Starting phenix.real_space_refine on Wed May 21 22:12:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x80_38131/05_2025/8x80_38131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x80_38131/05_2025/8x80_38131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x80_38131/05_2025/8x80_38131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x80_38131/05_2025/8x80_38131.map" model { file = "/net/cci-nas-00/data/ceres_data/8x80_38131/05_2025/8x80_38131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x80_38131/05_2025/8x80_38131.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 14083 2.51 5 N 3557 2.21 5 O 4100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21890 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6162 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 715} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 715} Chain breaks: 1 Chain: "E" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "D" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 809 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 715} Chain breaks: 1 Chain: "F" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 15.20, per 1000 atoms: 0.69 Number of scatterers: 21890 At special positions: 0 Unit cell: (147.9, 147.05, 209.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4100 8.00 N 3557 7.00 C 14083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 352 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 413 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 488 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS F 117 " - pdb=" SG CYS F 167 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " BETA1-6 " NAG G 1 " - " FUC G 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 3 " " NAG I 1 " - " FUC I 3 " NAG-ASN " NAG A 901 " - " ASN A 750 " " NAG A 902 " - " ASN A 624 " " NAG A 903 " - " ASN A 397 " " NAG A 904 " - " ASN A 516 " " NAG A 905 " - " ASN A 728 " " NAG B 901 " - " ASN B 750 " " NAG B 902 " - " ASN B 624 " " NAG B 904 " - " ASN B 516 " " NAG B 905 " - " ASN B 728 " " NAG C 901 " - " ASN C 750 " " NAG C 902 " - " ASN C 624 " " NAG C 904 " - " ASN C 516 " " NAG C 905 " - " ASN C 728 " " NAG G 1 " - " ASN A 347 " " NAG H 1 " - " ASN B 347 " " NAG I 1 " - " ASN C 347 " Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.5 seconds 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5172 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 50 sheets defined 15.2% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.981A pdb=" N LYS A 109 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.675A pdb=" N GLN A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.879A pdb=" N VAL A 535 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.906A pdb=" N ASN B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 732 through 737 removed outlier: 3.855A pdb=" N SER B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 737' Processing helix chain 'E' and resid 23 through 43 removed outlier: 3.578A pdb=" N VAL E 27 " --> pdb=" O PRO E 23 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 32 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 88 removed outlier: 3.619A pdb=" N SER E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 115 removed outlier: 3.681A pdb=" N ILE E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN E 96 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 130 through 138 removed outlier: 4.056A pdb=" N VAL E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 162 removed outlier: 4.089A pdb=" N ASP E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 45 removed outlier: 4.007A pdb=" N ILE D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 40 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 removed outlier: 4.123A pdb=" N GLN D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.911A pdb=" N GLN D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 143 through 164 removed outlier: 3.783A pdb=" N GLN D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP D 156 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 163 " --> pdb=" O TRP D 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.877A pdb=" N ILE C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 668 through 672 Processing helix chain 'C' and resid 733 through 737 Processing helix chain 'F' and resid 23 through 45 removed outlier: 3.606A pdb=" N ILE F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 removed outlier: 3.915A pdb=" N GLN F 49 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER F 50 " --> pdb=" O HIS F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 50' Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.850A pdb=" N GLN F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 115 Processing helix chain 'F' and resid 127 through 136 removed outlier: 3.600A pdb=" N GLU F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 164 Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.664A pdb=" N PHE A 33 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 34 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 164 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A 212 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 162 " --> pdb=" O CYS A 212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 216 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 158 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.664A pdb=" N PHE A 33 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 34 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 229 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 211 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 227 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.869A pdb=" N HIS A 244 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 256 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 253 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 295 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 271 Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.709A pdb=" N ILE A 334 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 353 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 336 " --> pdb=" O HIS A 351 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 351 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.709A pdb=" N ILE A 334 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 353 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 336 " --> pdb=" O HIS A 351 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 351 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 348 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS A 352 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 389 " --> pdb=" O CYS A 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 343 removed outlier: 5.873A pdb=" N ILE A 340 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 428 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 342 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 446 through 450 Processing sheet with id=AB3, first strand: chain 'A' and resid 462 through 465 removed outlier: 4.058A pdb=" N GLN A 463 " --> pdb=" O ARG A 514 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 462 through 465 removed outlier: 4.058A pdb=" N GLN A 463 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 509 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 527 " --> pdb=" O MET A 511 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.874A pdb=" N VAL A 596 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 584 through 588 removed outlier: 3.587A pdb=" N TYR A 574 " --> pdb=" O LYS A 584 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 586 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 645 through 649 Processing sheet with id=AB8, first strand: chain 'A' and resid 691 through 694 removed outlier: 3.727A pdb=" N ARG A 678 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 682 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 710 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 731 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 729 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 748 through 750 removed outlier: 6.861A pdb=" N ILE A 755 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 753 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 756 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 795 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 784 through 789 removed outlier: 4.401A pdb=" N LYS A 784 " --> pdb=" O TRP A 774 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 786 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 772 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 182 through 186 removed outlier: 3.998A pdb=" N LYS B 34 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 33 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 129 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP B 127 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 196 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 282 through 286 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.606A pdb=" N VAL B 410 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 408 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.606A pdb=" N VAL B 410 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 408 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.724A pdb=" N VAL B 348 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 434 through 438 removed outlier: 4.246A pdb=" N SER B 435 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG B 448 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.613A pdb=" N GLU B 484 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 466 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 461 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.613A pdb=" N GLU B 484 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 466 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 461 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 541 through 547 removed outlier: 6.214A pdb=" N SER B 542 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU B 559 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 544 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 584 through 588 removed outlier: 3.815A pdb=" N TYR B 574 " --> pdb=" O LYS B 584 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 570 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 612 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 645 through 649 removed outlier: 3.893A pdb=" N PHE B 701 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 679 through 684 removed outlier: 3.510A pdb=" N VAL B 680 " --> pdb=" O LEU B 715 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 710 " --> pdb=" O PHE B 731 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 741 through 750 removed outlier: 3.762A pdb=" N SER B 743 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 747 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 784 through 789 removed outlier: 3.790A pdb=" N LYS B 784 " --> pdb=" O TRP B 774 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B 774 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 786 " --> pdb=" O ILE B 772 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 771 " --> pdb=" O TYR B 812 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE B 809 " --> pdb=" O ILE B 825 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 97 through 98 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 209 through 217 current: chain 'C' and resid 127 through 133 Processing sheet with id=AD8, first strand: chain 'C' and resid 182 through 186 removed outlier: 4.267A pdb=" N VAL C 159 " --> pdb=" O CYS C 186 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 210 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.577A pdb=" N TYR C 273 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 284 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 275 through 276 Processing sheet with id=AE2, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AE3, first strand: chain 'C' and resid 342 through 343 removed outlier: 6.689A pdb=" N THR C 342 " --> pdb=" O ILE C 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AE5, first strand: chain 'C' and resid 366 through 370 removed outlier: 3.576A pdb=" N VAL C 367 " --> pdb=" O CYS C 413 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 435 through 438 removed outlier: 4.472A pdb=" N SER C 435 " --> pdb=" O ARG C 448 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 448 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 445 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS C 447 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 498 " --> pdb=" O CYS C 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 484 through 486 removed outlier: 3.768A pdb=" N GLU C 484 " --> pdb=" O TYR C 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 464 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 461 " --> pdb=" O ASN C 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN C 463 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 465 " --> pdb=" O TRP C 512 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 512 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 484 through 486 removed outlier: 3.768A pdb=" N GLU C 484 " --> pdb=" O TYR C 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 464 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 461 " --> pdb=" O ASN C 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN C 463 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 465 " --> pdb=" O TRP C 512 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 512 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 544 through 547 removed outlier: 3.558A pdb=" N VAL C 596 " --> pdb=" O ILE C 556 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 584 through 588 removed outlier: 3.590A pdb=" N PHE C 570 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 646 through 649 removed outlier: 3.578A pdb=" N PHE C 701 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 678 through 685 Processing sheet with id=AF4, first strand: chain 'C' and resid 741 through 747 removed outlier: 3.585A pdb=" N SER C 743 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 754 " --> pdb=" O ILE C 797 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 797 " --> pdb=" O VAL C 754 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 784 through 789 removed outlier: 3.719A pdb=" N LYS C 784 " --> pdb=" O TRP C 774 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 788 " --> pdb=" O PHE C 770 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR C 769 " --> pdb=" O ILE C 814 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1788 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: 8.98 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6755 1.34 - 1.47: 5512 1.47 - 1.59: 9988 1.59 - 1.71: 1 1.71 - 1.83: 210 Bond restraints: 22466 Sorted by residual: bond pdb=" C1 NAG C 904 " pdb=" O5 NAG C 904 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.586 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 22461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 30420 3.63 - 7.25: 161 7.25 - 10.88: 13 10.88 - 14.51: 5 14.51 - 18.14: 2 Bond angle restraints: 30601 Sorted by residual: angle pdb=" CA GLU B 459 " pdb=" CB GLU B 459 " pdb=" CG GLU B 459 " ideal model delta sigma weight residual 114.10 126.21 -12.11 2.00e+00 2.50e-01 3.67e+01 angle pdb=" CA ARG A 678 " pdb=" CB ARG A 678 " pdb=" CG ARG A 678 " ideal model delta sigma weight residual 114.10 125.30 -11.20 2.00e+00 2.50e-01 3.14e+01 angle pdb=" CG ARG A 678 " pdb=" CD ARG A 678 " pdb=" NE ARG A 678 " ideal model delta sigma weight residual 112.00 123.33 -11.33 2.20e+00 2.07e-01 2.65e+01 angle pdb=" C GLN B 331 " pdb=" N ASP B 332 " pdb=" CA ASP B 332 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" CA LEU C 253 " pdb=" CB LEU C 253 " pdb=" CG LEU C 253 " ideal model delta sigma weight residual 116.30 132.46 -16.16 3.50e+00 8.16e-02 2.13e+01 ... (remaining 30596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.84: 12419 24.84 - 49.69: 1278 49.69 - 74.53: 151 74.53 - 99.38: 41 99.38 - 124.22: 10 Dihedral angle restraints: 13899 sinusoidal: 5934 harmonic: 7965 Sorted by residual: dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 447 " pdb=" CB CYS A 447 " ideal model delta sinusoidal sigma weight residual 93.00 4.46 88.54 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 488 " pdb=" SG CYS A 488 " pdb=" SG CYS A 498 " pdb=" CB CYS A 498 " ideal model delta sinusoidal sigma weight residual -86.00 0.01 -86.01 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA GLN C 501 " pdb=" C GLN C 501 " pdb=" N PRO C 502 " pdb=" CA PRO C 502 " ideal model delta harmonic sigma weight residual -180.00 -139.85 -40.15 0 5.00e+00 4.00e-02 6.45e+01 ... (remaining 13896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3223 0.089 - 0.178: 306 0.178 - 0.267: 4 0.267 - 0.357: 3 0.357 - 0.446: 2 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG A 904 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 904 " pdb=" O5 NAG A 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" C1 NAG B 904 " pdb=" ND2 ASN B 516 " pdb=" C2 NAG B 904 " pdb=" O5 NAG B 904 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.24 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3535 not shown) Planarity restraints: 3806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 501 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO C 502 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 502 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 502 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 600 " -0.054 5.00e-02 4.00e+02 7.90e-02 9.97e+00 pdb=" N PRO B 601 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 601 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 601 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 624 " -0.004 2.00e-02 2.50e+03 2.37e-02 7.00e+00 pdb=" CG ASN A 624 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 624 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 624 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.027 2.00e-02 2.50e+03 ... (remaining 3803 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 372 2.65 - 3.22: 20155 3.22 - 3.78: 35021 3.78 - 4.34: 44916 4.34 - 4.90: 70931 Nonbonded interactions: 171395 Sorted by model distance: nonbonded pdb=" O VAL D 144 " pdb=" OG SER D 148 " model vdw 2.093 3.040 nonbonded pdb=" NZ LYS A 614 " pdb=" O ARG A 615 " model vdw 2.155 3.120 nonbonded pdb=" O HIS B 800 " pdb=" ND1 HIS B 800 " model vdw 2.190 3.120 nonbonded pdb=" OD1 ASN A 371 " pdb=" OH TYR E 140 " model vdw 2.196 3.040 nonbonded pdb=" O ALA D 80 " pdb=" NE2 GLN D 84 " model vdw 2.197 3.120 ... (remaining 171390 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' selection = (chain 'B' and (resid 23 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 829 or resid 901 through 905)) selection = (chain 'C' and (resid 23 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 829 or resid 901 through 905)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 16.460 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 51.670 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.003 0.099 22528 Z= 0.159 Angle : 0.756 19.651 30748 Z= 0.362 Chirality : 0.047 0.446 3538 Planarity : 0.004 0.081 3790 Dihedral : 18.696 124.221 8610 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.73 % Rotamer: Outliers : 0.72 % Allowed : 36.82 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: -0.19 (0.16), residues: 2672 helix: 1.11 (0.29), residues: 344 sheet: 0.03 (0.19), residues: 836 loop : -0.46 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 785 HIS 0.006 0.001 HIS F 47 PHE 0.017 0.001 PHE A 815 TYR 0.030 0.001 TYR B 354 ARG 0.015 0.000 ARG A 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 16) link_NAG-ASN : angle 4.97378 ( 48) link_BETA1-4 : bond 0.00775 ( 4) link_BETA1-4 : angle 4.10390 ( 12) hydrogen bonds : bond 0.28331 ( 620) hydrogen bonds : angle 9.86005 ( 1788) link_BETA1-6 : bond 0.00587 ( 3) link_BETA1-6 : angle 1.25012 ( 9) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.36155 ( 78) covalent geometry : bond 0.00339 (22466) covalent geometry : angle 0.72321 (30601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 437 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 VAL cc_start: 0.8187 (t) cc_final: 0.7700 (m) REVERT: A 634 MET cc_start: 0.6444 (ppp) cc_final: 0.6060 (ppp) REVERT: A 773 GLU cc_start: 0.7488 (pm20) cc_final: 0.7063 (pm20) REVERT: B 400 LYS cc_start: 0.8714 (mppt) cc_final: 0.8009 (mppt) REVERT: E 44 ASP cc_start: 0.7972 (t0) cc_final: 0.7754 (t0) REVERT: E 51 VAL cc_start: 0.8714 (m) cc_final: 0.8505 (t) REVERT: E 136 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 640 MET cc_start: 0.6723 (pmm) cc_final: 0.6498 (pmm) REVERT: C 807 TYR cc_start: 0.6424 (m-10) cc_final: 0.5891 (m-10) REVERT: F 51 VAL cc_start: 0.8035 (m) cc_final: 0.7471 (t) REVERT: F 96 GLN cc_start: 0.7671 (tp40) cc_final: 0.7464 (tp40) outliers start: 18 outliers final: 14 residues processed: 443 average time/residue: 0.3275 time to fit residues: 224.1445 Evaluate side-chains 442 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 428 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain F residue 82 TYR Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 107 optimal weight: 0.0370 chunk 208 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 126 optimal weight: 0.0040 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 ASN B 150 ASN B 182 GLN B 455 GLN B 698 HIS E 47 HIS E 109 HIS E 118 HIS E 151 GLN D 151 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.249904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.229767 restraints weight = 82243.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.228333 restraints weight = 76512.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.227623 restraints weight = 63550.104| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22528 Z= 0.146 Angle : 0.683 13.504 30748 Z= 0.338 Chirality : 0.047 0.430 3538 Planarity : 0.004 0.087 3790 Dihedral : 9.936 120.710 3415 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.93 % Favored : 95.88 % Rotamer: Outliers : 4.38 % Allowed : 32.84 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.14 (0.17), residues: 2672 helix: 1.38 (0.28), residues: 335 sheet: -0.10 (0.18), residues: 874 loop : -0.36 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 121 HIS 0.009 0.001 HIS E 109 PHE 0.023 0.001 PHE A 815 TYR 0.018 0.001 TYR C 466 ARG 0.007 0.001 ARG A 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 16) link_NAG-ASN : angle 3.56618 ( 48) link_BETA1-4 : bond 0.01199 ( 4) link_BETA1-4 : angle 3.26763 ( 12) hydrogen bonds : bond 0.05406 ( 620) hydrogen bonds : angle 7.19629 ( 1788) link_BETA1-6 : bond 0.00347 ( 3) link_BETA1-6 : angle 1.31660 ( 9) SS BOND : bond 0.00294 ( 39) SS BOND : angle 1.37625 ( 78) covalent geometry : bond 0.00322 (22466) covalent geometry : angle 0.66325 (30601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 432 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 VAL cc_start: 0.8154 (t) cc_final: 0.7728 (m) REVERT: A 504 PHE cc_start: 0.6652 (m-80) cc_final: 0.6413 (m-80) REVERT: A 550 ASN cc_start: 0.7417 (m110) cc_final: 0.6746 (p0) REVERT: A 634 MET cc_start: 0.6506 (ppp) cc_final: 0.5929 (ppp) REVERT: B 362 PRO cc_start: 0.8522 (Cg_exo) cc_final: 0.8284 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (t) REVERT: B 459 GLU cc_start: 0.6865 (pp20) cc_final: 0.6626 (pp20) REVERT: B 507 SER cc_start: 0.8379 (m) cc_final: 0.7901 (p) REVERT: B 565 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 584 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7559 (mtmm) REVERT: B 647 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7423 (tmt170) REVERT: E 44 ASP cc_start: 0.7859 (t0) cc_final: 0.7624 (t0) REVERT: E 51 VAL cc_start: 0.8710 (m) cc_final: 0.8507 (t) REVERT: E 61 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7718 (t0) REVERT: E 119 LEU cc_start: 0.8544 (mp) cc_final: 0.8179 (mp) REVERT: E 130 SER cc_start: 0.7170 (OUTLIER) cc_final: 0.6895 (p) REVERT: E 136 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6930 (tm-30) REVERT: D 84 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8332 (mm-40) REVERT: C 614 LYS cc_start: 0.7633 (tttm) cc_final: 0.6514 (tttm) REVERT: C 665 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7965 (mmtm) REVERT: C 683 HIS cc_start: 0.5790 (OUTLIER) cc_final: 0.1878 (m-70) REVERT: C 745 SER cc_start: 0.7759 (p) cc_final: 0.7216 (t) REVERT: C 784 LYS cc_start: 0.8397 (mttp) cc_final: 0.8187 (mttp) REVERT: C 807 TYR cc_start: 0.6293 (m-10) cc_final: 0.5760 (m-10) REVERT: F 51 VAL cc_start: 0.8129 (m) cc_final: 0.7586 (t) REVERT: F 77 GLN cc_start: 0.8114 (tp40) cc_final: 0.7634 (tp40) outliers start: 110 outliers final: 62 residues processed: 498 average time/residue: 0.3269 time to fit residues: 254.4410 Evaluate side-chains 479 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 411 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 109 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 262 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 239 optimal weight: 0.0040 chunk 60 optimal weight: 0.8980 chunk 125 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 206 optimal weight: 0.0980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 150 ASN B 397 ASN B 491 GLN B 742 GLN E 109 HIS E 118 HIS E 151 GLN D 151 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN C 684 HIS ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 49 GLN F 103 ASN F 109 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.249613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.229112 restraints weight = 81942.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.226773 restraints weight = 72385.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.225236 restraints weight = 66014.400| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22528 Z= 0.129 Angle : 0.662 12.376 30748 Z= 0.320 Chirality : 0.046 0.395 3538 Planarity : 0.004 0.095 3790 Dihedral : 9.322 120.447 3395 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 5.25 % Allowed : 33.04 % Favored : 61.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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 (0.16), residues: 2672 helix: 1.43 (0.28), residues: 331 sheet: -0.07 (0.18), residues: 866 loop : -0.40 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 121 HIS 0.017 0.001 HIS F 109 PHE 0.016 0.001 PHE C 394 TYR 0.014 0.001 TYR B 411 ARG 0.009 0.000 ARG A 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 16) link_NAG-ASN : angle 3.42435 ( 48) link_BETA1-4 : bond 0.00443 ( 4) link_BETA1-4 : angle 3.44428 ( 12) hydrogen bonds : bond 0.04763 ( 620) hydrogen bonds : angle 6.62486 ( 1788) link_BETA1-6 : bond 0.00472 ( 3) link_BETA1-6 : angle 1.32863 ( 9) SS BOND : bond 0.00293 ( 39) SS BOND : angle 1.26106 ( 78) covalent geometry : bond 0.00288 (22466) covalent geometry : angle 0.64276 (30601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 424 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 VAL cc_start: 0.8171 (t) cc_final: 0.7726 (m) REVERT: A 550 ASN cc_start: 0.7524 (m110) cc_final: 0.6830 (p0) REVERT: A 614 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6783 (tptt) REVERT: A 634 MET cc_start: 0.6488 (ppp) cc_final: 0.5811 (ppp) REVERT: A 768 MET cc_start: 0.6049 (pmm) cc_final: 0.5619 (pmm) REVERT: B 174 LEU cc_start: -0.3901 (OUTLIER) cc_final: -0.4114 (pt) REVERT: B 271 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7863 (m) REVERT: B 331 GLN cc_start: 0.7080 (pm20) cc_final: 0.6876 (pm20) REVERT: B 362 PRO cc_start: 0.8550 (Cg_exo) cc_final: 0.8129 (Cg_endo) REVERT: B 365 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: B 400 LYS cc_start: 0.8775 (mptt) cc_final: 0.8429 (mptt) REVERT: B 410 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8050 (t) REVERT: B 565 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 584 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7681 (mtmm) REVERT: B 647 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7223 (tmt170) REVERT: B 713 THR cc_start: 0.8407 (m) cc_final: 0.8047 (p) REVERT: B 768 MET cc_start: 0.7274 (mpp) cc_final: 0.7040 (mpp) REVERT: E 44 ASP cc_start: 0.7939 (t0) cc_final: 0.7664 (t0) REVERT: E 51 VAL cc_start: 0.8726 (m) cc_final: 0.8511 (t) REVERT: E 119 LEU cc_start: 0.8635 (mp) cc_final: 0.8303 (mp) REVERT: E 130 SER cc_start: 0.7281 (OUTLIER) cc_final: 0.6980 (p) REVERT: C 587 GLU cc_start: 0.5773 (tm-30) cc_final: 0.5572 (tm-30) REVERT: C 614 LYS cc_start: 0.7627 (tttm) cc_final: 0.6516 (tttm) REVERT: C 615 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7781 (mtp180) REVERT: C 745 SER cc_start: 0.7744 (p) cc_final: 0.7371 (t) REVERT: C 750 ASN cc_start: 0.5729 (t0) cc_final: 0.5227 (t0) REVERT: F 51 VAL cc_start: 0.8267 (m) cc_final: 0.7721 (t) REVERT: F 77 GLN cc_start: 0.8094 (tp40) cc_final: 0.7600 (tp40) REVERT: F 96 GLN cc_start: 0.7842 (tp40) cc_final: 0.7576 (tp40) outliers start: 132 outliers final: 80 residues processed: 512 average time/residue: 0.3215 time to fit residues: 258.1093 Evaluate side-chains 493 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 405 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 647 ARG Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 742 GLN Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 801 PHE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 28 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.0670 chunk 0 optimal weight: 90.0000 chunk 203 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 252 optimal weight: 0.5980 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 150 ASN B 351 HIS B 455 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 151 GLN E 160 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.243412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.222549 restraints weight = 80875.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.221619 restraints weight = 85571.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.219745 restraints weight = 62039.134| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 22528 Z= 0.270 Angle : 0.758 14.719 30748 Z= 0.379 Chirality : 0.050 0.376 3538 Planarity : 0.005 0.104 3790 Dihedral : 9.221 121.308 3390 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.01 % Favored : 94.80 % Rotamer: Outliers : 6.61 % Allowed : 32.92 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.44 (0.16), residues: 2672 helix: 1.12 (0.27), residues: 329 sheet: -0.25 (0.18), residues: 884 loop : -0.58 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 121 HIS 0.007 0.001 HIS E 47 PHE 0.024 0.002 PHE B 731 TYR 0.028 0.002 TYR A 407 ARG 0.009 0.001 ARG F 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 16) link_NAG-ASN : angle 3.63805 ( 48) link_BETA1-4 : bond 0.00574 ( 4) link_BETA1-4 : angle 3.34892 ( 12) hydrogen bonds : bond 0.05904 ( 620) hydrogen bonds : angle 6.66065 ( 1788) link_BETA1-6 : bond 0.00385 ( 3) link_BETA1-6 : angle 1.72873 ( 9) SS BOND : bond 0.00548 ( 39) SS BOND : angle 1.84800 ( 78) covalent geometry : bond 0.00609 (22466) covalent geometry : angle 0.73626 (30601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 418 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 THR cc_start: 0.7433 (p) cc_final: 0.6689 (m) REVERT: A 380 GLN cc_start: 0.8729 (mp10) cc_final: 0.8359 (mp10) REVERT: A 391 VAL cc_start: 0.7927 (p) cc_final: 0.7712 (t) REVERT: A 550 ASN cc_start: 0.7726 (m110) cc_final: 0.7341 (p0) REVERT: A 585 MET cc_start: 0.6654 (tpt) cc_final: 0.6439 (tpt) REVERT: A 614 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6749 (tptt) REVERT: A 634 MET cc_start: 0.6801 (ppp) cc_final: 0.5975 (ppp) REVERT: A 667 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6349 (mm) REVERT: A 713 THR cc_start: 0.1965 (OUTLIER) cc_final: 0.1266 (t) REVERT: A 760 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 794 LYS cc_start: 0.8093 (tptp) cc_final: 0.7697 (tptp) REVERT: A 795 TYR cc_start: 0.6912 (t80) cc_final: 0.6509 (t80) REVERT: B 271 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7956 (m) REVERT: B 350 PHE cc_start: 0.5813 (OUTLIER) cc_final: 0.5528 (m-80) REVERT: B 355 LYS cc_start: 0.8031 (tppt) cc_final: 0.7445 (tptm) REVERT: B 400 LYS cc_start: 0.8806 (mptt) cc_final: 0.8420 (mptt) REVERT: B 436 CYS cc_start: 0.5128 (m) cc_final: 0.4671 (m) REVERT: B 437 GLU cc_start: 0.7135 (pp20) cc_final: 0.6656 (pp20) REVERT: B 439 ASP cc_start: 0.7116 (p0) cc_final: 0.6891 (p0) REVERT: B 448 ARG cc_start: 0.7099 (ptp-170) cc_final: 0.6539 (ptp-170) REVERT: B 497 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: B 506 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7927 (mp) REVERT: B 507 SER cc_start: 0.8458 (m) cc_final: 0.8161 (p) REVERT: B 550 ASN cc_start: 0.8553 (m110) cc_final: 0.8007 (t0) REVERT: B 565 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 584 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7949 (mtmm) REVERT: B 634 MET cc_start: 0.7358 (tpt) cc_final: 0.7132 (tpt) REVERT: B 701 PHE cc_start: 0.7407 (t80) cc_final: 0.7205 (t80) REVERT: B 717 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7444 (tt) REVERT: B 764 ASP cc_start: 0.8254 (p0) cc_final: 0.8011 (p0) REVERT: B 768 MET cc_start: 0.7809 (mpp) cc_final: 0.7488 (mpp) REVERT: E 43 ASN cc_start: 0.7766 (t0) cc_final: 0.7309 (m-40) REVERT: E 44 ASP cc_start: 0.7886 (t0) cc_final: 0.7631 (t0) REVERT: E 106 ASP cc_start: 0.8464 (m-30) cc_final: 0.8245 (m-30) REVERT: E 109 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7648 (m170) REVERT: E 119 LEU cc_start: 0.8595 (mp) cc_final: 0.8272 (mp) REVERT: E 136 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 196 CYS cc_start: -0.0592 (OUTLIER) cc_final: -0.0814 (t) REVERT: C 493 ASP cc_start: 0.8542 (p0) cc_final: 0.8278 (p0) REVERT: C 587 GLU cc_start: 0.5983 (tm-30) cc_final: 0.5681 (tm-30) REVERT: C 665 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8305 (mmtm) REVERT: C 670 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7740 (p0) REVERT: C 683 HIS cc_start: 0.6189 (OUTLIER) cc_final: 0.2399 (m-70) REVERT: C 745 SER cc_start: 0.7751 (p) cc_final: 0.7312 (t) REVERT: C 787 ARG cc_start: 0.7331 (tmt170) cc_final: 0.7071 (tmm160) REVERT: F 51 VAL cc_start: 0.8558 (m) cc_final: 0.8281 (t) REVERT: F 84 GLN cc_start: 0.7727 (mp10) cc_final: 0.7523 (mp10) REVERT: F 96 GLN cc_start: 0.8077 (tp40) cc_final: 0.7820 (tp40) outliers start: 166 outliers final: 116 residues processed: 527 average time/residue: 0.3190 time to fit residues: 261.5560 Evaluate side-chains 527 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 397 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 LYS Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 254 optimal weight: 0.4980 chunk 172 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 92 optimal weight: 40.0000 chunk 207 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 188 optimal weight: 50.0000 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 182 GLN B 455 GLN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 160 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 103 ASN F 109 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.244283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.223578 restraints weight = 80734.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.221634 restraints weight = 75199.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.220505 restraints weight = 63316.569| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22528 Z= 0.195 Angle : 0.715 15.283 30748 Z= 0.349 Chirality : 0.048 0.378 3538 Planarity : 0.005 0.103 3790 Dihedral : 8.840 120.879 3385 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.45 % Favored : 95.36 % Rotamer: Outliers : 6.57 % Allowed : 33.16 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.43 (0.16), residues: 2672 helix: 1.26 (0.28), residues: 329 sheet: -0.24 (0.18), residues: 879 loop : -0.62 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 785 HIS 0.021 0.001 HIS F 109 PHE 0.025 0.002 PHE B 336 TYR 0.023 0.002 TYR A 411 ARG 0.013 0.001 ARG A 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00739 ( 16) link_NAG-ASN : angle 3.57052 ( 48) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 3.36630 ( 12) hydrogen bonds : bond 0.05134 ( 620) hydrogen bonds : angle 6.37686 ( 1788) link_BETA1-6 : bond 0.00336 ( 3) link_BETA1-6 : angle 1.44408 ( 9) SS BOND : bond 0.00404 ( 39) SS BOND : angle 1.79497 ( 78) covalent geometry : bond 0.00440 (22466) covalent geometry : angle 0.69270 (30601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 408 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLN cc_start: 0.8730 (mp10) cc_final: 0.8388 (mp10) REVERT: A 550 ASN cc_start: 0.7645 (m110) cc_final: 0.6920 (p0) REVERT: A 760 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8669 (pp) REVERT: A 768 MET cc_start: 0.6440 (pmm) cc_final: 0.5949 (pmm) REVERT: B 253 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5333 (tp) REVERT: B 271 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (m) REVERT: B 400 LYS cc_start: 0.8812 (mptt) cc_final: 0.8396 (mptt) REVERT: B 437 GLU cc_start: 0.7198 (pp20) cc_final: 0.6687 (pp20) REVERT: B 448 ARG cc_start: 0.7117 (ptp-170) cc_final: 0.6673 (ptp-170) REVERT: B 497 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: B 506 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7909 (mp) REVERT: B 507 SER cc_start: 0.8473 (m) cc_final: 0.8136 (p) REVERT: B 550 ASN cc_start: 0.8547 (m110) cc_final: 0.8010 (t0) REVERT: B 565 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 647 ARG cc_start: 0.8056 (tmt170) cc_final: 0.7595 (tmt170) REVERT: B 669 LYS cc_start: 0.8498 (tppp) cc_final: 0.8291 (tppp) REVERT: B 713 THR cc_start: 0.8470 (m) cc_final: 0.8235 (p) REVERT: B 717 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7423 (tt) REVERT: E 43 ASN cc_start: 0.8173 (t0) cc_final: 0.7715 (m-40) REVERT: E 44 ASP cc_start: 0.8051 (t0) cc_final: 0.7789 (t0) REVERT: E 119 LEU cc_start: 0.8583 (mp) cc_final: 0.8196 (mp) REVERT: E 136 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 196 CYS cc_start: -0.0755 (OUTLIER) cc_final: -0.1016 (t) REVERT: C 493 ASP cc_start: 0.8576 (p0) cc_final: 0.8054 (p0) REVERT: C 587 GLU cc_start: 0.5852 (tm-30) cc_final: 0.5509 (tm-30) REVERT: C 683 HIS cc_start: 0.5999 (OUTLIER) cc_final: 0.2306 (m-70) REVERT: C 745 SER cc_start: 0.7785 (p) cc_final: 0.7324 (t) REVERT: C 787 ARG cc_start: 0.7272 (tmt170) cc_final: 0.6981 (tmm160) REVERT: F 51 VAL cc_start: 0.8531 (m) cc_final: 0.8260 (t) REVERT: F 75 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6896 (tpp) REVERT: F 96 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7845 (tp40) REVERT: F 118 HIS cc_start: 0.7372 (t70) cc_final: 0.7126 (t-90) outliers start: 165 outliers final: 118 residues processed: 522 average time/residue: 0.3162 time to fit residues: 256.1922 Evaluate side-chains 518 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 391 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 670 ASN Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 11 optimal weight: 8.9990 chunk 251 optimal weight: 0.9980 chunk 131 optimal weight: 0.0770 chunk 109 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 240 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 123 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 455 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.246059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.225851 restraints weight = 80847.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222218 restraints weight = 73329.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.222591 restraints weight = 61606.186| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 22528 Z= 0.136 Angle : 0.705 14.070 30748 Z= 0.340 Chirality : 0.048 0.382 3538 Planarity : 0.004 0.098 3790 Dihedral : 8.460 120.099 3385 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 5.85 % Allowed : 34.24 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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 (0.16), residues: 2672 helix: 1.32 (0.28), residues: 331 sheet: -0.20 (0.18), residues: 875 loop : -0.57 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 664 HIS 0.013 0.001 HIS F 109 PHE 0.021 0.001 PHE B 336 TYR 0.018 0.001 TYR C 812 ARG 0.006 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 16) link_NAG-ASN : angle 3.49395 ( 48) link_BETA1-4 : bond 0.00368 ( 4) link_BETA1-4 : angle 3.36923 ( 12) hydrogen bonds : bond 0.04393 ( 620) hydrogen bonds : angle 6.13137 ( 1788) link_BETA1-6 : bond 0.00435 ( 3) link_BETA1-6 : angle 1.32337 ( 9) SS BOND : bond 0.00485 ( 39) SS BOND : angle 1.80222 ( 78) covalent geometry : bond 0.00318 (22466) covalent geometry : angle 0.68340 (30601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 405 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.3142 (OUTLIER) cc_final: 0.2698 (tm-30) REVERT: A 380 GLN cc_start: 0.8691 (mp10) cc_final: 0.8329 (mp10) REVERT: A 585 MET cc_start: 0.6445 (tpt) cc_final: 0.4891 (tpt) REVERT: A 675 SER cc_start: 0.2327 (OUTLIER) cc_final: 0.2060 (p) REVERT: A 773 GLU cc_start: 0.7854 (pm20) cc_final: 0.7092 (pm20) REVERT: A 794 LYS cc_start: 0.8050 (tptp) cc_final: 0.7756 (mmtm) REVERT: B 362 PRO cc_start: 0.8613 (Cg_exo) cc_final: 0.8345 (Cg_endo) REVERT: B 374 GLU cc_start: 0.8035 (pm20) cc_final: 0.7815 (pm20) REVERT: B 400 LYS cc_start: 0.8813 (mptt) cc_final: 0.8418 (mptt) REVERT: B 410 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7945 (t) REVERT: B 436 CYS cc_start: 0.5241 (m) cc_final: 0.5007 (m) REVERT: B 506 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 507 SER cc_start: 0.8457 (m) cc_final: 0.8061 (p) REVERT: B 550 ASN cc_start: 0.8551 (m110) cc_final: 0.8069 (t0) REVERT: B 565 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 717 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7401 (tt) REVERT: B 768 MET cc_start: 0.7671 (mpp) cc_final: 0.7463 (mpp) REVERT: E 43 ASN cc_start: 0.8204 (t0) cc_final: 0.7789 (m-40) REVERT: E 44 ASP cc_start: 0.7940 (t0) cc_final: 0.7656 (t0) REVERT: E 119 LEU cc_start: 0.8656 (mp) cc_final: 0.8179 (mp) REVERT: E 136 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7037 (tm-30) REVERT: E 160 GLN cc_start: 0.8398 (tp40) cc_final: 0.8110 (tt0) REVERT: C 196 CYS cc_start: -0.0760 (OUTLIER) cc_final: -0.1025 (t) REVERT: C 493 ASP cc_start: 0.8608 (p0) cc_final: 0.8115 (p0) REVERT: C 587 GLU cc_start: 0.5961 (tm-30) cc_final: 0.5678 (tm-30) REVERT: C 665 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8137 (mmtm) REVERT: C 683 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.2108 (m-70) REVERT: C 745 SER cc_start: 0.7850 (p) cc_final: 0.7411 (t) REVERT: F 51 VAL cc_start: 0.8569 (m) cc_final: 0.8252 (t) REVERT: F 96 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7732 (tp40) REVERT: F 118 HIS cc_start: 0.7292 (t70) cc_final: 0.7025 (t-90) outliers start: 147 outliers final: 108 residues processed: 510 average time/residue: 0.3231 time to fit residues: 256.9108 Evaluate side-chains 508 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 393 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 785 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 682 ASN Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 238 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 150 optimal weight: 0.0670 chunk 172 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 455 GLN B 501 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.244402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.223951 restraints weight = 80657.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.222203 restraints weight = 74590.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.220340 restraints weight = 65304.219| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22528 Z= 0.173 Angle : 0.716 16.737 30748 Z= 0.347 Chirality : 0.048 0.379 3538 Planarity : 0.005 0.100 3790 Dihedral : 8.212 120.318 3385 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 6.45 % Allowed : 32.96 % Favored : 60.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.37 (0.16), residues: 2672 helix: 1.34 (0.28), residues: 329 sheet: -0.23 (0.18), residues: 875 loop : -0.56 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 664 HIS 0.025 0.001 HIS F 109 PHE 0.023 0.001 PHE B 336 TYR 0.021 0.002 TYR A 411 ARG 0.007 0.001 ARG C 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 16) link_NAG-ASN : angle 3.57677 ( 48) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 3.35621 ( 12) hydrogen bonds : bond 0.04664 ( 620) hydrogen bonds : angle 6.09267 ( 1788) link_BETA1-6 : bond 0.00307 ( 3) link_BETA1-6 : angle 1.41111 ( 9) SS BOND : bond 0.00425 ( 39) SS BOND : angle 1.69521 ( 78) covalent geometry : bond 0.00400 (22466) covalent geometry : angle 0.69527 (30601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 410 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.3087 (OUTLIER) cc_final: 0.2628 (tm-30) REVERT: A 380 GLN cc_start: 0.8697 (mp10) cc_final: 0.8328 (mp10) REVERT: A 675 SER cc_start: 0.2798 (OUTLIER) cc_final: 0.2430 (p) REVERT: A 704 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8220 (pp) REVERT: A 794 LYS cc_start: 0.8011 (tptp) cc_final: 0.7524 (tptp) REVERT: A 796 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6519 (m-10) REVERT: B 355 LYS cc_start: 0.8086 (tppt) cc_final: 0.7450 (tptm) REVERT: B 362 PRO cc_start: 0.8640 (Cg_exo) cc_final: 0.8394 (Cg_endo) REVERT: B 400 LYS cc_start: 0.8814 (mptt) cc_final: 0.8405 (mptt) REVERT: B 436 CYS cc_start: 0.5409 (m) cc_final: 0.5087 (m) REVERT: B 506 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 507 SER cc_start: 0.8451 (m) cc_final: 0.8112 (p) REVERT: B 565 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7364 (mm-30) REVERT: B 676 VAL cc_start: 0.8247 (t) cc_final: 0.7954 (p) REVERT: B 682 ASN cc_start: 0.8183 (p0) cc_final: 0.7880 (p0) REVERT: B 717 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7267 (tt) REVERT: B 764 ASP cc_start: 0.8202 (p0) cc_final: 0.7844 (p0) REVERT: B 768 MET cc_start: 0.7846 (mpp) cc_final: 0.7552 (mpp) REVERT: B 786 LEU cc_start: 0.8523 (mm) cc_final: 0.8267 (mm) REVERT: B 823 LYS cc_start: 0.7958 (tptp) cc_final: 0.7593 (tptp) REVERT: E 43 ASN cc_start: 0.7971 (t0) cc_final: 0.7502 (m-40) REVERT: E 44 ASP cc_start: 0.8033 (t0) cc_final: 0.7795 (t0) REVERT: E 119 LEU cc_start: 0.8621 (mp) cc_final: 0.8285 (mp) REVERT: E 160 GLN cc_start: 0.8476 (tp40) cc_final: 0.8184 (tt0) REVERT: C 196 CYS cc_start: -0.0721 (OUTLIER) cc_final: -0.1009 (t) REVERT: C 299 LEU cc_start: 0.7200 (tp) cc_final: 0.6976 (tp) REVERT: C 493 ASP cc_start: 0.8647 (p0) cc_final: 0.8195 (p0) REVERT: C 582 GLN cc_start: 0.7072 (mp10) cc_final: 0.6862 (mp10) REVERT: C 587 GLU cc_start: 0.6009 (tm-30) cc_final: 0.5729 (tm-30) REVERT: C 745 SER cc_start: 0.7838 (p) cc_final: 0.7396 (t) REVERT: C 807 TYR cc_start: 0.6607 (m-10) cc_final: 0.6249 (m-80) REVERT: F 51 VAL cc_start: 0.8507 (m) cc_final: 0.8209 (t) REVERT: F 75 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6866 (tpp) REVERT: F 96 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7805 (tp40) outliers start: 162 outliers final: 126 residues processed: 528 average time/residue: 0.3197 time to fit residues: 263.5835 Evaluate side-chains 535 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 401 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 785 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 135 optimal weight: 0.0050 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 188 optimal weight: 40.0000 chunk 20 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 455 GLN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN F 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.244459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.224159 restraints weight = 80700.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.222698 restraints weight = 73071.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.221329 restraints weight = 65538.204| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22528 Z= 0.163 Angle : 0.730 16.010 30748 Z= 0.353 Chirality : 0.048 0.379 3538 Planarity : 0.004 0.098 3790 Dihedral : 7.977 120.197 3385 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.10 % Rotamer: Outliers : 6.21 % Allowed : 33.32 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.39 (0.16), residues: 2672 helix: 1.31 (0.28), residues: 329 sheet: -0.27 (0.18), residues: 872 loop : -0.55 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 664 HIS 0.020 0.001 HIS E 109 PHE 0.034 0.002 PHE B 701 TYR 0.020 0.001 TYR A 411 ARG 0.007 0.001 ARG C 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 16) link_NAG-ASN : angle 3.84927 ( 48) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 3.27165 ( 12) hydrogen bonds : bond 0.04590 ( 620) hydrogen bonds : angle 6.02612 ( 1788) link_BETA1-6 : bond 0.00388 ( 3) link_BETA1-6 : angle 1.41759 ( 9) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.80863 ( 78) covalent geometry : bond 0.00377 (22466) covalent geometry : angle 0.70685 (30601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 410 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.3077 (OUTLIER) cc_final: 0.2618 (tm-30) REVERT: A 380 GLN cc_start: 0.8697 (mp10) cc_final: 0.8320 (mp10) REVERT: A 675 SER cc_start: 0.2553 (OUTLIER) cc_final: 0.2303 (p) REVERT: A 704 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8246 (pp) REVERT: A 773 GLU cc_start: 0.7837 (pm20) cc_final: 0.7359 (pm20) REVERT: A 794 LYS cc_start: 0.8019 (tptp) cc_final: 0.7502 (tptp) REVERT: A 796 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6453 (m-10) REVERT: B 362 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8356 (Cg_endo) REVERT: B 400 LYS cc_start: 0.8816 (mptt) cc_final: 0.8393 (mptt) REVERT: B 436 CYS cc_start: 0.5281 (m) cc_final: 0.4928 (m) REVERT: B 506 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7891 (mp) REVERT: B 507 SER cc_start: 0.8328 (m) cc_final: 0.7965 (p) REVERT: B 565 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 647 ARG cc_start: 0.8031 (tmt170) cc_final: 0.7499 (tmt170) REVERT: B 669 LYS cc_start: 0.8498 (tppp) cc_final: 0.8295 (tppp) REVERT: B 676 VAL cc_start: 0.8023 (t) cc_final: 0.7692 (p) REVERT: B 682 ASN cc_start: 0.8170 (p0) cc_final: 0.7847 (p0) REVERT: B 764 ASP cc_start: 0.8247 (p0) cc_final: 0.7960 (p0) REVERT: B 768 MET cc_start: 0.7964 (mpp) cc_final: 0.7691 (mpp) REVERT: B 786 LEU cc_start: 0.8519 (mm) cc_final: 0.8243 (mm) REVERT: B 823 LYS cc_start: 0.7926 (tptp) cc_final: 0.7563 (tptp) REVERT: E 43 ASN cc_start: 0.8095 (t0) cc_final: 0.7574 (m-40) REVERT: E 44 ASP cc_start: 0.7965 (t0) cc_final: 0.7666 (t0) REVERT: E 119 LEU cc_start: 0.8603 (mp) cc_final: 0.8309 (mp) REVERT: E 136 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7041 (tm-30) REVERT: E 160 GLN cc_start: 0.8502 (tp40) cc_final: 0.8175 (tt0) REVERT: C 196 CYS cc_start: -0.0710 (OUTLIER) cc_final: -0.0969 (t) REVERT: C 299 LEU cc_start: 0.7180 (tp) cc_final: 0.6960 (tp) REVERT: C 493 ASP cc_start: 0.8681 (p0) cc_final: 0.8267 (p0) REVERT: C 582 GLN cc_start: 0.7141 (mp10) cc_final: 0.6920 (mp10) REVERT: C 587 GLU cc_start: 0.5964 (tm-30) cc_final: 0.5698 (tm-30) REVERT: C 745 SER cc_start: 0.7952 (p) cc_final: 0.7521 (t) REVERT: C 807 TYR cc_start: 0.6620 (m-10) cc_final: 0.6285 (m-10) REVERT: F 51 VAL cc_start: 0.8583 (m) cc_final: 0.8282 (t) REVERT: F 96 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7803 (tp40) outliers start: 156 outliers final: 129 residues processed: 523 average time/residue: 0.3138 time to fit residues: 254.7814 Evaluate side-chains 540 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 405 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 785 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.1980 chunk 166 optimal weight: 5.9990 chunk 233 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.219786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.171873 restraints weight = 61265.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177034 restraints weight = 33088.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176684 restraints weight = 22444.054| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22528 Z= 0.135 Angle : 0.733 16.546 30748 Z= 0.352 Chirality : 0.047 0.380 3538 Planarity : 0.004 0.097 3790 Dihedral : 7.729 119.724 3385 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.72 % Favored : 95.13 % Rotamer: Outliers : 5.49 % Allowed : 34.24 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2672 helix: 1.36 (0.28), residues: 329 sheet: -0.28 (0.18), residues: 875 loop : -0.55 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 664 HIS 0.016 0.001 HIS E 109 PHE 0.016 0.001 PHE C 394 TYR 0.018 0.001 TYR C 812 ARG 0.006 0.000 ARG A 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 16) link_NAG-ASN : angle 3.72712 ( 48) link_BETA1-4 : bond 0.00341 ( 4) link_BETA1-4 : angle 3.17403 ( 12) hydrogen bonds : bond 0.04222 ( 620) hydrogen bonds : angle 5.91291 ( 1788) link_BETA1-6 : bond 0.00428 ( 3) link_BETA1-6 : angle 1.31881 ( 9) SS BOND : bond 0.00323 ( 39) SS BOND : angle 1.63957 ( 78) covalent geometry : bond 0.00315 (22466) covalent geometry : angle 0.71149 (30601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 411 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.3464 (OUTLIER) cc_final: 0.3213 (tm-30) REVERT: A 348 VAL cc_start: 0.8358 (t) cc_final: 0.7962 (m) REVERT: A 380 GLN cc_start: 0.8716 (mp10) cc_final: 0.8377 (mp10) REVERT: A 421 ARG cc_start: 0.7152 (mmm160) cc_final: 0.6843 (mmm160) REVERT: A 704 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 768 MET cc_start: 0.7305 (pmm) cc_final: 0.7002 (pmm) REVERT: A 773 GLU cc_start: 0.8202 (pm20) cc_final: 0.7608 (pm20) REVERT: A 794 LYS cc_start: 0.8140 (tptp) cc_final: 0.7532 (tptp) REVERT: A 796 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6369 (m-10) REVERT: B 355 LYS cc_start: 0.8104 (tppt) cc_final: 0.7365 (tptm) REVERT: B 362 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8420 (Cg_endo) REVERT: B 400 LYS cc_start: 0.8776 (mptt) cc_final: 0.8392 (mptt) REVERT: B 410 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8196 (t) REVERT: B 436 CYS cc_start: 0.5561 (m) cc_final: 0.5213 (m) REVERT: B 506 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 507 SER cc_start: 0.8447 (m) cc_final: 0.8036 (p) REVERT: B 565 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 647 ARG cc_start: 0.7861 (tmt170) cc_final: 0.7437 (tmt170) REVERT: B 669 LYS cc_start: 0.8405 (tppp) cc_final: 0.7916 (tppp) REVERT: B 676 VAL cc_start: 0.7883 (t) cc_final: 0.7509 (p) REVERT: B 682 ASN cc_start: 0.8149 (p0) cc_final: 0.7781 (p0) REVERT: B 764 ASP cc_start: 0.8072 (p0) cc_final: 0.7795 (p0) REVERT: B 768 MET cc_start: 0.7870 (mpp) cc_final: 0.7648 (mpp) REVERT: B 786 LEU cc_start: 0.8521 (mm) cc_final: 0.8261 (mm) REVERT: B 823 LYS cc_start: 0.7819 (tptp) cc_final: 0.7497 (tptp) REVERT: E 43 ASN cc_start: 0.8309 (t0) cc_final: 0.7799 (m-40) REVERT: E 44 ASP cc_start: 0.8044 (t0) cc_final: 0.7745 (t0) REVERT: E 119 LEU cc_start: 0.8544 (mp) cc_final: 0.8235 (mp) REVERT: E 136 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7154 (tm-30) REVERT: E 160 GLN cc_start: 0.8430 (tp40) cc_final: 0.8136 (tt0) REVERT: C 196 CYS cc_start: -0.1168 (OUTLIER) cc_final: -0.1537 (t) REVERT: C 299 LEU cc_start: 0.7045 (tp) cc_final: 0.6822 (tp) REVERT: C 493 ASP cc_start: 0.8682 (p0) cc_final: 0.8259 (p0) REVERT: C 582 GLN cc_start: 0.7169 (mp10) cc_final: 0.6948 (mp10) REVERT: C 587 GLU cc_start: 0.5950 (tm-30) cc_final: 0.5706 (tm-30) REVERT: C 671 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7522 (t0) REVERT: C 742 GLN cc_start: 0.7920 (mp10) cc_final: 0.7675 (mp10) REVERT: C 745 SER cc_start: 0.7988 (p) cc_final: 0.7542 (t) REVERT: C 807 TYR cc_start: 0.6755 (m-10) cc_final: 0.6359 (m-10) REVERT: F 51 VAL cc_start: 0.8514 (m) cc_final: 0.8206 (t) REVERT: F 96 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7801 (tp40) outliers start: 138 outliers final: 113 residues processed: 506 average time/residue: 0.3239 time to fit residues: 253.6967 Evaluate side-chains 525 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 405 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 785 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 HIS Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 109 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 103 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 GLN B 150 ASN B 455 GLN B 726 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.244496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.224154 restraints weight = 81025.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.221124 restraints weight = 75227.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.220673 restraints weight = 69089.104| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22528 Z= 0.161 Angle : 0.742 17.124 30748 Z= 0.358 Chirality : 0.048 0.377 3538 Planarity : 0.004 0.097 3790 Dihedral : 7.660 119.924 3385 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.01 % Favored : 94.80 % Rotamer: Outliers : 5.10 % Allowed : 34.63 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2672 helix: 1.35 (0.28), residues: 327 sheet: -0.25 (0.18), residues: 876 loop : -0.56 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 664 HIS 0.011 0.001 HIS C 683 PHE 0.022 0.001 PHE B 350 TYR 0.020 0.001 TYR A 411 ARG 0.006 0.000 ARG C 678 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 16) link_NAG-ASN : angle 3.69042 ( 48) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 3.09309 ( 12) hydrogen bonds : bond 0.04440 ( 620) hydrogen bonds : angle 5.89717 ( 1788) link_BETA1-6 : bond 0.00364 ( 3) link_BETA1-6 : angle 1.35515 ( 9) SS BOND : bond 0.00356 ( 39) SS BOND : angle 1.66096 ( 78) covalent geometry : bond 0.00372 (22466) covalent geometry : angle 0.72120 (30601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 409 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.3132 (OUTLIER) cc_final: 0.2689 (tm-30) REVERT: A 380 GLN cc_start: 0.8690 (mp10) cc_final: 0.8321 (mp10) REVERT: A 704 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8261 (pp) REVERT: A 768 MET cc_start: 0.7013 (pmm) cc_final: 0.6672 (pmm) REVERT: A 773 GLU cc_start: 0.7926 (pm20) cc_final: 0.7444 (pm20) REVERT: A 794 LYS cc_start: 0.8056 (tptp) cc_final: 0.7438 (tptp) REVERT: A 796 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6186 (m-10) REVERT: B 355 LYS cc_start: 0.8125 (tppt) cc_final: 0.7418 (tptp) REVERT: B 362 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8374 (Cg_endo) REVERT: B 400 LYS cc_start: 0.8823 (mptt) cc_final: 0.8407 (mptt) REVERT: B 410 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7997 (t) REVERT: B 436 CYS cc_start: 0.5281 (m) cc_final: 0.4923 (m) REVERT: B 506 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 507 SER cc_start: 0.8365 (m) cc_final: 0.7977 (p) REVERT: B 565 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7321 (mm-30) REVERT: B 647 ARG cc_start: 0.7981 (tmt170) cc_final: 0.7527 (tmt170) REVERT: B 669 LYS cc_start: 0.8328 (tppp) cc_final: 0.8070 (tppp) REVERT: B 676 VAL cc_start: 0.8044 (t) cc_final: 0.7704 (p) REVERT: B 682 ASN cc_start: 0.8163 (p0) cc_final: 0.7757 (p0) REVERT: B 764 ASP cc_start: 0.8216 (p0) cc_final: 0.7973 (p0) REVERT: B 768 MET cc_start: 0.7990 (mpp) cc_final: 0.7740 (mpp) REVERT: B 786 LEU cc_start: 0.8533 (mm) cc_final: 0.8225 (mm) REVERT: B 823 LYS cc_start: 0.7884 (tptp) cc_final: 0.7512 (tptp) REVERT: E 43 ASN cc_start: 0.8128 (t0) cc_final: 0.7691 (m-40) REVERT: E 44 ASP cc_start: 0.7980 (t0) cc_final: 0.7718 (t0) REVERT: E 119 LEU cc_start: 0.8574 (mp) cc_final: 0.8274 (mp) REVERT: E 136 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7109 (tm-30) REVERT: E 151 GLN cc_start: 0.8017 (tt0) cc_final: 0.7805 (tt0) REVERT: E 160 GLN cc_start: 0.8517 (tp40) cc_final: 0.8207 (tt0) REVERT: C 196 CYS cc_start: -0.0840 (OUTLIER) cc_final: -0.1120 (t) REVERT: C 299 LEU cc_start: 0.7145 (tp) cc_final: 0.6927 (tp) REVERT: C 493 ASP cc_start: 0.8683 (p0) cc_final: 0.8255 (p0) REVERT: C 582 GLN cc_start: 0.7093 (mp10) cc_final: 0.6869 (mp10) REVERT: C 587 GLU cc_start: 0.6060 (tm-30) cc_final: 0.5804 (tm-30) REVERT: C 671 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7591 (t0) REVERT: C 742 GLN cc_start: 0.7878 (mp10) cc_final: 0.7659 (mp10) REVERT: C 745 SER cc_start: 0.7967 (p) cc_final: 0.7537 (t) REVERT: C 807 TYR cc_start: 0.6824 (m-10) cc_final: 0.6358 (m-10) REVERT: C 826 ASN cc_start: 0.6935 (t0) cc_final: 0.6581 (p0) REVERT: F 51 VAL cc_start: 0.8554 (m) cc_final: 0.8234 (t) REVERT: F 96 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7765 (tp40) outliers start: 128 outliers final: 115 residues processed: 500 average time/residue: 0.3246 time to fit residues: 253.7687 Evaluate side-chains 530 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 408 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 785 TRP Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 589 TYR Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 671 ASP Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 784 LYS Chi-restraints excluded: chain C residue 785 TRP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 14 optimal weight: 50.0000 chunk 213 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 203 optimal weight: 0.0060 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 50 optimal weight: 0.0980 chunk 246 optimal weight: 0.5980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 726 ASN B 778 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.246189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.230568 restraints weight = 81342.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.230973 restraints weight = 112477.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.231289 restraints weight = 92413.520| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22528 Z= 0.124 Angle : 0.732 17.309 30748 Z= 0.350 Chirality : 0.047 0.379 3538 Planarity : 0.004 0.096 3790 Dihedral : 7.462 119.314 3385 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 4.70 % Allowed : 35.19 % Favored : 60.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -0.32 (0.17), residues: 2672 helix: 1.35 (0.28), residues: 327 sheet: -0.19 (0.18), residues: 876 loop : -0.52 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 664 HIS 0.017 0.001 HIS E 109 PHE 0.016 0.001 PHE C 504 TYR 0.015 0.001 TYR B 812 ARG 0.008 0.001 ARG D 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 16) link_NAG-ASN : angle 3.52384 ( 48) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 3.00259 ( 12) hydrogen bonds : bond 0.03966 ( 620) hydrogen bonds : angle 5.71624 ( 1788) link_BETA1-6 : bond 0.00424 ( 3) link_BETA1-6 : angle 1.26318 ( 9) SS BOND : bond 0.00291 ( 39) SS BOND : angle 1.48660 ( 78) covalent geometry : bond 0.00288 (22466) covalent geometry : angle 0.71379 (30601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9141.66 seconds wall clock time: 161 minutes 2.08 seconds (9662.08 seconds total)