Starting phenix.real_space_refine on Sun Aug 24 18:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x81_38132/08_2025/8x81_38132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x81_38132/08_2025/8x81_38132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x81_38132/08_2025/8x81_38132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x81_38132/08_2025/8x81_38132.map" model { file = "/net/cci-nas-00/data/ceres_data/8x81_38132/08_2025/8x81_38132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x81_38132/08_2025/8x81_38132.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 14073 2.51 5 N 3565 2.21 5 O 4087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 21875 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 715} Chain breaks: 1 Chain: "B" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 715} Chain breaks: 1 Chain: "D" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 819 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 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: "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: "C" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 715} Chain breaks: 1 Chain: "G" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.73, per 1000 atoms: 0.26 Number of scatterers: 21875 At special positions: 0 Unit cell: (167.45, 153.85, 215.9, 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 4087 8.00 N 3565 7.00 C 14073 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=2.03 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 D 117 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS F 117 " - pdb=" SG CYS F 167 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 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=2.04 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 674 " distance=2.03 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 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... 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 903 " - " ASN B 516 " " NAG B 904 " - " ASN B 697 " " NAG B 905 " - " ASN B 659 " " NAG B 906 " - " ASN B 728 " " NAG B 907 " - " ASN B 397 " " NAG C 901 " - " ASN C 750 " " NAG C 902 " - " ASN C 624 " " NAG C 903 " - " ASN C 397 " " NAG C 904 " - " ASN C 347 " " NAG C 905 " - " ASN C 697 " " NAG C 906 " - " ASN C 659 " " NAG C 907 " - " ASN C 728 " " NAG G 1 " - " ASN A 347 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 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: 38 helices and 60 sheets defined 15.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.570A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.581A pdb=" N MET A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 235 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.095A pdb=" N GLN A 455 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.927A pdb=" N LYS A 737 " --> pdb=" O PRO A 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.637A pdb=" N ASN B 206 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 233 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.206A pdb=" N GLN B 380 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 381 " --> pdb=" O GLN B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.766A pdb=" N SER B 456 " --> pdb=" O THR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.831A pdb=" N VAL B 535 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 733 through 737 removed outlier: 3.927A pdb=" N LYS B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 733 through 737' Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 30 through 46 removed outlier: 4.234A pdb=" N LEU D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR D 40 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 4.022A pdb=" N MET D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 144 through 159 removed outlier: 4.146A pdb=" N SER D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'F' and resid 23 through 44 Processing helix chain 'F' and resid 71 through 88 removed outlier: 3.931A pdb=" N SER F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 115 Processing helix chain 'F' and resid 128 through 161 removed outlier: 3.959A pdb=" N GLY F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER F 141 " --> pdb=" O ALA F 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 44 Processing helix chain 'E' and resid 71 through 87 Processing helix chain 'E' and resid 91 through 115 removed outlier: 3.650A pdb=" N LYS E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.998A pdb=" N LEU E 128 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 129 " --> pdb=" O GLU E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 125 through 129' Processing helix chain 'E' and resid 130 through 162 removed outlier: 4.474A pdb=" N GLU E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.728A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 230 through 235 removed outlier: 3.853A pdb=" N VAL C 235 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' 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 452 through 457 removed outlier: 3.641A pdb=" N LEU C 457 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 673 Processing helix chain 'C' and resid 734 through 738 removed outlier: 3.639A pdb=" N VAL C 738 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.573A pdb=" N PHE A 91 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 98 " --> pdb=" O PHE A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 133 removed outlier: 4.087A pdb=" N ASN A 128 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 4.776A pdb=" N LYS A 158 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A 216 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS A 160 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS A 214 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.858A pdb=" N VAL A 164 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 210 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET A 211 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET A 227 " --> pdb=" O MET A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 248 removed outlier: 3.719A pdb=" N ASN A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 253 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 295 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 255 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 293 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 288 removed outlier: 3.540A pdb=" N TYR A 273 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 286 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 271 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 268 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS A 311 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 270 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 309 " --> pdb=" O GLN A 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AB1, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.609A pdb=" N VAL A 348 " --> pdb=" O PHE A 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 339 through 343 removed outlier: 6.382A pdb=" N ILE A 340 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 428 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 342 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AB4, first strand: chain 'A' and resid 461 through 469 Processing sheet with id=AB5, first strand: chain 'A' and resid 461 through 469 removed outlier: 3.912A pdb=" N TYR A 509 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 529 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.668A pdb=" N LEU A 598 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 584 through 588 removed outlier: 3.788A pdb=" N LYS A 584 " --> pdb=" O TYR A 574 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 574 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 645 through 649 removed outlier: 3.602A pdb=" N PHE A 701 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 693 through 694 removed outlier: 3.678A pdb=" N THR A 711 " --> pdb=" O HIS A 684 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS A 710 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 731 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 743 through 748 removed outlier: 3.740A pdb=" N VAL A 756 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR A 795 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 784 through 789 removed outlier: 3.525A pdb=" N LYS A 784 " --> pdb=" O TRP A 774 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.518A pdb=" N PHE B 87 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 223 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.736A pdb=" N PHE B 91 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 128 through 129 removed outlier: 4.128A pdb=" N ASN B 128 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 145 " --> pdb=" O ASN B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 133 through 134 removed outlier: 7.113A pdb=" N LEU B 133 " --> pdb=" O LYS B 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.785A pdb=" N LEU B 161 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 184 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AC9, first strand: chain 'B' and resid 267 through 268 removed outlier: 4.096A pdb=" N GLN B 268 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS B 311 " --> pdb=" O GLN B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 339 through 343 removed outlier: 3.877A pdb=" N ILE B 428 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 374 through 375 removed outlier: 3.602A pdb=" N MET B 370 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 382 through 383 removed outlier: 3.631A pdb=" N ASP B 382 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 390 " --> pdb=" O ASP B 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AD5, first strand: chain 'B' and resid 435 through 438 removed outlier: 3.886A pdb=" N ARG B 448 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 437 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.305A pdb=" N LEU B 464 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.305A pdb=" N LEU B 464 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 541 through 547 removed outlier: 5.961A pdb=" N SER B 542 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU B 559 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 584 through 588 removed outlier: 3.503A pdb=" N VAL B 609 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 645 through 650 Processing sheet with id=AE2, first strand: chain 'B' and resid 693 through 696 removed outlier: 5.983A pdb=" N TYR B 679 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 745 through 748 removed outlier: 3.674A pdb=" N VAL B 756 " --> pdb=" O TYR B 795 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 795 " --> pdb=" O VAL B 756 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 784 through 789 removed outlier: 3.936A pdb=" N LYS B 784 " --> pdb=" O TRP B 774 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR B 769 " --> pdb=" O ILE B 814 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 814 " --> pdb=" O TYR B 769 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 771 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 35 through 36 removed outlier: 4.808A pdb=" N SER C 36 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS C 90 " --> pdb=" O SER C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 85 through 88 removed outlier: 6.824A pdb=" N THR C 85 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN C 223 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE C 87 " --> pdb=" O GLN C 223 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 214 " --> pdb=" O HIS C 160 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 158 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 128 through 133 removed outlier: 4.196A pdb=" N ASN C 128 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 145 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 141 " --> pdb=" O TRP C 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AE9, first strand: chain 'C' and resid 241 through 247 removed outlier: 5.567A pdb=" N GLY C 242 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 258 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 268 through 271 removed outlier: 4.116A pdb=" N GLN C 268 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 275 through 276 removed outlier: 3.952A pdb=" N GLU C 275 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 282 " --> pdb=" O GLU C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 334 through 335 removed outlier: 4.342A pdb=" N ILE C 334 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 353 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 348 " --> pdb=" O PHE C 393 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 341 through 343 removed outlier: 3.729A pdb=" N THR C 342 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 428 " --> pdb=" O THR C 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 355 through 356 Processing sheet with id=AF6, first strand: chain 'C' and resid 366 through 370 Processing sheet with id=AF7, first strand: chain 'C' and resid 437 through 438 Processing sheet with id=AF8, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AF9, first strand: chain 'C' and resid 461 through 469 removed outlier: 3.611A pdb=" N TYR C 509 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 527 " --> pdb=" O MET C 511 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 544 through 547 Processing sheet with id=AG2, first strand: chain 'C' and resid 583 through 588 Processing sheet with id=AG3, first strand: chain 'C' and resid 645 through 650 removed outlier: 3.687A pdb=" N THR C 661 " --> pdb=" O ILE C 648 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN C 650 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 659 " --> pdb=" O ASN C 650 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 691 through 694 removed outlier: 4.053A pdb=" N TRP C 691 " --> pdb=" O HIS C 683 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 741 through 748 Processing sheet with id=AG6, first strand: chain 'C' and resid 785 through 789 612 hydrogen bonds defined for protein. 1581 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: 4.71 Time building geometry restraints manager: 2.46 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: 6704 1.34 - 1.46: 4801 1.46 - 1.58: 10732 1.58 - 1.70: 5 1.70 - 1.82: 210 Bond restraints: 22452 Sorted by residual: bond pdb=" C1 NAG C 905 " pdb=" O5 NAG C 905 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CB PRO C 531 " pdb=" CG PRO C 531 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.35e+00 bond pdb=" CB PRO C 643 " pdb=" CG PRO C 643 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.16e+00 bond pdb=" CB PRO E 23 " pdb=" CG PRO E 23 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.72e+00 bond pdb=" CB PRO B 813 " pdb=" CG PRO B 813 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.84e+00 ... (remaining 22447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 30200 2.66 - 5.32: 311 5.32 - 7.98: 50 7.98 - 10.64: 14 10.64 - 13.30: 3 Bond angle restraints: 30578 Sorted by residual: angle pdb=" CA PRO C 531 " pdb=" N PRO C 531 " pdb=" CD PRO C 531 " ideal model delta sigma weight residual 112.00 100.73 11.27 1.40e+00 5.10e-01 6.48e+01 angle pdb=" CA PRO E 23 " pdb=" N PRO E 23 " pdb=" CD PRO E 23 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" N CYS B 447 " pdb=" CA CYS B 447 " pdb=" C CYS B 447 " ideal model delta sigma weight residual 108.74 115.84 -7.10 1.38e+00 5.25e-01 2.65e+01 angle pdb=" CA PRO C 643 " pdb=" N PRO C 643 " pdb=" CD PRO C 643 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.34e+01 angle pdb=" N CYS B 436 " pdb=" CA CYS B 436 " pdb=" C CYS B 436 " ideal model delta sigma weight residual 108.24 114.25 -6.01 1.32e+00 5.74e-01 2.07e+01 ... (remaining 30573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 12644 23.42 - 46.84: 1056 46.84 - 70.25: 125 70.25 - 93.67: 28 93.67 - 117.09: 5 Dihedral angle restraints: 13858 sinusoidal: 5893 harmonic: 7965 Sorted by residual: dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 412 " pdb=" CB CYS B 412 " ideal model delta sinusoidal sigma weight residual -86.00 -161.76 75.76 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 447 " pdb=" CB CYS B 447 " ideal model delta sinusoidal sigma weight residual 93.00 17.76 75.24 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C 488 " pdb=" SG CYS C 488 " pdb=" SG CYS C 498 " pdb=" CB CYS C 498 " ideal model delta sinusoidal sigma weight residual -86.00 -11.29 -74.71 1 1.00e+01 1.00e-02 7.07e+01 ... (remaining 13855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3248 0.093 - 0.186: 270 0.186 - 0.279: 5 0.279 - 0.372: 0 0.372 - 0.465: 1 Chirality restraints: 3524 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 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 750 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 659 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3521 not shown) Planarity restraints: 3813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 400 " 0.084 5.00e-02 4.00e+02 1.25e-01 2.48e+01 pdb=" N PRO B 401 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO B 401 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 401 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 530 " 0.072 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO C 531 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 531 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 531 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 299 " 0.056 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO B 300 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " 0.046 5.00e-02 4.00e+02 ... (remaining 3810 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 793 2.72 - 3.26: 20407 3.26 - 3.81: 33158 3.81 - 4.35: 37696 4.35 - 4.90: 63253 Nonbonded interactions: 155307 Sorted by model distance: nonbonded pdb=" O SER F 52 " pdb=" OG SER F 148 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASN A 516 " pdb=" OG SER A 521 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS C 536 " pdb=" O TRP C 622 " model vdw 2.204 3.120 nonbonded pdb=" O THR D 37 " pdb=" OG1 THR D 40 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR C 248 " pdb=" OD1 ASP C 250 " model vdw 2.251 3.040 ... (remaining 155302 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 905) selection = (chain 'C' and resid 23 through 905) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 15.510 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: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.250 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 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 : 0.004 0.136 22513 Z= 0.165 Angle : 0.737 13.297 30722 Z= 0.391 Chirality : 0.046 0.465 3524 Planarity : 0.005 0.125 3793 Dihedral : 16.023 117.089 8569 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.78 % Favored : 96.00 % Rotamer: Outliers : 0.40 % Allowed : 25.17 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.16), residues: 2672 helix: 0.24 (0.31), residues: 316 sheet: 0.62 (0.20), residues: 700 loop : -0.63 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 573 TYR 0.032 0.001 TYR B 769 PHE 0.029 0.001 PHE C 703 TRP 0.042 0.001 TRP C 625 HIS 0.012 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00369 (22452) covalent geometry : angle 0.72308 (30578) SS BOND : bond 0.00185 ( 39) SS BOND : angle 1.52230 ( 78) hydrogen bonds : bond 0.16568 ( 587) hydrogen bonds : angle 6.98667 ( 1581) link_BETA1-4 : bond 0.00502 ( 1) link_BETA1-4 : angle 0.83709 ( 3) link_BETA1-6 : bond 0.00687 ( 1) link_BETA1-6 : angle 1.28231 ( 3) link_NAG-ASN : bond 0.00624 ( 20) link_NAG-ASN : angle 2.94543 ( 60) *********************** 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 431 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 421 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 SER cc_start: 0.8718 (t) cc_final: 0.8471 (p) REVERT: A 546 GLU cc_start: 0.5240 (tp30) cc_final: 0.4826 (tp30) REVERT: A 707 GLU cc_start: 0.7328 (pp20) cc_final: 0.6966 (pp20) REVERT: F 26 LYS cc_start: 0.6818 (tptp) cc_final: 0.6521 (tptp) REVERT: F 134 VAL cc_start: 0.6993 (t) cc_final: 0.6787 (t) REVERT: E 136 GLU cc_start: 0.6705 (pp20) cc_final: 0.6496 (pp20) REVERT: C 307 GLN cc_start: 0.7776 (mp-120) cc_final: 0.7532 (mp10) REVERT: C 615 ARG cc_start: 0.8081 (ttt-90) cc_final: 0.7722 (ttt90) outliers start: 10 outliers final: 10 residues processed: 422 average time/residue: 0.1653 time to fit residues: 107.1847 Evaluate side-chains 422 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 412 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 668 MET Chi-restraints excluded: chain C residue 681 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 223 GLN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 223 GLN B 517 HIS E 96 GLN E 118 HIS C 798 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.215908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167426 restraints weight = 50174.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171894 restraints weight = 25053.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174753 restraints weight = 15786.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176552 restraints weight = 11432.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.177625 restraints weight = 9168.587| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22513 Z= 0.212 Angle : 0.677 10.458 30722 Z= 0.339 Chirality : 0.047 0.310 3524 Planarity : 0.005 0.078 3793 Dihedral : 7.462 97.514 3353 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 3.50 % Allowed : 22.23 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2672 helix: 1.11 (0.30), residues: 303 sheet: 0.54 (0.19), residues: 746 loop : -0.65 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 573 TYR 0.026 0.002 TYR A 335 PHE 0.030 0.001 PHE B 500 TRP 0.021 0.002 TRP A 512 HIS 0.009 0.001 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.00473 (22452) covalent geometry : angle 0.66040 (30578) SS BOND : bond 0.00442 ( 39) SS BOND : angle 1.60949 ( 78) hydrogen bonds : bond 0.05902 ( 587) hydrogen bonds : angle 5.54486 ( 1581) link_BETA1-4 : bond 0.00867 ( 1) link_BETA1-4 : angle 0.45598 ( 3) link_BETA1-6 : bond 0.01478 ( 1) link_BETA1-6 : angle 3.10434 ( 3) link_NAG-ASN : bond 0.01023 ( 20) link_NAG-ASN : angle 2.90351 ( 60) *********************** 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 535 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 447 time to evaluate : 0.978 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 270 GLN cc_start: 0.7542 (pm20) cc_final: 0.7210 (pm20) REVERT: A 422 TYR cc_start: 0.8447 (p90) cc_final: 0.7491 (p90) REVERT: A 449 TRP cc_start: 0.7884 (p-90) cc_final: 0.7555 (p-90) REVERT: A 506 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7182 (tp) REVERT: A 669 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8591 (mmmm) REVERT: A 694 ASP cc_start: 0.6545 (t0) cc_final: 0.6324 (t0) REVERT: A 707 GLU cc_start: 0.7569 (pp20) cc_final: 0.7243 (pp20) REVERT: B 439 ASP cc_start: 0.8032 (t0) cc_final: 0.7718 (t0) REVERT: B 444 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8210 (ptpp) REVERT: B 550 ASN cc_start: 0.7823 (t0) cc_final: 0.7418 (t0) REVERT: B 558 TRP cc_start: 0.8609 (p90) cc_final: 0.7960 (p90) REVERT: B 787 ARG cc_start: 0.7356 (ttt180) cc_final: 0.7111 (tpp80) REVERT: F 26 LYS cc_start: 0.7500 (tptp) cc_final: 0.7180 (tptp) REVERT: F 43 ASN cc_start: 0.8232 (m-40) cc_final: 0.7834 (m-40) REVERT: F 89 MET cc_start: 0.7733 (mtt) cc_final: 0.7522 (mtt) REVERT: E 89 MET cc_start: 0.8159 (mpp) cc_final: 0.6996 (mtm) REVERT: E 96 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7381 (tp-100) REVERT: E 159 TRP cc_start: 0.7642 (t60) cc_final: 0.7213 (t60) REVERT: E 160 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7810 (mm-40) REVERT: C 307 GLN cc_start: 0.7265 (mp-120) cc_final: 0.6972 (mp10) REVERT: C 387 HIS cc_start: 0.8963 (m-70) cc_final: 0.8753 (m-70) REVERT: C 544 LYS cc_start: 0.8160 (tptt) cc_final: 0.7859 (tptt) REVERT: C 615 ARG cc_start: 0.8351 (ttt-90) cc_final: 0.8027 (mtp85) REVERT: C 625 TRP cc_start: 0.7339 (m100) cc_final: 0.7078 (m100) REVERT: C 662 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7154 (mm) outliers start: 88 outliers final: 52 residues processed: 492 average time/residue: 0.1614 time to fit residues: 122.9728 Evaluate side-chains 485 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 430 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 194 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 190 optimal weight: 60.0000 chunk 242 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 358 ASN A 395 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN B 683 HIS B 710 HIS F 47 HIS E 47 HIS E 55 GLN C 726 ASN C 798 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.202746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151982 restraints weight = 48103.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156182 restraints weight = 24011.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158852 restraints weight = 15001.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.160496 restraints weight = 10834.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.161566 restraints weight = 8691.474| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.173 22513 Z= 0.464 Angle : 0.866 12.483 30722 Z= 0.449 Chirality : 0.053 0.305 3524 Planarity : 0.007 0.085 3793 Dihedral : 7.393 95.792 3338 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.68 % Rotamer: Outliers : 6.08 % Allowed : 21.19 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.16), residues: 2672 helix: 0.33 (0.28), residues: 294 sheet: -0.16 (0.18), residues: 772 loop : -0.98 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 678 TYR 0.042 0.003 TYR B 422 PHE 0.048 0.002 PHE B 500 TRP 0.028 0.003 TRP B 774 HIS 0.012 0.002 HIS B 467 Details of bonding type rmsd covalent geometry : bond 0.01028 (22452) covalent geometry : angle 0.85246 (30578) SS BOND : bond 0.00497 ( 39) SS BOND : angle 1.78538 ( 78) hydrogen bonds : bond 0.08059 ( 587) hydrogen bonds : angle 6.27850 ( 1581) link_BETA1-4 : bond 0.01162 ( 1) link_BETA1-4 : angle 0.67545 ( 3) link_BETA1-6 : bond 0.01835 ( 1) link_BETA1-6 : angle 2.72398 ( 3) link_NAG-ASN : bond 0.00543 ( 20) link_NAG-ASN : angle 2.96875 ( 60) *********************** 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 627 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 474 time to evaluate : 0.869 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 246 GLU cc_start: 0.7278 (tp30) cc_final: 0.6939 (tp30) REVERT: A 270 GLN cc_start: 0.7731 (pm20) cc_final: 0.7337 (pm20) REVERT: A 339 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8200 (mttp) REVERT: A 374 GLU cc_start: 0.6790 (mp0) cc_final: 0.6475 (mp0) REVERT: A 469 SER cc_start: 0.7744 (m) cc_final: 0.7472 (t) REVERT: A 506 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 574 TYR cc_start: 0.8077 (p90) cc_final: 0.7854 (p90) REVERT: A 584 LYS cc_start: 0.8759 (pptt) cc_final: 0.8384 (pttp) REVERT: A 587 GLU cc_start: 0.7922 (mp0) cc_final: 0.7713 (mp0) REVERT: A 729 LEU cc_start: 0.6400 (tp) cc_final: 0.6176 (tp) REVERT: A 731 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: A 768 MET cc_start: 0.5680 (pmm) cc_final: 0.5471 (pmm) REVERT: A 769 TYR cc_start: 0.7319 (p90) cc_final: 0.7105 (p90) REVERT: A 823 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7035 (ttpp) REVERT: B 272 LYS cc_start: 0.7699 (mptt) cc_final: 0.7373 (mmtt) REVERT: B 355 LYS cc_start: 0.7717 (tppp) cc_final: 0.7505 (tptm) REVERT: B 375 LYS cc_start: 0.7680 (tptm) cc_final: 0.7400 (tptm) REVERT: B 392 THR cc_start: 0.8502 (t) cc_final: 0.8251 (p) REVERT: B 407 TYR cc_start: 0.8117 (p90) cc_final: 0.7766 (p90) REVERT: B 448 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7703 (ptp-170) REVERT: B 517 HIS cc_start: 0.8433 (t-90) cc_final: 0.8100 (t-90) REVERT: B 544 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7525 (mtmm) REVERT: B 550 ASN cc_start: 0.7973 (t0) cc_final: 0.7543 (t0) REVERT: B 700 LYS cc_start: 0.8401 (tttt) cc_final: 0.8167 (tttt) REVERT: B 764 ASP cc_start: 0.8651 (p0) cc_final: 0.8446 (p0) REVERT: B 795 TYR cc_start: 0.7844 (t80) cc_final: 0.7544 (t80) REVERT: B 812 TYR cc_start: 0.8290 (m-10) cc_final: 0.7995 (m-10) REVERT: B 815 PHE cc_start: 0.6623 (m-80) cc_final: 0.6408 (m-80) REVERT: D 26 LYS cc_start: 0.8024 (pttp) cc_final: 0.7730 (pttp) REVERT: F 26 LYS cc_start: 0.7906 (tptp) cc_final: 0.7494 (tptp) REVERT: F 43 ASN cc_start: 0.8382 (m-40) cc_final: 0.8037 (m-40) REVERT: F 44 ASP cc_start: 0.7744 (t0) cc_final: 0.7378 (t70) REVERT: F 89 MET cc_start: 0.8317 (mtt) cc_final: 0.8053 (mtt) REVERT: E 89 MET cc_start: 0.8370 (mpp) cc_final: 0.7780 (mpp) REVERT: E 96 GLN cc_start: 0.8488 (tp40) cc_final: 0.8132 (tm-30) REVERT: E 143 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6750 (mm-30) REVERT: E 144 VAL cc_start: 0.8481 (p) cc_final: 0.8267 (p) REVERT: E 159 TRP cc_start: 0.8023 (t60) cc_final: 0.7531 (t60) REVERT: E 160 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7901 (mm-40) REVERT: C 307 GLN cc_start: 0.7550 (mp-120) cc_final: 0.7186 (mp10) REVERT: C 350 PHE cc_start: 0.7654 (m-10) cc_final: 0.7448 (m-10) REVERT: C 428 ILE cc_start: 0.4029 (OUTLIER) cc_final: 0.3742 (mp) REVERT: C 457 LEU cc_start: 0.2772 (OUTLIER) cc_final: 0.1563 (mm) REVERT: C 523 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7331 (t70) REVERT: C 544 LYS cc_start: 0.8208 (tptt) cc_final: 0.7950 (tptt) REVERT: C 574 TYR cc_start: 0.6808 (p90) cc_final: 0.6531 (p90) REVERT: C 583 TRP cc_start: 0.6381 (m100) cc_final: 0.6065 (m100) REVERT: C 587 GLU cc_start: 0.7592 (mp0) cc_final: 0.7291 (mp0) REVERT: C 615 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.8354 (ttt-90) outliers start: 153 outliers final: 88 residues processed: 570 average time/residue: 0.1615 time to fit residues: 142.6056 Evaluate side-chains 549 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 453 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 ASN Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 630 TYR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 798 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS B 710 HIS B 800 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 47 HIS C 670 ASN C 726 ASN C 798 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.208471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159956 restraints weight = 49053.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165478 restraints weight = 25735.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167068 restraints weight = 13878.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167942 restraints weight = 10417.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168394 restraints weight = 9302.249| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22513 Z= 0.199 Angle : 0.677 12.388 30722 Z= 0.341 Chirality : 0.048 0.457 3524 Planarity : 0.005 0.072 3793 Dihedral : 6.642 94.059 3336 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.98 % Favored : 94.84 % Rotamer: Outliers : 4.57 % Allowed : 23.74 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.16), residues: 2672 helix: 0.73 (0.29), residues: 308 sheet: -0.09 (0.18), residues: 777 loop : -0.90 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 678 TYR 0.021 0.002 TYR A 795 PHE 0.023 0.001 PHE B 500 TRP 0.037 0.002 TRP A 449 HIS 0.007 0.001 HIS C 798 Details of bonding type rmsd covalent geometry : bond 0.00445 (22452) covalent geometry : angle 0.66397 (30578) SS BOND : bond 0.00354 ( 39) SS BOND : angle 1.56780 ( 78) hydrogen bonds : bond 0.05738 ( 587) hydrogen bonds : angle 5.72228 ( 1581) link_BETA1-4 : bond 0.00579 ( 1) link_BETA1-4 : angle 0.75675 ( 3) link_BETA1-6 : bond 0.01498 ( 1) link_BETA1-6 : angle 0.87935 ( 3) link_NAG-ASN : bond 0.00491 ( 20) link_NAG-ASN : angle 2.64492 ( 60) *********************** 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 572 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 457 time to evaluate : 0.843 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 246 GLU cc_start: 0.7283 (tp30) cc_final: 0.6942 (tp30) REVERT: A 270 GLN cc_start: 0.7787 (pm20) cc_final: 0.7290 (pm20) REVERT: A 469 SER cc_start: 0.7761 (m) cc_final: 0.7450 (t) REVERT: A 521 SER cc_start: 0.7999 (p) cc_final: 0.7741 (m) REVERT: A 584 LYS cc_start: 0.8780 (pptt) cc_final: 0.8414 (pttp) REVERT: A 669 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8730 (mmmm) REVERT: A 729 LEU cc_start: 0.6330 (tp) cc_final: 0.6099 (tp) REVERT: A 812 TYR cc_start: 0.6848 (m-10) cc_final: 0.6638 (m-10) REVERT: A 823 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7084 (ttmm) REVERT: B 355 LYS cc_start: 0.7492 (tppp) cc_final: 0.7275 (tptm) REVERT: B 365 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5448 (tm-30) REVERT: B 390 LYS cc_start: 0.8513 (tttt) cc_final: 0.8179 (tttt) REVERT: B 407 TYR cc_start: 0.8185 (p90) cc_final: 0.7914 (p90) REVERT: B 439 ASP cc_start: 0.8094 (t0) cc_final: 0.7641 (t70) REVERT: B 448 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6964 (mtp85) REVERT: B 517 HIS cc_start: 0.8276 (t-90) cc_final: 0.8064 (t-90) REVERT: B 544 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7403 (mtmm) REVERT: B 558 TRP cc_start: 0.8621 (p90) cc_final: 0.8055 (p90) REVERT: B 700 LYS cc_start: 0.8358 (tttt) cc_final: 0.8136 (tttt) REVERT: B 787 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7129 (tpp80) REVERT: B 788 ILE cc_start: 0.8157 (tp) cc_final: 0.7847 (tp) REVERT: B 795 TYR cc_start: 0.7816 (t80) cc_final: 0.7564 (t80) REVERT: D 26 LYS cc_start: 0.8106 (pttp) cc_final: 0.7876 (pttp) REVERT: D 105 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7722 (tmm-80) REVERT: F 26 LYS cc_start: 0.7670 (tptp) cc_final: 0.7329 (tptp) REVERT: F 43 ASN cc_start: 0.8268 (m-40) cc_final: 0.7820 (m-40) REVERT: F 44 ASP cc_start: 0.7740 (t0) cc_final: 0.7420 (t70) REVERT: F 75 MET cc_start: 0.8191 (ttt) cc_final: 0.7924 (mtp) REVERT: F 89 MET cc_start: 0.8170 (mtt) cc_final: 0.7952 (mtt) REVERT: F 157 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6803 (tpt) REVERT: E 96 GLN cc_start: 0.8473 (tp40) cc_final: 0.7894 (tm-30) REVERT: C 307 GLN cc_start: 0.7314 (mp-120) cc_final: 0.7016 (mp10) REVERT: C 394 PHE cc_start: 0.6145 (OUTLIER) cc_final: 0.4951 (m-10) REVERT: C 457 LEU cc_start: 0.2731 (OUTLIER) cc_final: 0.1803 (mm) REVERT: C 544 LYS cc_start: 0.8167 (tptt) cc_final: 0.7792 (tptt) REVERT: C 610 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7384 (mm-40) REVERT: C 662 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7361 (mm) outliers start: 115 outliers final: 86 residues processed: 515 average time/residue: 0.1606 time to fit residues: 128.6134 Evaluate side-chains 532 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 437 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 630 TYR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 665 LYS Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 798 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 149 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 81 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 232 optimal weight: 5.9990 chunk 195 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 215 optimal weight: 0.0970 chunk 222 optimal weight: 5.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS B 710 HIS F 109 HIS F 160 GLN E 47 HIS E 55 GLN C 268 GLN C 798 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.209504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.160122 restraints weight = 48983.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.164599 restraints weight = 24128.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167354 restraints weight = 15003.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.169115 restraints weight = 10852.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170288 restraints weight = 8701.970| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22513 Z= 0.179 Angle : 0.664 13.072 30722 Z= 0.332 Chirality : 0.047 0.311 3524 Planarity : 0.005 0.070 3793 Dihedral : 6.323 91.084 3336 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.35 % Rotamer: Outliers : 5.49 % Allowed : 23.74 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.16), residues: 2672 helix: 1.10 (0.30), residues: 302 sheet: -0.07 (0.18), residues: 766 loop : -0.84 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 647 TYR 0.017 0.001 TYR B 466 PHE 0.022 0.001 PHE B 500 TRP 0.038 0.002 TRP A 449 HIS 0.010 0.001 HIS C 800 Details of bonding type rmsd covalent geometry : bond 0.00405 (22452) covalent geometry : angle 0.65111 (30578) SS BOND : bond 0.00347 ( 39) SS BOND : angle 1.66173 ( 78) hydrogen bonds : bond 0.05334 ( 587) hydrogen bonds : angle 5.53423 ( 1581) link_BETA1-4 : bond 0.00616 ( 1) link_BETA1-4 : angle 0.75930 ( 3) link_BETA1-6 : bond 0.01524 ( 1) link_BETA1-6 : angle 1.05948 ( 3) link_NAG-ASN : bond 0.00419 ( 20) link_NAG-ASN : angle 2.47602 ( 60) *********************** 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 593 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 455 time to evaluate : 0.932 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 246 GLU cc_start: 0.7242 (tp30) cc_final: 0.6898 (tp30) REVERT: A 270 GLN cc_start: 0.7681 (pm20) cc_final: 0.7299 (pm20) REVERT: A 335 TYR cc_start: 0.7800 (m-10) cc_final: 0.7329 (m-80) REVERT: A 339 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8194 (mmtp) REVERT: A 395 ASN cc_start: 0.7544 (p0) cc_final: 0.7142 (p0) REVERT: A 434 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7469 (mt) REVERT: A 469 SER cc_start: 0.7755 (m) cc_final: 0.7436 (t) REVERT: A 497 GLU cc_start: 0.6727 (tt0) cc_final: 0.6456 (tp30) REVERT: A 521 SER cc_start: 0.7969 (p) cc_final: 0.7723 (m) REVERT: A 584 LYS cc_start: 0.8784 (pptt) cc_final: 0.8494 (pttp) REVERT: A 667 LEU cc_start: 0.8047 (mm) cc_final: 0.7792 (mp) REVERT: A 729 LEU cc_start: 0.6219 (tp) cc_final: 0.5956 (tp) REVERT: A 823 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7063 (ttpp) REVERT: B 355 LYS cc_start: 0.7431 (tppp) cc_final: 0.7212 (tptm) REVERT: B 365 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5401 (tm-30) REVERT: B 390 LYS cc_start: 0.8502 (tttt) cc_final: 0.8148 (tttt) REVERT: B 407 TYR cc_start: 0.8191 (p90) cc_final: 0.7941 (p90) REVERT: B 439 ASP cc_start: 0.8078 (t0) cc_final: 0.7691 (t70) REVERT: B 544 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7381 (mtmm) REVERT: B 641 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7371 (mtm110) REVERT: B 700 LYS cc_start: 0.8369 (tttt) cc_final: 0.8161 (tttt) REVERT: B 737 LYS cc_start: 0.7885 (mttt) cc_final: 0.7680 (mtmt) REVERT: B 787 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7108 (tpp80) REVERT: B 788 ILE cc_start: 0.8074 (tp) cc_final: 0.7739 (tp) REVERT: B 795 TYR cc_start: 0.7863 (t80) cc_final: 0.7651 (t80) REVERT: B 815 PHE cc_start: 0.6596 (m-80) cc_final: 0.6371 (m-80) REVERT: D 26 LYS cc_start: 0.8080 (pttp) cc_final: 0.7821 (pttp) REVERT: D 105 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7576 (tmm-80) REVERT: F 26 LYS cc_start: 0.7579 (tptp) cc_final: 0.7277 (tptp) REVERT: F 43 ASN cc_start: 0.8234 (m-40) cc_final: 0.7846 (m-40) REVERT: F 44 ASP cc_start: 0.7669 (t0) cc_final: 0.7293 (t70) REVERT: E 96 GLN cc_start: 0.8420 (tp40) cc_final: 0.7810 (tm-30) REVERT: E 159 TRP cc_start: 0.8068 (t60) cc_final: 0.7663 (t60) REVERT: C 243 LEU cc_start: 0.0535 (OUTLIER) cc_final: -0.0764 (tt) REVERT: C 307 GLN cc_start: 0.7333 (mp-120) cc_final: 0.7056 (mp10) REVERT: C 394 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5043 (m-10) REVERT: C 428 ILE cc_start: 0.4014 (OUTLIER) cc_final: 0.3759 (mp) REVERT: C 457 LEU cc_start: 0.2629 (OUTLIER) cc_final: 0.1506 (mm) REVERT: C 506 LEU cc_start: 0.8776 (mt) cc_final: 0.7521 (tt) REVERT: C 523 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7266 (t70) REVERT: C 544 LYS cc_start: 0.8197 (tptt) cc_final: 0.7790 (tptt) REVERT: C 587 GLU cc_start: 0.7607 (mp0) cc_final: 0.7359 (mp0) REVERT: C 592 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8011 (ptpp) REVERT: C 610 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7622 (mm110) REVERT: C 615 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8368 (ttt-90) REVERT: C 662 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7122 (mm) REVERT: C 754 VAL cc_start: 0.5126 (OUTLIER) cc_final: 0.4911 (t) outliers start: 138 outliers final: 87 residues processed: 536 average time/residue: 0.1562 time to fit residues: 130.9524 Evaluate side-chains 551 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 449 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL 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 742 GLN Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 798 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 154 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 191 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 202 optimal weight: 50.0000 chunk 0 optimal weight: 80.0000 chunk 199 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS A 798 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS B 710 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS E 96 GLN C 798 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.208039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158864 restraints weight = 48861.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163296 restraints weight = 23992.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.166093 restraints weight = 14876.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167855 restraints weight = 10658.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.168947 restraints weight = 8499.758| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22513 Z= 0.199 Angle : 0.673 13.473 30722 Z= 0.337 Chirality : 0.046 0.261 3524 Planarity : 0.005 0.069 3793 Dihedral : 6.148 89.362 3334 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.35 % Rotamer: Outliers : 5.92 % Allowed : 23.58 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.16), residues: 2672 helix: 1.16 (0.30), residues: 296 sheet: -0.08 (0.19), residues: 751 loop : -0.88 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 468 TYR 0.019 0.001 TYR B 422 PHE 0.025 0.001 PHE C 703 TRP 0.042 0.002 TRP A 449 HIS 0.009 0.001 HIS C 800 Details of bonding type rmsd covalent geometry : bond 0.00448 (22452) covalent geometry : angle 0.66063 (30578) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.67457 ( 78) hydrogen bonds : bond 0.05438 ( 587) hydrogen bonds : angle 5.56451 ( 1581) link_BETA1-4 : bond 0.00532 ( 1) link_BETA1-4 : angle 0.73181 ( 3) link_BETA1-6 : bond 0.01592 ( 1) link_BETA1-6 : angle 1.05514 ( 3) link_NAG-ASN : bond 0.00401 ( 20) link_NAG-ASN : angle 2.43935 ( 60) *********************** 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 603 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 454 time to evaluate : 0.917 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 246 GLU cc_start: 0.7253 (tp30) cc_final: 0.6946 (tp30) REVERT: A 270 GLN cc_start: 0.7704 (pm20) cc_final: 0.7329 (pm20) REVERT: A 339 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8168 (mttm) REVERT: A 395 ASN cc_start: 0.7662 (p0) cc_final: 0.7244 (p0) REVERT: A 434 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7475 (mt) REVERT: A 463 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6239 (tm-30) REVERT: A 469 SER cc_start: 0.7795 (m) cc_final: 0.7468 (t) REVERT: A 497 GLU cc_start: 0.6717 (tt0) cc_final: 0.6452 (tp30) REVERT: A 521 SER cc_start: 0.7931 (p) cc_final: 0.7669 (m) REVERT: A 584 LYS cc_start: 0.8717 (pptt) cc_final: 0.8443 (pttp) REVERT: A 667 LEU cc_start: 0.7954 (mm) cc_final: 0.7747 (mp) REVERT: A 669 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8744 (mmmm) REVERT: A 694 ASP cc_start: 0.6808 (t0) cc_final: 0.6482 (t0) REVERT: A 729 LEU cc_start: 0.6231 (tp) cc_final: 0.5865 (tp) REVERT: A 731 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: A 823 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7285 (ttmm) REVERT: B 355 LYS cc_start: 0.7436 (tppp) cc_final: 0.7209 (tptm) REVERT: B 365 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5393 (tm-30) REVERT: B 390 LYS cc_start: 0.8517 (tttt) cc_final: 0.8182 (tttt) REVERT: B 402 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8044 (mtt-85) REVERT: B 407 TYR cc_start: 0.8198 (p90) cc_final: 0.7947 (p90) REVERT: B 439 ASP cc_start: 0.8086 (t0) cc_final: 0.7697 (t70) REVERT: B 452 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 544 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7398 (mtmm) REVERT: B 641 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7388 (mtm110) REVERT: B 669 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8543 (mtpp) REVERT: B 737 LYS cc_start: 0.7921 (mttt) cc_final: 0.7693 (mtmt) REVERT: B 788 ILE cc_start: 0.8065 (tp) cc_final: 0.7700 (tp) REVERT: B 815 PHE cc_start: 0.6574 (m-80) cc_final: 0.6339 (m-80) REVERT: D 26 LYS cc_start: 0.8140 (pttp) cc_final: 0.7908 (pttp) REVERT: D 105 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7560 (tmm-80) REVERT: F 26 LYS cc_start: 0.7605 (tptp) cc_final: 0.7300 (tptp) REVERT: F 43 ASN cc_start: 0.8238 (m-40) cc_final: 0.7864 (m-40) REVERT: E 96 GLN cc_start: 0.8426 (tp-100) cc_final: 0.7770 (tm-30) REVERT: E 159 TRP cc_start: 0.8120 (t60) cc_final: 0.7732 (t60) REVERT: C 243 LEU cc_start: 0.0552 (OUTLIER) cc_final: -0.0744 (tt) REVERT: C 307 GLN cc_start: 0.7331 (mp-120) cc_final: 0.7053 (mp10) REVERT: C 394 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5177 (m-10) REVERT: C 457 LEU cc_start: 0.2682 (OUTLIER) cc_final: 0.1531 (mm) REVERT: C 506 LEU cc_start: 0.8760 (mt) cc_final: 0.7493 (tt) REVERT: C 523 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7289 (t70) REVERT: C 544 LYS cc_start: 0.8217 (tptt) cc_final: 0.7814 (tptt) REVERT: C 592 LYS cc_start: 0.8525 (ptpp) cc_final: 0.8179 (ptpp) REVERT: C 615 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8359 (ttt-90) REVERT: C 631 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 662 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7147 (mm) REVERT: C 754 VAL cc_start: 0.5140 (OUTLIER) cc_final: 0.4919 (t) REVERT: C 771 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7131 (tt) outliers start: 149 outliers final: 99 residues processed: 545 average time/residue: 0.1606 time to fit residues: 135.6977 Evaluate side-chains 563 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 445 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 800 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 181 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 1 optimal weight: 50.0000 chunk 130 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 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 517 HIS A 798 HIS B 351 HIS B 683 HIS E 43 ASN E 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.209013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159233 restraints weight = 48944.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.163693 restraints weight = 24281.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166487 restraints weight = 15165.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168289 restraints weight = 10939.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169368 restraints weight = 8740.601| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22513 Z= 0.193 Angle : 0.681 13.500 30722 Z= 0.339 Chirality : 0.047 0.268 3524 Planarity : 0.005 0.082 3793 Dihedral : 6.033 87.345 3332 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.43 % Favored : 94.35 % Rotamer: Outliers : 5.53 % Allowed : 24.33 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.16), residues: 2672 helix: 0.98 (0.30), residues: 307 sheet: -0.08 (0.19), residues: 763 loop : -0.89 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 468 TYR 0.019 0.001 TYR B 466 PHE 0.024 0.001 PHE B 500 TRP 0.046 0.002 TRP A 449 HIS 0.025 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00438 (22452) covalent geometry : angle 0.66843 (30578) SS BOND : bond 0.00377 ( 39) SS BOND : angle 1.74710 ( 78) hydrogen bonds : bond 0.05342 ( 587) hydrogen bonds : angle 5.54444 ( 1581) link_BETA1-4 : bond 0.00541 ( 1) link_BETA1-4 : angle 0.77139 ( 3) link_BETA1-6 : bond 0.01381 ( 1) link_BETA1-6 : angle 1.02168 ( 3) link_NAG-ASN : bond 0.00393 ( 20) link_NAG-ASN : angle 2.39272 ( 60) *********************** 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 584 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 445 time to evaluate : 0.719 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 246 GLU cc_start: 0.7275 (tp30) cc_final: 0.7004 (tp30) REVERT: A 270 GLN cc_start: 0.7685 (pm20) cc_final: 0.7313 (pm20) REVERT: A 339 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: A 395 ASN cc_start: 0.7730 (p0) cc_final: 0.7353 (p0) REVERT: A 434 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7476 (mt) REVERT: A 463 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: A 469 SER cc_start: 0.7764 (m) cc_final: 0.7444 (t) REVERT: A 497 GLU cc_start: 0.6683 (tt0) cc_final: 0.6420 (tp30) REVERT: A 521 SER cc_start: 0.7912 (p) cc_final: 0.7608 (m) REVERT: A 548 THR cc_start: 0.7514 (p) cc_final: 0.6178 (m) REVERT: A 555 LYS cc_start: 0.7890 (tppt) cc_final: 0.7667 (tppt) REVERT: A 641 ARG cc_start: 0.7418 (tpm170) cc_final: 0.7109 (tpm170) REVERT: A 667 LEU cc_start: 0.7896 (mm) cc_final: 0.7433 (mp) REVERT: A 694 ASP cc_start: 0.6849 (t0) cc_final: 0.6513 (t0) REVERT: A 729 LEU cc_start: 0.6252 (tp) cc_final: 0.5852 (tp) REVERT: A 731 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: A 823 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7148 (ttmm) REVERT: B 355 LYS cc_start: 0.7410 (tppp) cc_final: 0.7182 (tptm) REVERT: B 365 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5415 (tm-30) REVERT: B 390 LYS cc_start: 0.8532 (tttt) cc_final: 0.8198 (tttt) REVERT: B 402 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8068 (mtt-85) REVERT: B 407 TYR cc_start: 0.8209 (p90) cc_final: 0.7961 (p90) REVERT: B 439 ASP cc_start: 0.8034 (t0) cc_final: 0.7658 (t70) REVERT: B 452 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7552 (p) REVERT: B 544 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7396 (mtmm) REVERT: B 669 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8452 (mtpp) REVERT: B 737 LYS cc_start: 0.7893 (mttt) cc_final: 0.7665 (mtmt) REVERT: B 788 ILE cc_start: 0.8088 (tp) cc_final: 0.7832 (tp) REVERT: B 815 PHE cc_start: 0.6534 (m-80) cc_final: 0.6288 (m-80) REVERT: D 26 LYS cc_start: 0.8131 (pttp) cc_final: 0.7881 (pttp) REVERT: D 105 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (tmm-80) REVERT: D 149 ARG cc_start: 0.7371 (ptp-170) cc_final: 0.7116 (ptp-170) REVERT: F 26 LYS cc_start: 0.7594 (tptp) cc_final: 0.7290 (tptp) REVERT: F 43 ASN cc_start: 0.8239 (m-40) cc_final: 0.7861 (m-40) REVERT: E 96 GLN cc_start: 0.8402 (tp-100) cc_final: 0.7752 (tm-30) REVERT: E 159 TRP cc_start: 0.8122 (t60) cc_final: 0.7768 (t60) REVERT: C 243 LEU cc_start: 0.0552 (OUTLIER) cc_final: -0.0479 (tt) REVERT: C 307 GLN cc_start: 0.7342 (mp-120) cc_final: 0.7060 (mp10) REVERT: C 394 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5558 (m-80) REVERT: C 457 LEU cc_start: 0.2494 (OUTLIER) cc_final: 0.1434 (mm) REVERT: C 523 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7294 (t70) REVERT: C 544 LYS cc_start: 0.8198 (tptt) cc_final: 0.7782 (tptt) REVERT: C 587 GLU cc_start: 0.7548 (mp0) cc_final: 0.7264 (mp0) REVERT: C 592 LYS cc_start: 0.8494 (ptpp) cc_final: 0.8130 (ptpp) REVERT: C 615 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8308 (ttt-90) REVERT: C 631 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.7788 (p) REVERT: C 662 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7091 (mm) REVERT: C 754 VAL cc_start: 0.5221 (OUTLIER) cc_final: 0.4999 (t) REVERT: C 771 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7126 (tt) outliers start: 139 outliers final: 102 residues processed: 533 average time/residue: 0.1585 time to fit residues: 130.9958 Evaluate side-chains 561 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 441 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 796 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 152 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS E 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.209431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159841 restraints weight = 48948.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.164306 restraints weight = 24299.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167096 restraints weight = 15112.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168896 restraints weight = 10895.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170016 restraints weight = 8705.125| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22513 Z= 0.167 Angle : 0.689 13.982 30722 Z= 0.340 Chirality : 0.046 0.280 3524 Planarity : 0.005 0.068 3793 Dihedral : 5.917 85.414 3332 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 5.29 % Allowed : 24.89 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.59 (0.16), residues: 2672 helix: 0.91 (0.30), residues: 312 sheet: -0.00 (0.19), residues: 762 loop : -0.85 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 468 TYR 0.016 0.001 TYR B 466 PHE 0.027 0.001 PHE C 703 TRP 0.051 0.002 TRP A 449 HIS 0.025 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00382 (22452) covalent geometry : angle 0.67570 (30578) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.87119 ( 78) hydrogen bonds : bond 0.05039 ( 587) hydrogen bonds : angle 5.45157 ( 1581) link_BETA1-4 : bond 0.00553 ( 1) link_BETA1-4 : angle 0.77431 ( 3) link_BETA1-6 : bond 0.01400 ( 1) link_BETA1-6 : angle 0.98818 ( 3) link_NAG-ASN : bond 0.00411 ( 20) link_NAG-ASN : angle 2.32771 ( 60) *********************** 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 578 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 445 time to evaluate : 0.686 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 246 GLU cc_start: 0.7247 (tp30) cc_final: 0.6986 (tp30) REVERT: A 270 GLN cc_start: 0.7595 (pm20) cc_final: 0.7309 (pm20) REVERT: A 335 TYR cc_start: 0.7834 (m-10) cc_final: 0.7438 (m-10) REVERT: A 395 ASN cc_start: 0.7781 (p0) cc_final: 0.7405 (p0) REVERT: A 434 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7471 (mt) REVERT: A 463 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6260 (tm-30) REVERT: A 469 SER cc_start: 0.7756 (m) cc_final: 0.7431 (t) REVERT: A 497 GLU cc_start: 0.6706 (tt0) cc_final: 0.6453 (tp30) REVERT: A 521 SER cc_start: 0.7896 (p) cc_final: 0.7585 (m) REVERT: A 548 THR cc_start: 0.7515 (p) cc_final: 0.6076 (m) REVERT: A 641 ARG cc_start: 0.7404 (tpm170) cc_final: 0.7188 (tpm170) REVERT: A 669 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8913 (mmmt) REVERT: A 694 ASP cc_start: 0.6748 (t0) cc_final: 0.6348 (t0) REVERT: A 729 LEU cc_start: 0.6204 (tp) cc_final: 0.5805 (tp) REVERT: A 731 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6177 (m-80) REVERT: A 823 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7158 (ttmm) REVERT: B 365 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5387 (tm-30) REVERT: B 390 LYS cc_start: 0.8511 (tttt) cc_final: 0.8169 (tttt) REVERT: B 402 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8034 (mtt-85) REVERT: B 407 TYR cc_start: 0.8217 (p90) cc_final: 0.7997 (p90) REVERT: B 439 ASP cc_start: 0.8030 (t0) cc_final: 0.7651 (t70) REVERT: B 544 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7359 (mtmm) REVERT: B 669 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8462 (mtmm) REVERT: B 700 LYS cc_start: 0.8443 (pttt) cc_final: 0.8231 (pttt) REVERT: B 737 LYS cc_start: 0.7877 (mttt) cc_final: 0.7641 (mtmt) REVERT: B 788 ILE cc_start: 0.8034 (tp) cc_final: 0.7770 (tp) REVERT: D 26 LYS cc_start: 0.8141 (pttp) cc_final: 0.7887 (pttp) REVERT: D 105 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7569 (tmm-80) REVERT: D 149 ARG cc_start: 0.7343 (ptp-170) cc_final: 0.7088 (ptp-170) REVERT: F 26 LYS cc_start: 0.7565 (tptp) cc_final: 0.7254 (tptp) REVERT: F 43 ASN cc_start: 0.8228 (m-40) cc_final: 0.7994 (m-40) REVERT: E 75 MET cc_start: 0.7610 (tmm) cc_final: 0.7334 (tmm) REVERT: E 96 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7739 (tm-30) REVERT: E 159 TRP cc_start: 0.8122 (t60) cc_final: 0.7763 (t60) REVERT: C 243 LEU cc_start: 0.0512 (OUTLIER) cc_final: -0.0835 (tt) REVERT: C 307 GLN cc_start: 0.7345 (mp-120) cc_final: 0.7071 (mp10) REVERT: C 394 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5623 (m-80) REVERT: C 457 LEU cc_start: 0.2514 (OUTLIER) cc_final: 0.1438 (mm) REVERT: C 472 TYR cc_start: 0.7042 (m-80) cc_final: 0.6795 (m-80) REVERT: C 523 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7288 (t70) REVERT: C 544 LYS cc_start: 0.8229 (tptt) cc_final: 0.7810 (tptt) REVERT: C 587 GLU cc_start: 0.7524 (mp0) cc_final: 0.7304 (mp0) REVERT: C 592 LYS cc_start: 0.8467 (ptpp) cc_final: 0.8188 (ptpp) REVERT: C 615 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8277 (ttt-90) REVERT: C 641 ARG cc_start: 0.7111 (tpm170) cc_final: 0.6114 (tpp-160) REVERT: C 662 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7068 (mm) REVERT: C 754 VAL cc_start: 0.5370 (OUTLIER) cc_final: 0.5147 (t) REVERT: C 771 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7104 (tt) outliers start: 133 outliers final: 97 residues processed: 526 average time/residue: 0.1559 time to fit residues: 127.2693 Evaluate side-chains 556 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 444 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 796 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 94 optimal weight: 3.9990 chunk 123 optimal weight: 0.1980 chunk 180 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 73 optimal weight: 0.0060 chunk 139 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 150 optimal weight: 0.3980 chunk 222 optimal weight: 7.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 798 HIS B 351 HIS B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.210291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160850 restraints weight = 49327.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165303 restraints weight = 24350.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168117 restraints weight = 15164.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.169876 restraints weight = 10915.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.171060 restraints weight = 8717.171| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22513 Z= 0.134 Angle : 0.694 14.489 30722 Z= 0.341 Chirality : 0.046 0.274 3524 Planarity : 0.004 0.068 3793 Dihedral : 5.718 83.543 3332 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 4.21 % Allowed : 25.96 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.52 (0.16), residues: 2672 helix: 1.07 (0.31), residues: 306 sheet: 0.05 (0.19), residues: 759 loop : -0.82 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 678 TYR 0.013 0.001 TYR B 807 PHE 0.021 0.001 PHE A 801 TRP 0.055 0.002 TRP A 449 HIS 0.005 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00312 (22452) covalent geometry : angle 0.68241 (30578) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.85459 ( 78) hydrogen bonds : bond 0.04629 ( 587) hydrogen bonds : angle 5.34142 ( 1581) link_BETA1-4 : bond 0.00491 ( 1) link_BETA1-4 : angle 0.72063 ( 3) link_BETA1-6 : bond 0.01314 ( 1) link_BETA1-6 : angle 0.88473 ( 3) link_NAG-ASN : bond 0.00402 ( 20) link_NAG-ASN : angle 2.25099 ( 60) *********************** 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 551 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 445 time to evaluate : 0.815 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 246 GLU cc_start: 0.7248 (tp30) cc_final: 0.7019 (tp30) REVERT: A 270 GLN cc_start: 0.7608 (pm20) cc_final: 0.7327 (pm20) REVERT: A 335 TYR cc_start: 0.7752 (m-10) cc_final: 0.7153 (m-10) REVERT: A 395 ASN cc_start: 0.7766 (p0) cc_final: 0.7372 (p0) REVERT: A 424 GLU cc_start: 0.8027 (pt0) cc_final: 0.7732 (pt0) REVERT: A 434 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7417 (mt) REVERT: A 463 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6247 (tm-30) REVERT: A 469 SER cc_start: 0.7772 (m) cc_final: 0.7476 (t) REVERT: A 497 GLU cc_start: 0.6710 (tt0) cc_final: 0.6431 (tp30) REVERT: A 521 SER cc_start: 0.7855 (p) cc_final: 0.7529 (m) REVERT: A 548 THR cc_start: 0.7526 (p) cc_final: 0.6032 (m) REVERT: A 669 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8879 (mmmt) REVERT: A 729 LEU cc_start: 0.6094 (tp) cc_final: 0.5687 (tp) REVERT: A 731 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: A 771 ILE cc_start: 0.8715 (mm) cc_final: 0.8491 (mm) REVERT: A 787 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8062 (ttp80) REVERT: A 823 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7133 (ttmm) REVERT: B 365 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5352 (tm-30) REVERT: B 390 LYS cc_start: 0.8453 (tttt) cc_final: 0.8094 (tttt) REVERT: B 402 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7889 (mtt-85) REVERT: B 407 TYR cc_start: 0.8212 (p90) cc_final: 0.7992 (p90) REVERT: B 439 ASP cc_start: 0.8051 (t0) cc_final: 0.7657 (t70) REVERT: B 452 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7528 (p) REVERT: B 497 GLU cc_start: 0.7906 (tt0) cc_final: 0.7661 (tt0) REVERT: B 544 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7338 (mtmm) REVERT: B 669 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8311 (mtmm) REVERT: B 682 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6651 (t0) REVERT: B 700 LYS cc_start: 0.8414 (pttt) cc_final: 0.8185 (pttt) REVERT: B 737 LYS cc_start: 0.7838 (mttt) cc_final: 0.7596 (mtmt) REVERT: B 788 ILE cc_start: 0.8000 (tp) cc_final: 0.7714 (tp) REVERT: D 26 LYS cc_start: 0.8171 (pttp) cc_final: 0.7923 (pttp) REVERT: D 105 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7527 (tmm-80) REVERT: D 149 ARG cc_start: 0.7311 (ptp-170) cc_final: 0.7037 (ptp-170) REVERT: F 26 LYS cc_start: 0.7506 (tptp) cc_final: 0.7182 (tptp) REVERT: F 43 ASN cc_start: 0.8196 (m-40) cc_final: 0.7940 (m-40) REVERT: F 156 ASP cc_start: 0.7576 (m-30) cc_final: 0.7337 (m-30) REVERT: E 96 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7687 (tm-30) REVERT: E 159 TRP cc_start: 0.8107 (t60) cc_final: 0.7752 (t60) REVERT: C 243 LEU cc_start: 0.0415 (OUTLIER) cc_final: -0.0622 (tt) REVERT: C 307 GLN cc_start: 0.7313 (mp-120) cc_final: 0.7037 (mp10) REVERT: C 394 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: C 457 LEU cc_start: 0.2358 (OUTLIER) cc_final: 0.1291 (mm) REVERT: C 472 TYR cc_start: 0.6996 (m-80) cc_final: 0.6745 (m-80) REVERT: C 544 LYS cc_start: 0.8217 (tptt) cc_final: 0.7804 (tptt) REVERT: C 615 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8255 (ttt-90) REVERT: C 662 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7096 (mm) REVERT: C 771 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7012 (tt) outliers start: 106 outliers final: 78 residues processed: 511 average time/residue: 0.1477 time to fit residues: 116.9523 Evaluate side-chains 533 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 440 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 796 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 119 optimal weight: 0.3980 chunk 78 optimal weight: 50.0000 chunk 145 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 224 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 245 optimal weight: 0.4980 chunk 160 optimal weight: 0.0470 chunk 230 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS A 798 HIS B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.212564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163144 restraints weight = 49422.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.167674 restraints weight = 24447.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170473 restraints weight = 15139.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172224 restraints weight = 10889.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.173347 restraints weight = 8726.560| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22513 Z= 0.135 Angle : 0.701 14.459 30722 Z= 0.343 Chirality : 0.046 0.280 3524 Planarity : 0.005 0.068 3793 Dihedral : 5.620 81.529 3332 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 4.10 % Allowed : 26.04 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.52 (0.16), residues: 2672 helix: 1.06 (0.31), residues: 306 sheet: 0.09 (0.19), residues: 749 loop : -0.83 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 641 TYR 0.014 0.001 TYR B 807 PHE 0.028 0.001 PHE C 703 TRP 0.061 0.002 TRP A 449 HIS 0.012 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00313 (22452) covalent geometry : angle 0.68948 (30578) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.88914 ( 78) hydrogen bonds : bond 0.04520 ( 587) hydrogen bonds : angle 5.30645 ( 1581) link_BETA1-4 : bond 0.00554 ( 1) link_BETA1-4 : angle 0.75691 ( 3) link_BETA1-6 : bond 0.01411 ( 1) link_BETA1-6 : angle 0.93865 ( 3) link_NAG-ASN : bond 0.00424 ( 20) link_NAG-ASN : angle 2.23020 ( 60) ********************** 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 541 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 438 time to evaluate : 0.853 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 246 GLU cc_start: 0.7274 (tp30) cc_final: 0.7013 (tp30) REVERT: A 270 GLN cc_start: 0.7610 (pm20) cc_final: 0.7322 (pm20) REVERT: A 335 TYR cc_start: 0.7741 (m-10) cc_final: 0.7129 (m-10) REVERT: A 339 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8218 (mmtp) REVERT: A 395 ASN cc_start: 0.7762 (p0) cc_final: 0.7367 (p0) REVERT: A 424 GLU cc_start: 0.8022 (pt0) cc_final: 0.7798 (pt0) REVERT: A 434 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7404 (mt) REVERT: A 463 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: A 469 SER cc_start: 0.7852 (m) cc_final: 0.7484 (t) REVERT: A 497 GLU cc_start: 0.6712 (tt0) cc_final: 0.6449 (tp30) REVERT: A 521 SER cc_start: 0.7827 (p) cc_final: 0.7512 (m) REVERT: A 548 THR cc_start: 0.7481 (p) cc_final: 0.5970 (m) REVERT: A 669 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8854 (mmmt) REVERT: A 729 LEU cc_start: 0.6070 (tp) cc_final: 0.5659 (tp) REVERT: A 731 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: A 771 ILE cc_start: 0.8702 (mm) cc_final: 0.8468 (mm) REVERT: A 787 ARG cc_start: 0.8263 (ttp80) cc_final: 0.8023 (ttp80) REVERT: A 823 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7145 (ttmm) REVERT: B 365 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5350 (tm-30) REVERT: B 390 LYS cc_start: 0.8445 (tttt) cc_final: 0.8081 (tttt) REVERT: B 402 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: B 407 TYR cc_start: 0.8195 (p90) cc_final: 0.7967 (p90) REVERT: B 439 ASP cc_start: 0.8061 (t0) cc_final: 0.7679 (t70) REVERT: B 452 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 497 GLU cc_start: 0.7901 (tt0) cc_final: 0.7667 (tt0) REVERT: B 544 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7339 (mtmm) REVERT: B 558 TRP cc_start: 0.8485 (p90) cc_final: 0.8032 (p90) REVERT: B 668 MET cc_start: 0.7297 (tpt) cc_final: 0.7058 (tpt) REVERT: B 682 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6659 (t0) REVERT: B 700 LYS cc_start: 0.8434 (pttt) cc_final: 0.8219 (pttt) REVERT: B 737 LYS cc_start: 0.7815 (mttt) cc_final: 0.7567 (mtmt) REVERT: B 788 ILE cc_start: 0.8046 (tp) cc_final: 0.7746 (tp) REVERT: B 801 PHE cc_start: 0.7061 (m-80) cc_final: 0.6004 (m-80) REVERT: D 26 LYS cc_start: 0.8263 (pttp) cc_final: 0.8034 (pttp) REVERT: D 105 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7509 (tmm-80) REVERT: D 149 ARG cc_start: 0.7390 (ptp-170) cc_final: 0.7079 (ptp-170) REVERT: F 26 LYS cc_start: 0.7465 (tptp) cc_final: 0.7156 (tptp) REVERT: F 43 ASN cc_start: 0.8191 (m-40) cc_final: 0.7937 (m-40) REVERT: F 156 ASP cc_start: 0.7594 (m-30) cc_final: 0.7347 (m-30) REVERT: E 96 GLN cc_start: 0.8347 (tp-100) cc_final: 0.7653 (tm-30) REVERT: E 159 TRP cc_start: 0.8091 (t60) cc_final: 0.7745 (t60) REVERT: C 243 LEU cc_start: 0.0405 (OUTLIER) cc_final: -0.0899 (tt) REVERT: C 307 GLN cc_start: 0.7321 (mp-120) cc_final: 0.7048 (mp10) REVERT: C 394 PHE cc_start: 0.6321 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: C 457 LEU cc_start: 0.2340 (OUTLIER) cc_final: 0.1289 (mm) REVERT: C 472 TYR cc_start: 0.7012 (m-80) cc_final: 0.6762 (m-80) REVERT: C 544 LYS cc_start: 0.8210 (tptt) cc_final: 0.7802 (tptt) REVERT: C 615 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (ttt-90) REVERT: C 662 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.6986 (mm) REVERT: C 754 VAL cc_start: 0.5057 (OUTLIER) cc_final: 0.4753 (t) REVERT: C 771 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7059 (tt) outliers start: 103 outliers final: 80 residues processed: 506 average time/residue: 0.1446 time to fit residues: 114.1854 Evaluate side-chains 529 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 432 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 796 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 100 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 147 optimal weight: 0.0970 chunk 243 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS B 710 HIS F 47 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 47 HIS ** C 566 ASN ** 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 = 0.4562 r_free = 0.4562 target = 0.210183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160472 restraints weight = 49102.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164938 restraints weight = 24323.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167750 restraints weight = 15137.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169490 restraints weight = 10881.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170616 restraints weight = 8735.917| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 22513 Z= 0.216 Angle : 0.744 14.775 30722 Z= 0.367 Chirality : 0.047 0.324 3524 Planarity : 0.005 0.069 3793 Dihedral : 5.765 79.470 3332 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.82 % Rotamer: Outliers : 4.29 % Allowed : 26.04 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.66 (0.16), residues: 2672 helix: 0.88 (0.30), residues: 306 sheet: -0.04 (0.19), residues: 750 loop : -0.89 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 678 TYR 0.021 0.001 TYR B 422 PHE 0.027 0.001 PHE B 500 TRP 0.065 0.002 TRP A 449 HIS 0.029 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00489 (22452) covalent geometry : angle 0.73129 (30578) SS BOND : bond 0.00580 ( 39) SS BOND : angle 2.03688 ( 78) hydrogen bonds : bond 0.05397 ( 587) hydrogen bonds : angle 5.47652 ( 1581) link_BETA1-4 : bond 0.00569 ( 1) link_BETA1-4 : angle 0.76336 ( 3) link_BETA1-6 : bond 0.01376 ( 1) link_BETA1-6 : angle 1.07128 ( 3) link_NAG-ASN : bond 0.00415 ( 20) link_NAG-ASN : angle 2.33159 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.76 seconds wall clock time: 104 minutes 25.06 seconds (6265.06 seconds total)