.042246 restraints weight = 174914.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.043488 restraints weight = 79218.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.044274 restraints weight = 45913.263| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3748 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= 0.114 Angle : 0.536 8.466 10905 Z= 0.276 Chirality : 0.044 0.239 1351 Planarity : 0.004 0.034 1378 Dihedral : 6.409 51.727 1317 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.60 % Allowed : 6.65 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1094 helix: 2.23 (0.47), residues: 133 sheet: -0.09 (0.23), residues: 491 loop : -0.69 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 PHE 0.009 0.001 PHE C 116 TYR 0.007 0.001 TYR D 26 ARG 0.002 0.000 ARG D 7 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 4) link_NAG-ASN : angle 3.33612 ( 12) link_BETA1-4 : bond 0.00779 ( 3) link_BETA1-4 : angle 2.41521 ( 9) hydrogen bonds : bond 0.03646 ( 390) hydrogen bonds : angle 5.10008 ( 993) SS BOND : bond 0.00433 ( 12) SS BOND : angle 0.76895 ( 24) covalent geometry : bond 0.00250 ( 7893) covalent geometry : angle 0.51996 (10860) *********************** 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 25 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 289 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7530 (ptm) REVERT: D 36 MET cc_start: 0.9178 (ppp) cc_final: 0.8177 (ppp) outliers start: 4 outliers final: 2 residues processed: 24 average time/residue: 0.2272 time to fit residues: 10.0645 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 : 1.211 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.049682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.041938 restraints weight = 177595.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043162 restraints weight = 81215.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043818 restraints weight = 47477.434| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3865 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= 0.141 Angle : 0.544 7.869 10905 Z= 0.281 Chirality : 0.044 0.241 1351 Planarity : 0.004 0.033 1378 Dihedral : 6.391 51.526 1317 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.60 % Allowed : 6.65 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1094 helix: 2.13 (0.47), residues: 133 sheet: -0.11 (0.23), residues: 491 loop : -0.76 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 66 HIS 0.004 0.001 HIS A 185 PHE 0.010 0.001 PHE C 116 TYR 0.009 0.001 TYR D 26 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 4) link_NAG-ASN : angle 3.33719 ( 12) link_BETA1-4 : bond 0.00635 ( 3) link_BETA1-4 : angle 2.30191 ( 9) hydrogen bonds : bond 0.03855 ( 390) hydrogen bonds : angle 5.14086 ( 993) SS BOND : bond 0.00454 ( 12) SS BOND : angle 0.97662 ( 24) covalent geometry : bond 0.00309 ( 7893) covalent geometry : angle 0.52777 (10860) ********************** 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 24 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7903 (tp) REVERT: A 289 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7581 (ptm) REVERT: D 36 MET cc_start: 0.9185 (ppp) cc_final: 0.8275 (ppp) outliers start: 4 outliers final: 2 residues processed: 23 average time/residue: 0.2580 time to fit residues: 11.1272 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 : 1.303 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 21 optimal weight: 0.0060 chunk 98 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.050340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042586 restraints weight = 175266.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043844 restraints weight = 79236.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044653 restraints weight = 45817.203| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7912 Z= 0.087 Angle : 0.516 7.952 10905 Z= 0.263 Chirality : 0.044 0.221 1351 Planarity : 0.004 0.032 1378 Dihedral : 6.091 51.605 1317 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.45 % Allowed : 6.80 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.27), residues: 1094 helix: 2.43 (0.48), residues: 134 sheet: -0.04 (0.23), residues: 501 loop : -0.58 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 66 HIS 0.003 0.001 HIS A 185 PHE 0.010 0.001 PHE B 63 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 4) link_NAG-ASN : angle 3.19591 ( 12) link_BETA1-4 : bond 0.00735 ( 3) link_BETA1-4 : angle 2.49851 ( 9) hydrogen bonds : bond 0.03267 ( 390) hydrogen bonds : angle 4.90049 ( 993) SS BOND : bond 0.00379 ( 12) SS BOND : angle 0.70918 ( 24) covalent geometry : bond 0.00190 ( 7893) covalent geometry : angle 0.49936 (10860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4201.76 seconds wall clock time: 73 minutes 17.92 seconds (4397.92 seconds total)