Starting phenix.real_space_refine on Sun Aug 24 18:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x80_38131/08_2025/8x80_38131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x80_38131/08_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_38131/08_2025/8x80_38131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x80_38131/08_2025/8x80_38131.map" model { file = "/net/cci-nas-00/data/ceres_data/8x80_38131/08_2025/8x80_38131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x80_38131/08_2025/8x80_38131.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.89, per 1000 atoms: 0.27 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.77 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: 4.16 Time building geometry restraints manager: 2.32 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 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 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: 15.540 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.300 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- 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 : 15.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.000 ARG A 678 TYR 0.030 0.001 TYR B 354 PHE 0.017 0.001 PHE A 815 TRP 0.037 0.002 TRP C 785 HIS 0.006 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00339 (22466) covalent geometry : angle 0.72321 (30601) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.36155 ( 78) hydrogen bonds : bond 0.28331 ( 620) hydrogen bonds : angle 9.86005 ( 1788) link_BETA1-4 : bond 0.00775 ( 4) link_BETA1-4 : angle 4.10390 ( 12) link_BETA1-6 : bond 0.00587 ( 3) link_BETA1-6 : angle 1.25012 ( 9) link_NAG-ASN : bond 0.00839 ( 16) link_NAG-ASN : angle 4.97378 ( 48) *********************** 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 : 0.718 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: 0.6061 (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: 0.1292 time to fit residues: 88.9900 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 : 0.538 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A 776 ASN B 150 ASN B 182 GLN B 331 GLN B 351 HIS ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 151 GLN D 151 GLN C 276 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.246288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.225982 restraints weight = 81390.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.225228 restraints weight = 76151.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.223135 restraints weight = 60171.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.223506 restraints weight = 59513.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.223610 restraints weight = 51151.524| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22528 Z= 0.216 Angle : 0.725 13.352 30748 Z= 0.362 Chirality : 0.049 0.412 3538 Planarity : 0.005 0.092 3790 Dihedral : 9.986 121.908 3415 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 5.41 % Allowed : 32.36 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2672 helix: 1.31 (0.28), residues: 335 sheet: -0.20 (0.18), residues: 877 loop : -0.45 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 678 TYR 0.027 0.002 TYR C 466 PHE 0.034 0.002 PHE A 815 TRP 0.029 0.002 TRP E 121 HIS 0.007 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00483 (22466) covalent geometry : angle 0.70438 (30601) SS BOND : bond 0.00340 ( 39) SS BOND : angle 1.58142 ( 78) hydrogen bonds : bond 0.05984 ( 620) hydrogen bonds : angle 7.18999 ( 1788) link_BETA1-4 : bond 0.00670 ( 4) link_BETA1-4 : angle 3.24421 ( 12) link_BETA1-6 : bond 0.00513 ( 3) link_BETA1-6 : angle 1.58210 ( 9) link_NAG-ASN : bond 0.00719 ( 16) link_NAG-ASN : angle 3.62169 ( 48) *********************** 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 560 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 424 time to evaluate : 0.588 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: A 357 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7121 (pp20) REVERT: A 433 ASN cc_start: 0.7969 (p0) cc_final: 0.7762 (p0) REVERT: A 550 ASN cc_start: 0.7574 (m110) cc_final: 0.6739 (p0) REVERT: A 634 MET cc_start: 0.6665 (ppp) cc_final: 0.5891 (ppp) REVERT: A 760 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8669 (pp) REVERT: A 821 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8164 (ptpp) REVERT: B 350 PHE cc_start: 0.5280 (OUTLIER) cc_final: 0.4995 (m-80) REVERT: B 459 GLU cc_start: 0.6969 (pp20) cc_final: 0.6758 (pp20) REVERT: B 507 SER cc_start: 0.8459 (m) cc_final: 0.8007 (p) REVERT: B 669 LYS cc_start: 0.8451 (tppp) cc_final: 0.8234 (tppp) REVERT: B 742 GLN cc_start: 0.7825 (mp10) cc_final: 0.7563 (mm-40) REVERT: E 44 ASP cc_start: 0.7888 (t0) cc_final: 0.7553 (t0) REVERT: E 119 LEU cc_start: 0.8534 (mp) cc_final: 0.8162 (mp) REVERT: E 130 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.7142 (p) REVERT: D 84 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8353 (mm-40) REVERT: C 493 ASP cc_start: 0.8345 (p0) cc_final: 0.8061 (p0) REVERT: C 495 PHE cc_start: 0.7664 (m-80) cc_final: 0.7460 (m-10) REVERT: C 501 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: C 614 LYS cc_start: 0.7715 (tttm) cc_final: 0.6552 (tttm) REVERT: C 683 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.1926 (m-70) REVERT: C 694 ASP cc_start: 0.7333 (t0) cc_final: 0.7084 (t0) REVERT: C 745 SER cc_start: 0.7671 (p) cc_final: 0.7352 (t) REVERT: F 51 VAL cc_start: 0.8462 (m) cc_final: 0.8008 (t) outliers start: 136 outliers final: 80 residues processed: 507 average time/residue: 0.1288 time to fit residues: 103.0926 Evaluate side-chains 497 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 410 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 294 LEU 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 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 587 GLU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 160 HIS 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 328 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 LEU 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 399 THR Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 528 CYS 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 682 ASN 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 B residue 824 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 109 HIS Chi-restraints excluded: chain E residue 111 LEU 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 34 LEU 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 D residue 151 GLN 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 466 TYR Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 501 GLN 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 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 683 HIS 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 47 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 58 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 27 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 235 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN B 397 ASN B 491 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS E 109 HIS E 118 HIS E 151 GLN E 160 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 HIS ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 49 GLN F 96 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.220112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.165691 restraints weight = 61629.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169483 restraints weight = 32927.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.172100 restraints weight = 22023.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.173608 restraints weight = 16861.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174383 restraints weight = 14634.374| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22528 Z= 0.187 Angle : 0.695 12.701 30748 Z= 0.342 Chirality : 0.048 0.390 3538 Planarity : 0.005 0.098 3790 Dihedral : 9.414 121.040 3391 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.42 % Favored : 95.40 % Rotamer: Outliers : 5.81 % Allowed : 33.16 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.16), residues: 2672 helix: 1.37 (0.28), residues: 331 sheet: -0.21 (0.18), residues: 880 loop : -0.52 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 678 TYR 0.021 0.002 TYR C 466 PHE 0.030 0.002 PHE B 701 TRP 0.020 0.002 TRP B 774 HIS 0.013 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00420 (22466) covalent geometry : angle 0.67416 (30601) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.50549 ( 78) hydrogen bonds : bond 0.05417 ( 620) hydrogen bonds : angle 6.76780 ( 1788) link_BETA1-4 : bond 0.00596 ( 4) link_BETA1-4 : angle 3.37862 ( 12) link_BETA1-6 : bond 0.00376 ( 3) link_BETA1-6 : angle 1.45999 ( 9) link_NAG-ASN : bond 0.00766 ( 16) link_NAG-ASN : angle 3.58286 ( 48) *********************** 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 561 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 415 time to evaluate : 0.583 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: A 380 GLN cc_start: 0.8653 (mp10) cc_final: 0.8380 (mp10) REVERT: A 550 ASN cc_start: 0.7484 (m110) cc_final: 0.6671 (p0) REVERT: A 585 MET cc_start: 0.6018 (tpt) cc_final: 0.5808 (tpt) REVERT: A 614 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6838 (tmtt) REVERT: A 634 MET cc_start: 0.6710 (ppp) cc_final: 0.6036 (ppp) REVERT: A 760 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8651 (pp) REVERT: B 362 PRO cc_start: 0.8680 (Cg_exo) cc_final: 0.8443 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8336 (t) REVERT: B 448 ARG cc_start: 0.6914 (ptp-170) cc_final: 0.6513 (ptp-170) REVERT: B 459 GLU cc_start: 0.6858 (pp20) cc_final: 0.6561 (pp20) REVERT: B 468 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7735 (ttp80) REVERT: B 497 GLU cc_start: 0.7418 (tt0) cc_final: 0.6967 (tt0) REVERT: B 506 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7959 (mp) REVERT: B 507 SER cc_start: 0.8520 (m) cc_final: 0.8128 (p) REVERT: B 647 ARG cc_start: 0.7758 (tmt170) cc_final: 0.7367 (tmt170) REVERT: B 786 LEU cc_start: 0.8490 (mm) cc_final: 0.8239 (mm) REVERT: E 43 ASN cc_start: 0.8403 (t0) cc_final: 0.7927 (m-40) REVERT: E 44 ASP cc_start: 0.7913 (t0) cc_final: 0.7676 (t0) REVERT: E 119 LEU cc_start: 0.8431 (mp) cc_final: 0.8094 (mp) REVERT: E 130 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7496 (p) REVERT: E 136 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7036 (tm-30) REVERT: C 493 ASP cc_start: 0.8377 (p0) cc_final: 0.7909 (p0) REVERT: C 665 LYS cc_start: 0.8427 (mmtm) cc_final: 0.8084 (mmtm) REVERT: C 683 HIS cc_start: 0.5542 (OUTLIER) cc_final: 0.1952 (m-70) REVERT: C 745 SER cc_start: 0.7699 (p) cc_final: 0.7274 (t) REVERT: F 51 VAL cc_start: 0.8505 (m) cc_final: 0.8127 (t) outliers start: 146 outliers final: 91 residues processed: 522 average time/residue: 0.1312 time to fit residues: 108.0209 Evaluate side-chains 497 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 400 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 295 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 406 THR 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 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 614 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 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 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 221 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 382 ASP 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 446 THR Chi-restraints excluded: chain B residue 483 SER 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 611 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 715 LEU 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 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 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 130 SER 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 370 MET Chi-restraints excluded: chain C residue 489 TYR 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 613 CYS Chi-restraints excluded: chain C residue 616 LEU 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 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 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 119 LEU 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 184 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 150 ASN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS E 160 GLN D 151 GLN ** C 98 ASN ** 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 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS F 96 GLN F 103 ASN F 109 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.245569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.225139 restraints weight = 80975.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222081 restraints weight = 74030.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.221481 restraints weight = 66458.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.221573 restraints weight = 54580.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.221855 restraints weight = 45935.455| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22528 Z= 0.174 Angle : 0.700 14.678 30748 Z= 0.342 Chirality : 0.048 0.392 3538 Planarity : 0.004 0.096 3790 Dihedral : 9.084 120.765 3387 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 6.37 % Allowed : 33.24 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2672 helix: 1.38 (0.28), residues: 329 sheet: -0.21 (0.18), residues: 879 loop : -0.55 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 678 TYR 0.018 0.002 TYR C 466 PHE 0.028 0.002 PHE A 336 TRP 0.029 0.002 TRP E 121 HIS 0.007 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00395 (22466) covalent geometry : angle 0.67917 (30601) SS BOND : bond 0.00386 ( 39) SS BOND : angle 1.47351 ( 78) hydrogen bonds : bond 0.04997 ( 620) hydrogen bonds : angle 6.49119 ( 1788) link_BETA1-4 : bond 0.00466 ( 4) link_BETA1-4 : angle 3.37481 ( 12) link_BETA1-6 : bond 0.00380 ( 3) link_BETA1-6 : angle 1.40842 ( 9) link_NAG-ASN : bond 0.00734 ( 16) link_NAG-ASN : angle 3.56384 ( 48) *********************** 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 562 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 402 time to evaluate : 0.501 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: A 328 PHE cc_start: 0.7447 (t80) cc_final: 0.7140 (t80) REVERT: A 380 GLN cc_start: 0.8703 (mp10) cc_final: 0.8352 (mp10) REVERT: A 422 TYR cc_start: 0.8537 (p90) cc_final: 0.8171 (p90) REVERT: A 550 ASN cc_start: 0.7609 (m110) cc_final: 0.6801 (p0) REVERT: A 634 MET cc_start: 0.6771 (ppp) cc_final: 0.6044 (ppp) REVERT: A 760 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8688 (pp) REVERT: A 768 MET cc_start: 0.6431 (pmm) cc_final: 0.6113 (pmm) REVERT: B 350 PHE cc_start: 0.5563 (OUTLIER) cc_final: 0.5232 (m-80) REVERT: B 362 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.8390 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8057 (t) REVERT: B 436 CYS cc_start: 0.5120 (m) cc_final: 0.4675 (m) REVERT: B 448 ARG cc_start: 0.6959 (ptp-170) cc_final: 0.6548 (ptp-170) REVERT: B 506 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 507 SER cc_start: 0.8453 (m) cc_final: 0.8039 (p) REVERT: B 647 ARG cc_start: 0.7974 (tmt170) cc_final: 0.7483 (tmt170) REVERT: B 669 LYS cc_start: 0.8424 (tppp) cc_final: 0.8141 (tppp) REVERT: B 713 THR cc_start: 0.8473 (m) cc_final: 0.8141 (p) REVERT: B 717 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7264 (tt) REVERT: B 786 LEU cc_start: 0.8434 (mm) cc_final: 0.8146 (mm) REVERT: E 43 ASN cc_start: 0.8048 (t0) cc_final: 0.7441 (m-40) REVERT: E 44 ASP cc_start: 0.7893 (t0) cc_final: 0.7639 (t0) REVERT: E 119 LEU cc_start: 0.8631 (mp) cc_final: 0.8264 (mp) REVERT: E 130 SER cc_start: 0.7350 (OUTLIER) cc_final: 0.7122 (p) REVERT: E 136 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 196 CYS cc_start: -0.0619 (OUTLIER) cc_final: -0.0851 (t) REVERT: C 484 GLU cc_start: 0.7814 (mp0) cc_final: 0.7451 (mp0) REVERT: C 493 ASP cc_start: 0.8365 (p0) cc_final: 0.8075 (p0) REVERT: C 587 GLU cc_start: 0.5983 (tm-30) cc_final: 0.5565 (tm-30) REVERT: C 614 LYS cc_start: 0.7812 (tttm) cc_final: 0.6590 (tttm) REVERT: C 745 SER cc_start: 0.7793 (p) cc_final: 0.7353 (t) REVERT: F 51 VAL cc_start: 0.8490 (m) cc_final: 0.8175 (t) outliers start: 160 outliers final: 122 residues processed: 506 average time/residue: 0.1318 time to fit residues: 104.2983 Evaluate side-chains 521 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 392 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 334 ILE Chi-restraints excluded: chain A residue 357 GLU 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 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 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 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 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 379 SER Chi-restraints excluded: chain B residue 382 ASP 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 446 THR Chi-restraints excluded: chain B residue 483 SER 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 523 ASP 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 598 LEU 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 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 715 LEU 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 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 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 130 SER 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 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 172 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 CYS 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 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 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 676 VAL 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 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 70 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU 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 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 210 optimal weight: 0.1980 chunk 241 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 164 optimal weight: 0.6980 chunk 82 optimal weight: 30.0000 chunk 113 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 739 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS E 160 GLN D 151 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.245876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.225540 restraints weight = 80418.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 92)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.222640 restraints weight = 72822.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.222431 restraints weight = 64014.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.222502 restraints weight = 49781.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222772 restraints weight = 43358.686| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22528 Z= 0.154 Angle : 0.689 12.969 30748 Z= 0.336 Chirality : 0.048 0.396 3538 Planarity : 0.004 0.096 3790 Dihedral : 8.742 120.448 3387 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 6.77 % Allowed : 32.92 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2672 helix: 1.40 (0.28), residues: 331 sheet: -0.22 (0.18), residues: 889 loop : -0.56 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 647 TYR 0.016 0.001 TYR B 411 PHE 0.031 0.002 PHE B 701 TRP 0.023 0.002 TRP B 774 HIS 0.008 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00351 (22466) covalent geometry : angle 0.66873 (30601) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.43833 ( 78) hydrogen bonds : bond 0.04648 ( 620) hydrogen bonds : angle 6.26442 ( 1788) link_BETA1-4 : bond 0.00460 ( 4) link_BETA1-4 : angle 3.40290 ( 12) link_BETA1-6 : bond 0.00254 ( 3) link_BETA1-6 : angle 1.39548 ( 9) link_NAG-ASN : bond 0.00730 ( 16) link_NAG-ASN : angle 3.54924 ( 48) *********************** 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 585 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 415 time to evaluate : 0.786 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 328 PHE cc_start: 0.7487 (t80) cc_final: 0.7162 (t80) REVERT: A 380 GLN cc_start: 0.8690 (mp10) cc_final: 0.8322 (mp10) REVERT: A 422 TYR cc_start: 0.8494 (p90) cc_final: 0.8167 (p90) REVERT: A 550 ASN cc_start: 0.7643 (m110) cc_final: 0.7246 (p0) REVERT: A 614 LYS cc_start: 0.7012 (tmtt) cc_final: 0.6672 (tptt) REVERT: A 615 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7327 (tpp80) REVERT: A 760 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8713 (pp) REVERT: A 773 GLU cc_start: 0.7852 (pm20) cc_final: 0.7481 (pm20) REVERT: B 362 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8361 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7960 (t) REVERT: B 448 ARG cc_start: 0.7090 (ptp-170) cc_final: 0.6431 (ptp-170) REVERT: B 497 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: B 506 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7910 (mp) REVERT: B 507 SER cc_start: 0.8445 (m) cc_final: 0.8003 (p) REVERT: B 658 LYS cc_start: 0.7269 (mmmt) cc_final: 0.7050 (mmmt) REVERT: B 669 LYS cc_start: 0.8413 (tppp) cc_final: 0.8009 (tppp) REVERT: B 713 THR cc_start: 0.8488 (m) cc_final: 0.8161 (p) REVERT: B 717 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7327 (tt) REVERT: B 786 LEU cc_start: 0.8375 (mm) cc_final: 0.8055 (mm) REVERT: E 43 ASN cc_start: 0.8095 (t0) cc_final: 0.7550 (m-40) REVERT: E 44 ASP cc_start: 0.8073 (t0) cc_final: 0.7800 (t0) REVERT: E 119 LEU cc_start: 0.8633 (mp) cc_final: 0.8233 (mp) REVERT: E 130 SER cc_start: 0.7318 (OUTLIER) cc_final: 0.7080 (p) REVERT: E 136 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7250 (tm-30) REVERT: E 160 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: C 196 CYS cc_start: -0.0729 (OUTLIER) cc_final: -0.1049 (t) REVERT: C 493 ASP cc_start: 0.8440 (p0) cc_final: 0.8136 (p0) REVERT: C 587 GLU cc_start: 0.6010 (tm-30) cc_final: 0.5619 (tm-30) REVERT: C 614 LYS cc_start: 0.7766 (tttm) cc_final: 0.6514 (tttm) REVERT: C 665 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8163 (mmtm) REVERT: C 683 HIS cc_start: 0.5867 (OUTLIER) cc_final: 0.2081 (m-70) REVERT: C 745 SER cc_start: 0.7863 (p) cc_final: 0.7405 (t) REVERT: F 51 VAL cc_start: 0.8468 (m) cc_final: 0.8158 (t) REVERT: F 75 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6869 (tpp) outliers start: 170 outliers final: 121 residues processed: 535 average time/residue: 0.1422 time to fit residues: 119.5568 Evaluate side-chains 530 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 399 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 273 TYR 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 352 CYS Chi-restraints excluded: chain A residue 357 GLU 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 427 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 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 593 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 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 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 410 VAL Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 483 SER 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 517 HIS 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 598 LEU 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 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 715 LEU 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 743 SER 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 79 LEU 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 E residue 130 SER 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 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 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 613 CYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 633 VAL 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 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 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 75 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 230 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 131 optimal weight: 0.0970 chunk 105 optimal weight: 0.3980 chunk 240 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 chunk 156 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 158 optimal weight: 0.4980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 182 GLN B 455 GLN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS E 160 GLN D 151 GLN ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4872 r_free = 0.4872 target = 0.247910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.227965 restraints weight = 81576.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.226931 restraints weight = 79885.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.225412 restraints weight = 65634.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225779 restraints weight = 56790.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.225911 restraints weight = 50095.658| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22528 Z= 0.119 Angle : 0.687 16.899 30748 Z= 0.331 Chirality : 0.047 0.405 3538 Planarity : 0.004 0.092 3790 Dihedral : 8.335 119.811 3387 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.51 % Rotamer: Outliers : 5.85 % Allowed : 33.68 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2672 helix: 1.50 (0.28), residues: 329 sheet: -0.21 (0.18), residues: 881 loop : -0.51 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 647 TYR 0.015 0.001 TYR B 812 PHE 0.028 0.001 PHE A 336 TRP 0.036 0.001 TRP E 121 HIS 0.034 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00276 (22466) covalent geometry : angle 0.66603 (30601) SS BOND : bond 0.00441 ( 39) SS BOND : angle 1.63012 ( 78) hydrogen bonds : bond 0.04106 ( 620) hydrogen bonds : angle 6.06162 ( 1788) link_BETA1-4 : bond 0.00270 ( 4) link_BETA1-4 : angle 3.38553 ( 12) link_BETA1-6 : bond 0.00463 ( 3) link_BETA1-6 : angle 1.22235 ( 9) link_NAG-ASN : bond 0.00723 ( 16) link_NAG-ASN : angle 3.50357 ( 48) *********************** 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 559 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 412 time to evaluate : 0.737 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: A 348 VAL cc_start: 0.8281 (t) cc_final: 0.7884 (m) REVERT: A 380 GLN cc_start: 0.8667 (mp10) cc_final: 0.8293 (mp10) REVERT: A 422 TYR cc_start: 0.8430 (p90) cc_final: 0.8113 (p90) REVERT: A 614 LYS cc_start: 0.6998 (tmtt) cc_final: 0.6797 (tptt) REVERT: A 615 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7169 (tpp80) REVERT: A 704 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 773 GLU cc_start: 0.7687 (pm20) cc_final: 0.7154 (pm20) REVERT: A 794 LYS cc_start: 0.7899 (tptp) cc_final: 0.7625 (mmtm) REVERT: B 362 PRO cc_start: 0.8576 (Cg_exo) cc_final: 0.8319 (Cg_endo) REVERT: B 410 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7689 (t) REVERT: B 448 ARG cc_start: 0.6978 (ptp-170) cc_final: 0.6650 (ptp-170) REVERT: B 497 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: B 506 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7858 (mp) REVERT: B 647 ARG cc_start: 0.7885 (tmt170) cc_final: 0.7316 (tmt170) REVERT: B 669 LYS cc_start: 0.8399 (tppp) cc_final: 0.7975 (tppp) REVERT: B 676 VAL cc_start: 0.8055 (t) cc_final: 0.7752 (p) REVERT: B 713 THR cc_start: 0.8478 (m) cc_final: 0.8161 (p) REVERT: B 715 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7983 (mt) REVERT: B 717 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7382 (tt) REVERT: B 786 LEU cc_start: 0.8369 (mm) cc_final: 0.8051 (mm) REVERT: E 43 ASN cc_start: 0.7953 (t0) cc_final: 0.7395 (m-40) REVERT: E 44 ASP cc_start: 0.8009 (t0) cc_final: 0.7742 (t0) REVERT: E 119 LEU cc_start: 0.8629 (mp) cc_final: 0.8146 (mp) REVERT: E 136 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7000 (tm-30) REVERT: E 160 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: C 196 CYS cc_start: -0.0704 (OUTLIER) cc_final: -0.0958 (t) REVERT: C 493 ASP cc_start: 0.8366 (p0) cc_final: 0.8017 (p0) REVERT: C 587 GLU cc_start: 0.6068 (tm-30) cc_final: 0.5717 (tm-30) REVERT: C 614 LYS cc_start: 0.7724 (tttm) cc_final: 0.6543 (tttm) REVERT: C 745 SER cc_start: 0.7798 (p) cc_final: 0.7374 (t) REVERT: C 807 TYR cc_start: 0.6370 (m-10) cc_final: 0.5998 (m-10) REVERT: F 51 VAL cc_start: 0.8491 (m) cc_final: 0.8128 (t) REVERT: F 75 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6798 (tpp) REVERT: F 82 TYR cc_start: 0.7898 (m-80) cc_final: 0.7638 (m-80) outliers start: 147 outliers final: 105 residues processed: 507 average time/residue: 0.1357 time to fit residues: 108.5544 Evaluate side-chains 512 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 398 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 273 TYR Chi-restraints excluded: chain A residue 288 VAL 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 372 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 427 VAL 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 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 680 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 128 ASN 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 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL 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 567 ASN Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE 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 743 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 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 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain D residue 104 LEU 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 370 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 489 TYR 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 584 LYS 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 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 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 70 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 148 optimal weight: 0.0470 chunk 39 optimal weight: 0.0010 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 30.0000 chunk 128 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 48 optimal weight: 0.0870 chunk 104 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 258 optimal weight: 0.5980 chunk 8 optimal weight: 40.0000 overall best weight: 0.2662 ------------------------------------------------------------------------------- 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 118 HIS ** D 151 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 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.222148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168614 restraints weight = 62136.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172176 restraints weight = 33492.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.174746 restraints weight = 22091.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175889 restraints weight = 17019.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177160 restraints weight = 14789.032| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22528 Z= 0.121 Angle : 0.687 15.676 30748 Z= 0.330 Chirality : 0.047 0.400 3538 Planarity : 0.004 0.092 3790 Dihedral : 7.965 119.525 3385 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % Rotamer: Outliers : 5.45 % Allowed : 34.04 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2672 helix: 1.51 (0.28), residues: 329 sheet: -0.17 (0.18), residues: 875 loop : -0.50 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 647 TYR 0.014 0.001 TYR C 795 PHE 0.041 0.001 PHE B 701 TRP 0.027 0.001 TRP C 664 HIS 0.017 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00279 (22466) covalent geometry : angle 0.66505 (30601) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.58626 ( 78) hydrogen bonds : bond 0.03931 ( 620) hydrogen bonds : angle 5.93735 ( 1788) link_BETA1-4 : bond 0.00269 ( 4) link_BETA1-4 : angle 3.34623 ( 12) link_BETA1-6 : bond 0.00438 ( 3) link_BETA1-6 : angle 1.29507 ( 9) link_NAG-ASN : bond 0.00729 ( 16) link_NAG-ASN : angle 3.68681 ( 48) *********************** 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 551 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 414 time to evaluate : 0.833 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 348 VAL cc_start: 0.8243 (t) cc_final: 0.7872 (m) REVERT: A 380 GLN cc_start: 0.8686 (mp10) cc_final: 0.8377 (mp10) REVERT: A 422 TYR cc_start: 0.8415 (p90) cc_final: 0.8162 (p90) REVERT: A 585 MET cc_start: 0.6022 (tpt) cc_final: 0.5698 (tpt) REVERT: A 704 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8154 (pp) REVERT: A 794 LYS cc_start: 0.7931 (tptp) cc_final: 0.7350 (tptp) REVERT: A 796 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6174 (m-10) REVERT: B 362 PRO cc_start: 0.8623 (Cg_exo) cc_final: 0.8388 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8209 (t) REVERT: B 468 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7709 (ttp80) REVERT: B 506 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 507 SER cc_start: 0.8470 (m) cc_final: 0.8086 (p) REVERT: B 669 LYS cc_start: 0.8316 (tppp) cc_final: 0.8008 (tppp) REVERT: B 676 VAL cc_start: 0.7989 (t) cc_final: 0.7610 (p) REVERT: B 713 THR cc_start: 0.8342 (m) cc_final: 0.8127 (p) REVERT: B 717 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7339 (tt) REVERT: B 786 LEU cc_start: 0.8380 (mm) cc_final: 0.8071 (mm) REVERT: E 43 ASN cc_start: 0.8332 (t0) cc_final: 0.7867 (m-40) REVERT: E 44 ASP cc_start: 0.7962 (t0) cc_final: 0.7711 (t0) REVERT: E 119 LEU cc_start: 0.8370 (mp) cc_final: 0.8096 (mp) REVERT: E 136 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7005 (tm-30) REVERT: D 84 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8328 (mm-40) REVERT: C 493 ASP cc_start: 0.8250 (p0) cc_final: 0.7913 (p0) REVERT: C 587 GLU cc_start: 0.6068 (tm-30) cc_final: 0.5758 (tm-30) REVERT: C 614 LYS cc_start: 0.7935 (tttm) cc_final: 0.6842 (tttm) REVERT: C 745 SER cc_start: 0.7673 (p) cc_final: 0.7262 (t) REVERT: C 807 TYR cc_start: 0.6141 (m-10) cc_final: 0.5876 (m-10) REVERT: F 51 VAL cc_start: 0.8493 (m) cc_final: 0.8103 (t) REVERT: F 75 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6582 (tpp) REVERT: F 89 MET cc_start: 0.7271 (mpp) cc_final: 0.7019 (mpp) REVERT: F 136 GLU cc_start: 0.6943 (pm20) cc_final: 0.6629 (pm20) outliers start: 137 outliers final: 104 residues processed: 509 average time/residue: 0.1489 time to fit residues: 119.5500 Evaluate side-chains 514 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 404 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 273 TYR 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 372 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 427 VAL 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 457 LEU Chi-restraints excluded: chain A residue 462 LEU 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 680 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 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 196 CYS Chi-restraints excluded: chain B residue 211 MET 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 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 482 ILE 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 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN 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 743 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 802 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 117 CYS Chi-restraints excluded: chain E residue 143 GLU 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 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 471 LEU Chi-restraints excluded: chain C residue 489 TYR 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 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 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 772 ILE 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 75 MET 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 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 262 optimal weight: 0.0070 chunk 55 optimal weight: 0.1980 chunk 76 optimal weight: 30.0000 chunk 105 optimal weight: 0.5980 chunk 156 optimal weight: 0.0970 chunk 198 optimal weight: 8.9990 chunk 227 optimal weight: 0.0970 chunk 215 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 87 optimal weight: 50.0000 chunk 197 optimal weight: 0.9980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN B 150 ASN B 455 GLN B 778 ASN E 109 HIS E 118 HIS ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** C 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.222764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168514 restraints weight = 62224.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172049 restraints weight = 33748.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.174533 restraints weight = 22812.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176383 restraints weight = 17883.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.176845 restraints weight = 15570.886| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22528 Z= 0.116 Angle : 0.698 15.696 30748 Z= 0.334 Chirality : 0.047 0.398 3538 Planarity : 0.004 0.090 3790 Dihedral : 7.623 119.214 3385 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % Rotamer: Outliers : 5.57 % Allowed : 34.12 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2672 helix: 1.53 (0.28), residues: 329 sheet: -0.24 (0.18), residues: 874 loop : -0.47 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 647 TYR 0.012 0.001 TYR C 769 PHE 0.027 0.001 PHE A 336 TRP 0.031 0.001 TRP C 664 HIS 0.021 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00265 (22466) covalent geometry : angle 0.67633 (30601) SS BOND : bond 0.00370 ( 39) SS BOND : angle 1.74752 ( 78) hydrogen bonds : bond 0.03724 ( 620) hydrogen bonds : angle 5.80141 ( 1788) link_BETA1-4 : bond 0.00339 ( 4) link_BETA1-4 : angle 3.25636 ( 12) link_BETA1-6 : bond 0.00437 ( 3) link_BETA1-6 : angle 1.27957 ( 9) link_NAG-ASN : bond 0.00694 ( 16) link_NAG-ASN : angle 3.60202 ( 48) *********************** 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 553 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 413 time to evaluate : 0.726 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 348 VAL cc_start: 0.8230 (t) cc_final: 0.7835 (m) REVERT: A 380 GLN cc_start: 0.8667 (mp10) cc_final: 0.8350 (mp10) REVERT: A 422 TYR cc_start: 0.8400 (p90) cc_final: 0.8089 (p90) REVERT: A 585 MET cc_start: 0.6093 (tpt) cc_final: 0.5754 (tpt) REVERT: A 634 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.5971 (ppp) REVERT: A 704 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 773 GLU cc_start: 0.7847 (pm20) cc_final: 0.7370 (pm20) REVERT: A 794 LYS cc_start: 0.7899 (tptp) cc_final: 0.7660 (mmtt) REVERT: B 362 PRO cc_start: 0.8607 (Cg_exo) cc_final: 0.8358 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8177 (t) REVERT: B 506 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7966 (mp) REVERT: B 647 ARG cc_start: 0.7639 (tmt170) cc_final: 0.7218 (tmt170) REVERT: B 676 VAL cc_start: 0.7938 (t) cc_final: 0.7549 (p) REVERT: B 717 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7296 (tt) REVERT: E 43 ASN cc_start: 0.8306 (t0) cc_final: 0.7883 (m-40) REVERT: E 44 ASP cc_start: 0.7953 (t0) cc_final: 0.7687 (t0) REVERT: E 119 LEU cc_start: 0.8526 (mp) cc_final: 0.8199 (mp) REVERT: E 136 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7056 (tm-30) REVERT: C 557 SER cc_start: 0.7527 (m) cc_final: 0.6778 (p) REVERT: C 587 GLU cc_start: 0.6000 (tm-30) cc_final: 0.5721 (tm-30) REVERT: C 614 LYS cc_start: 0.7841 (tttm) cc_final: 0.6813 (tttm) REVERT: C 664 TRP cc_start: 0.6790 (p-90) cc_final: 0.6501 (p-90) REVERT: C 683 HIS cc_start: 0.4632 (OUTLIER) cc_final: 0.1960 (m90) REVERT: C 745 SER cc_start: 0.7732 (p) cc_final: 0.7312 (t) REVERT: C 807 TYR cc_start: 0.6295 (m-10) cc_final: 0.5915 (m-10) REVERT: F 51 VAL cc_start: 0.8417 (m) cc_final: 0.8024 (t) REVERT: F 75 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6648 (tpp) outliers start: 140 outliers final: 108 residues processed: 512 average time/residue: 0.1360 time to fit residues: 109.9110 Evaluate side-chains 521 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 406 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 357 GLU 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 427 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 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 128 ASN 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 211 MET 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 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 482 ILE 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 633 VAL Chi-restraints excluded: chain B residue 634 MET 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 743 SER 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 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 104 LEU 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 229 VAL Chi-restraints excluded: chain C residue 291 THR 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 471 LEU Chi-restraints excluded: chain C residue 489 TYR 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 613 CYS 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 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 772 ILE 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 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 ASN Chi-restraints excluded: chain F residue 145 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 194 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 251 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 229 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN B 150 ASN ** B 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 HIS E 118 HIS E 151 GLN E 160 GLN ** 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.247123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.226296 restraints weight = 81471.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.224546 restraints weight = 75123.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.223483 restraints weight = 62367.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.223697 restraints weight = 53715.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.223823 restraints weight = 44966.797| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 22528 Z= 0.135 Angle : 0.711 15.779 30748 Z= 0.340 Chirality : 0.047 0.394 3538 Planarity : 0.005 0.112 3790 Dihedral : 7.500 119.401 3385 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 5.10 % Allowed : 34.24 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2672 helix: 1.45 (0.28), residues: 329 sheet: -0.23 (0.18), residues: 868 loop : -0.50 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 468 TYR 0.014 0.001 TYR B 411 PHE 0.035 0.001 PHE A 336 TRP 0.031 0.001 TRP C 664 HIS 0.028 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00315 (22466) covalent geometry : angle 0.68909 (30601) SS BOND : bond 0.00418 ( 39) SS BOND : angle 1.80524 ( 78) hydrogen bonds : bond 0.04021 ( 620) hydrogen bonds : angle 5.76169 ( 1788) link_BETA1-4 : bond 0.00337 ( 4) link_BETA1-4 : angle 3.15338 ( 12) link_BETA1-6 : bond 0.00314 ( 3) link_BETA1-6 : angle 1.35797 ( 9) link_NAG-ASN : bond 0.00676 ( 16) link_NAG-ASN : angle 3.54355 ( 48) *********************** 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 543 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 415 time to evaluate : 0.856 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: 0.8289 (t) cc_final: 0.7858 (m) REVERT: A 380 GLN cc_start: 0.8662 (mp10) cc_final: 0.8277 (mp10) REVERT: A 634 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.5984 (ppp) REVERT: A 704 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 773 GLU cc_start: 0.7862 (pm20) cc_final: 0.7495 (pm20) REVERT: B 362 PRO cc_start: 0.8539 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: B 410 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7956 (t) REVERT: B 506 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7857 (mp) REVERT: B 647 ARG cc_start: 0.7904 (tmt170) cc_final: 0.7410 (tmt170) REVERT: B 676 VAL cc_start: 0.8176 (t) cc_final: 0.7839 (p) REVERT: B 717 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7343 (tt) REVERT: E 43 ASN cc_start: 0.8103 (t0) cc_final: 0.7458 (m-40) REVERT: E 44 ASP cc_start: 0.7982 (t0) cc_final: 0.7704 (t0) REVERT: E 109 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7391 (t70) REVERT: E 119 LEU cc_start: 0.8580 (mp) cc_final: 0.8228 (mp) REVERT: E 136 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7013 (tm-30) REVERT: E 160 GLN cc_start: 0.8545 (tt0) cc_final: 0.8313 (tt0) REVERT: D 84 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8339 (mm-40) REVERT: C 557 SER cc_start: 0.7650 (m) cc_final: 0.6857 (p) REVERT: C 587 GLU cc_start: 0.6022 (tm-30) cc_final: 0.5715 (tm-30) REVERT: C 614 LYS cc_start: 0.7669 (tttm) cc_final: 0.6493 (tttm) REVERT: C 664 TRP cc_start: 0.7062 (p-90) cc_final: 0.6809 (p-90) REVERT: C 683 HIS cc_start: 0.5407 (OUTLIER) cc_final: 0.2515 (m90) REVERT: C 745 SER cc_start: 0.7824 (p) cc_final: 0.7389 (t) REVERT: C 807 TYR cc_start: 0.6595 (m-10) cc_final: 0.6201 (m-10) REVERT: F 51 VAL cc_start: 0.8478 (m) cc_final: 0.8128 (t) REVERT: F 75 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6833 (tpp) outliers start: 128 outliers final: 110 residues processed: 506 average time/residue: 0.1204 time to fit residues: 96.6547 Evaluate side-chains 525 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 407 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 288 VAL 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 372 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 427 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 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 28 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 128 ASN 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 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 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 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 482 ILE 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 633 VAL Chi-restraints excluded: chain B residue 634 MET 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 743 SER 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 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 E residue 143 GLU 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 229 VAL Chi-restraints excluded: chain C residue 291 THR 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 471 LEU Chi-restraints excluded: chain C residue 489 TYR 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 613 CYS 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 650 ASN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 684 HIS Chi-restraints excluded: chain C residue 727 PHE Chi-restraints excluded: chain C residue 772 ILE 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 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 103 ASN 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 20 optimal weight: 0.0270 chunk 55 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 218 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 252 optimal weight: 0.0570 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN 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 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.248092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.227748 restraints weight = 82094.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.225616 restraints weight = 75927.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.223228 restraints weight = 76497.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.223799 restraints weight = 65337.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.224182 restraints weight = 53233.710| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 22528 Z= 0.119 Angle : 0.722 16.722 30748 Z= 0.344 Chirality : 0.047 0.394 3538 Planarity : 0.004 0.090 3790 Dihedral : 7.367 119.030 3385 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.04 % Favored : 95.81 % Rotamer: Outliers : 5.18 % Allowed : 34.43 % Favored : 60.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2672 helix: 1.46 (0.28), residues: 327 sheet: -0.19 (0.18), residues: 861 loop : -0.47 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 647 TYR 0.012 0.001 TYR C 812 PHE 0.038 0.001 PHE A 336 TRP 0.033 0.001 TRP A 774 HIS 0.022 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00275 (22466) covalent geometry : angle 0.70248 (30601) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.69931 ( 78) hydrogen bonds : bond 0.03782 ( 620) hydrogen bonds : angle 5.70955 ( 1788) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 3.05710 ( 12) link_BETA1-6 : bond 0.00436 ( 3) link_BETA1-6 : angle 1.26596 ( 9) link_NAG-ASN : bond 0.00672 ( 16) link_NAG-ASN : angle 3.45459 ( 48) ********************** 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 544 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 414 time to evaluate : 1.040 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: A 348 VAL cc_start: 0.8278 (t) cc_final: 0.7846 (m) REVERT: A 380 GLN cc_start: 0.8649 (mp10) cc_final: 0.8250 (mp10) REVERT: A 511 MET cc_start: 0.3961 (pmm) cc_final: 0.3592 (pmm) REVERT: A 634 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.5931 (ppp) REVERT: A 704 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8174 (pp) REVERT: A 773 GLU cc_start: 0.7843 (pm20) cc_final: 0.7239 (pm20) REVERT: B 355 LYS cc_start: 0.7532 (tptm) cc_final: 0.7316 (tppt) REVERT: B 362 PRO cc_start: 0.8510 (Cg_exo) cc_final: 0.8225 (Cg_endo) REVERT: B 374 GLU cc_start: 0.7508 (pm20) cc_final: 0.7242 (pm20) REVERT: B 410 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7917 (t) REVERT: B 506 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7794 (mp) REVERT: B 647 ARG cc_start: 0.7830 (tmt170) cc_final: 0.7375 (tmt170) REVERT: B 668 MET cc_start: 0.7359 (mmm) cc_final: 0.7114 (tmm) REVERT: B 676 VAL cc_start: 0.7995 (t) cc_final: 0.7677 (p) REVERT: B 717 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7363 (tt) REVERT: B 786 LEU cc_start: 0.8383 (mm) cc_final: 0.8158 (mm) REVERT: E 44 ASP cc_start: 0.7921 (t0) cc_final: 0.7649 (t0) REVERT: E 109 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7349 (t70) REVERT: E 119 LEU cc_start: 0.8580 (mp) cc_final: 0.8215 (mp) REVERT: E 136 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7067 (tm-30) REVERT: E 160 GLN cc_start: 0.8521 (tt0) cc_final: 0.8277 (tt0) REVERT: C 557 SER cc_start: 0.7643 (m) cc_final: 0.6829 (p) REVERT: C 587 GLU cc_start: 0.6036 (tm-30) cc_final: 0.5751 (tm-30) REVERT: C 614 LYS cc_start: 0.7619 (tttm) cc_final: 0.6490 (tttm) REVERT: C 665 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7947 (mmtm) REVERT: C 683 HIS cc_start: 0.5257 (OUTLIER) cc_final: 0.2507 (m90) REVERT: C 745 SER cc_start: 0.7866 (p) cc_final: 0.7438 (t) REVERT: C 807 TYR cc_start: 0.6764 (m-10) cc_final: 0.6291 (m-10) REVERT: F 51 VAL cc_start: 0.8404 (m) cc_final: 0.8020 (t) REVERT: F 75 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6815 (tpp) outliers start: 130 outliers final: 111 residues processed: 506 average time/residue: 0.1260 time to fit residues: 100.8396 Evaluate side-chains 523 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 404 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 357 GLU 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 427 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 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 705 TRP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 729 LEU 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 28 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 128 ASN 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 211 MET 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 383 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 482 ILE 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 551 ILE Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 634 MET Chi-restraints excluded: chain B residue 654 MET 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 743 SER 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 106 ASP Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 117 CYS Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain D residue 108 LEU 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 229 VAL Chi-restraints excluded: chain C residue 291 THR 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 471 LEU Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 489 TYR 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 589 TYR 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 649 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 684 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 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 75 MET Chi-restraints excluded: chain F residue 85 ILE 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 74 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 52 optimal weight: 0.0000 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 192 optimal weight: 0.0970 chunk 147 optimal weight: 2.9990 chunk 78 optimal weight: 40.0000 chunk 162 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 E 151 GLN ** 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** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.220316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167764 restraints weight = 61952.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.171117 restraints weight = 33436.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.173536 restraints weight = 21951.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174763 restraints weight = 16641.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.175840 restraints weight = 14392.516| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22528 Z= 0.156 Angle : 0.742 16.992 30748 Z= 0.356 Chirality : 0.047 0.387 3538 Planarity : 0.004 0.092 3790 Dihedral : 7.356 119.573 3385 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.79 % Favored : 94.99 % Rotamer: Outliers : 4.98 % Allowed : 34.59 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.22 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2672 helix: 1.43 (0.28), residues: 327 sheet: -0.21 (0.18), residues: 876 loop : -0.50 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 678 TYR 0.016 0.001 TYR A 411 PHE 0.035 0.002 PHE A 336 TRP 0.044 0.002 TRP C 646 HIS 0.023 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00363 (22466) covalent geometry : angle 0.71910 (30601) SS BOND : bond 0.00513 ( 39) SS BOND : angle 2.01785 ( 78) hydrogen bonds : bond 0.04263 ( 620) hydrogen bonds : angle 5.73895 ( 1788) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 3.23268 ( 12) link_BETA1-6 : bond 0.00354 ( 3) link_BETA1-6 : angle 1.45213 ( 9) link_NAG-ASN : bond 0.00650 ( 16) link_NAG-ASN : angle 3.63928 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.11 seconds wall clock time: 93 minutes 40.54 seconds (5620.54 seconds total)