Starting phenix.real_space_refine on Wed May 21 21:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x81_38132/05_2025/8x81_38132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x81_38132/05_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_38132/05_2025/8x81_38132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x81_38132/05_2025/8x81_38132.map" model { file = "/net/cci-nas-00/data/ceres_data/8x81_38132/05_2025/8x81_38132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x81_38132/05_2025/8x81_38132.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.88, per 1000 atoms: 0.68 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: 6.05 Conformation dependent library (CDL) restraints added in 2.8 seconds 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5172 Finding SS restraints... Secondary structure from input PDB file: 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: 3.29 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: 8.04 Time building geometry restraints manager: 6.84 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 829 or resid 901 through 905)) selection = (chain 'C' and (resid 23 through 829 or resid 901 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: 13.950 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: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 51.720 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.960 ------------------------------------------------------------------------------- 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 : 9.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), 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 TRP 0.042 0.001 TRP C 625 HIS 0.012 0.001 HIS A 467 PHE 0.029 0.001 PHE C 703 TYR 0.032 0.001 TYR B 769 ARG 0.010 0.000 ARG B 573 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 20) link_NAG-ASN : angle 2.94543 ( 60) link_BETA1-4 : bond 0.00502 ( 1) link_BETA1-4 : angle 0.83709 ( 3) hydrogen bonds : bond 0.16568 ( 587) hydrogen bonds : angle 6.98667 ( 1581) link_BETA1-6 : bond 0.00687 ( 1) link_BETA1-6 : angle 1.28231 ( 3) SS BOND : bond 0.00185 ( 39) SS BOND : angle 1.52230 ( 78) covalent geometry : bond 0.00369 (22452) covalent geometry : angle 0.72308 (30578) *********************** 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 : 2.346 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: 0.3349 time to fit residues: 216.3285 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 : 2.421 ------------------------------------------------------------------------------- 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 224 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 208 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 126 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS C 798 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.214787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166520 restraints weight = 50049.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171049 restraints weight = 24880.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.173845 restraints weight = 15534.932| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22513 Z= 0.218 Angle : 0.687 10.968 30722 Z= 0.344 Chirality : 0.047 0.288 3524 Planarity : 0.005 0.075 3793 Dihedral : 7.390 96.156 3353 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 3.62 % Allowed : 21.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2672 helix: 1.10 (0.30), residues: 303 sheet: 0.51 (0.19), residues: 745 loop : -0.66 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 512 HIS 0.010 0.001 HIS B 467 PHE 0.032 0.002 PHE B 500 TYR 0.026 0.002 TYR A 335 ARG 0.012 0.001 ARG B 573 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 20) link_NAG-ASN : angle 2.90030 ( 60) link_BETA1-4 : bond 0.00127 ( 1) link_BETA1-4 : angle 0.29926 ( 3) hydrogen bonds : bond 0.05661 ( 587) hydrogen bonds : angle 5.49322 ( 1581) link_BETA1-6 : bond 0.01461 ( 1) link_BETA1-6 : angle 3.10031 ( 3) SS BOND : bond 0.00444 ( 39) SS BOND : angle 1.59846 ( 78) covalent geometry : bond 0.00481 (22452) covalent geometry : angle 0.67107 (30578) *********************** 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 547 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 456 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.7600 (pm20) cc_final: 0.7229 (pm20) REVERT: A 422 TYR cc_start: 0.8459 (p90) cc_final: 0.7500 (p90) REVERT: A 449 TRP cc_start: 0.7853 (p-90) cc_final: 0.7531 (p-90) REVERT: A 506 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7270 (tp) REVERT: A 694 ASP cc_start: 0.6645 (t0) cc_final: 0.6428 (t0) REVERT: A 707 GLU cc_start: 0.7593 (pp20) cc_final: 0.7285 (pp20) REVERT: B 439 ASP cc_start: 0.8069 (t0) cc_final: 0.7740 (t0) REVERT: B 444 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8201 (ptpp) REVERT: B 544 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7452 (mtmm) REVERT: B 550 ASN cc_start: 0.7854 (t0) cc_final: 0.7430 (t0) REVERT: B 558 TRP cc_start: 0.8617 (p90) cc_final: 0.7879 (p90) REVERT: B 559 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 573 ARG cc_start: 0.7460 (ptt90) cc_final: 0.6589 (ptm-80) REVERT: B 787 ARG cc_start: 0.7415 (ttt180) cc_final: 0.7193 (tpp80) REVERT: B 788 ILE cc_start: 0.7966 (tp) cc_final: 0.7752 (tp) REVERT: F 26 LYS cc_start: 0.7558 (tptp) cc_final: 0.7262 (tptp) REVERT: F 43 ASN cc_start: 0.8219 (m-40) cc_final: 0.7802 (m-40) REVERT: F 89 MET cc_start: 0.7790 (mtt) cc_final: 0.7522 (mtt) REVERT: E 74 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7215 (ttmt) REVERT: E 83 GLN cc_start: 0.8175 (tp40) cc_final: 0.7966 (tp-100) REVERT: E 89 MET cc_start: 0.8152 (mpp) cc_final: 0.7499 (mtm) REVERT: E 159 TRP cc_start: 0.7727 (t60) cc_final: 0.7248 (t60) REVERT: E 160 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7784 (mm-40) REVERT: C 307 GLN cc_start: 0.7273 (mp-120) cc_final: 0.6981 (mp10) REVERT: C 387 HIS cc_start: 0.8973 (m-70) cc_final: 0.8752 (m-70) REVERT: C 457 LEU cc_start: 0.2662 (OUTLIER) cc_final: 0.1782 (mm) REVERT: C 544 LYS cc_start: 0.8187 (tptt) cc_final: 0.7824 (tptt) REVERT: C 615 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8049 (mtp85) REVERT: C 625 TRP cc_start: 0.7343 (m100) cc_final: 0.7088 (m100) REVERT: C 662 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7125 (mm) outliers start: 91 outliers final: 53 residues processed: 505 average time/residue: 0.3252 time to fit residues: 253.5861 Evaluate side-chains 495 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 439 time to evaluate : 2.424 ------------------------------------------------------------------------------- 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 329 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 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 457 LEU 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 170 optimal weight: 0.8980 chunk 247 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 190 optimal weight: 80.0000 chunk 196 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 395 ASN B 358 ASN B 610 GLN B 683 HIS B 710 HIS E 96 GLN C 798 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.217153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.168451 restraints weight = 49490.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.173011 restraints weight = 25098.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175872 restraints weight = 15756.971| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22513 Z= 0.140 Angle : 0.604 10.831 30722 Z= 0.301 Chirality : 0.045 0.221 3524 Planarity : 0.004 0.062 3793 Dihedral : 6.355 95.376 3338 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.73 % Rotamer: Outliers : 3.58 % Allowed : 22.78 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2672 helix: 1.50 (0.31), residues: 303 sheet: 0.52 (0.19), residues: 753 loop : -0.63 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 369 HIS 0.007 0.001 HIS C 798 PHE 0.017 0.001 PHE B 500 TYR 0.015 0.001 TYR B 422 ARG 0.006 0.001 ARG A 787 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 20) link_NAG-ASN : angle 2.33704 ( 60) link_BETA1-4 : bond 0.00698 ( 1) link_BETA1-4 : angle 0.46627 ( 3) hydrogen bonds : bond 0.04707 ( 587) hydrogen bonds : angle 5.19764 ( 1581) link_BETA1-6 : bond 0.01929 ( 1) link_BETA1-6 : angle 2.80305 ( 3) SS BOND : bond 0.00261 ( 39) SS BOND : angle 1.46873 ( 78) covalent geometry : bond 0.00317 (22452) covalent geometry : angle 0.59101 (30578) *********************** 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 533 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 443 time to evaluate : 2.569 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 254 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7737 (mmtt) REVERT: A 422 TYR cc_start: 0.8466 (p90) cc_final: 0.8151 (p90) REVERT: A 424 GLU cc_start: 0.7967 (pt0) cc_final: 0.7745 (pt0) REVERT: A 449 TRP cc_start: 0.7821 (p-90) cc_final: 0.7380 (p-90) REVERT: A 463 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: A 469 SER cc_start: 0.7777 (m) cc_final: 0.7259 (p) REVERT: A 787 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8167 (ttp80) REVERT: A 823 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7298 (tttp) REVERT: B 272 LYS cc_start: 0.7723 (mptt) cc_final: 0.7387 (mmtt) REVERT: B 375 LYS cc_start: 0.7356 (tptm) cc_final: 0.7100 (tptm) REVERT: B 407 TYR cc_start: 0.8097 (p90) cc_final: 0.7852 (p90) REVERT: B 439 ASP cc_start: 0.8051 (t0) cc_final: 0.7700 (t0) REVERT: B 444 LYS cc_start: 0.8452 (ptpt) cc_final: 0.8225 (ptpp) REVERT: B 448 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6632 (mtp85) REVERT: B 544 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7343 (mtmm) REVERT: B 550 ASN cc_start: 0.7862 (t0) cc_final: 0.7415 (t0) REVERT: B 788 ILE cc_start: 0.8029 (tp) cc_final: 0.7723 (tp) REVERT: B 795 TYR cc_start: 0.7157 (t80) cc_final: 0.6930 (t80) REVERT: D 89 MET cc_start: 0.7489 (tpp) cc_final: 0.7256 (tpp) REVERT: F 26 LYS cc_start: 0.7454 (tptp) cc_final: 0.7155 (tptp) REVERT: F 43 ASN cc_start: 0.8181 (m-40) cc_final: 0.7742 (m-40) REVERT: F 47 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7252 (m170) REVERT: F 89 MET cc_start: 0.7769 (mtt) cc_final: 0.7522 (mtt) REVERT: E 89 MET cc_start: 0.8300 (mpp) cc_final: 0.7906 (mtm) REVERT: E 159 TRP cc_start: 0.7711 (t60) cc_final: 0.7337 (t60) REVERT: E 160 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7814 (mm-40) REVERT: C 307 GLN cc_start: 0.7392 (mp-120) cc_final: 0.7079 (mp10) REVERT: C 387 HIS cc_start: 0.8932 (m-70) cc_final: 0.8711 (m-70) REVERT: C 544 LYS cc_start: 0.8230 (tptt) cc_final: 0.7954 (tptt) REVERT: C 584 LYS cc_start: 0.8813 (tptm) cc_final: 0.8547 (tppt) REVERT: C 615 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.8042 (mtp85) REVERT: C 625 TRP cc_start: 0.7409 (m100) cc_final: 0.7146 (m100) REVERT: C 662 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7050 (mm) REVERT: C 826 ASN cc_start: 0.7642 (m-40) cc_final: 0.7440 (m-40) outliers start: 90 outliers final: 63 residues processed: 495 average time/residue: 0.3226 time to fit residues: 245.8504 Evaluate side-chains 497 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 429 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 505 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 588 VAL Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 674 CYS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR 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 324 THR Chi-restraints excluded: chain B residue 359 LYS 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 383 VAL Chi-restraints excluded: chain B residue 400 LYS 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 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 154 LEU 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 114 SER 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 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 529 VAL 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 631 THR Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 798 HIS Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 85 optimal weight: 50.0000 chunk 184 optimal weight: 0.6980 chunk 254 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 108 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS F 47 HIS F 155 GLN E 55 GLN C 798 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.211501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162542 restraints weight = 49464.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167032 restraints weight = 24540.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169850 restraints weight = 15215.429| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22513 Z= 0.208 Angle : 0.646 10.820 30722 Z= 0.325 Chirality : 0.046 0.499 3524 Planarity : 0.005 0.064 3793 Dihedral : 6.112 91.783 3336 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 4.61 % Allowed : 22.35 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2672 helix: 1.38 (0.30), residues: 301 sheet: 0.35 (0.19), residues: 754 loop : -0.64 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 368 HIS 0.015 0.001 HIS B 710 PHE 0.027 0.001 PHE B 500 TYR 0.021 0.001 TYR B 422 ARG 0.007 0.001 ARG E 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 20) link_NAG-ASN : angle 2.48314 ( 60) link_BETA1-4 : bond 0.00623 ( 1) link_BETA1-4 : angle 0.69436 ( 3) hydrogen bonds : bond 0.05289 ( 587) hydrogen bonds : angle 5.25791 ( 1581) link_BETA1-6 : bond 0.01625 ( 1) link_BETA1-6 : angle 0.73249 ( 3) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.57848 ( 78) covalent geometry : bond 0.00465 (22452) covalent geometry : angle 0.63301 (30578) *********************** 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 557 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 441 time to evaluate : 2.159 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 254 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7754 (mmtt) REVERT: A 374 GLU cc_start: 0.6679 (mp0) cc_final: 0.6212 (mp0) REVERT: A 434 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7301 (mt) REVERT: A 449 TRP cc_start: 0.7844 (p-90) cc_final: 0.7582 (p-90) REVERT: A 469 SER cc_start: 0.7754 (m) cc_final: 0.7391 (t) REVERT: A 506 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7496 (tp) REVERT: A 521 SER cc_start: 0.7988 (p) cc_final: 0.7687 (m) REVERT: A 584 LYS cc_start: 0.8792 (pptt) cc_final: 0.8416 (pttp) REVERT: A 587 GLU cc_start: 0.7476 (mp0) cc_final: 0.7176 (mp0) REVERT: A 707 GLU cc_start: 0.7477 (pp20) cc_final: 0.7029 (pp20) REVERT: A 731 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: A 769 TYR cc_start: 0.7251 (p90) cc_final: 0.6987 (p90) REVERT: A 823 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7266 (tttm) REVERT: B 375 LYS cc_start: 0.7535 (tptm) cc_final: 0.7244 (tptm) REVERT: B 407 TYR cc_start: 0.8136 (p90) cc_final: 0.7836 (p90) REVERT: B 448 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6841 (mtp85) REVERT: B 544 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7393 (mtmm) REVERT: B 550 ASN cc_start: 0.7900 (t0) cc_final: 0.7474 (t0) REVERT: B 787 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7089 (tpp80) REVERT: B 788 ILE cc_start: 0.8073 (tp) cc_final: 0.7765 (tp) REVERT: D 26 LYS cc_start: 0.8024 (pttp) cc_final: 0.7813 (pttp) REVERT: D 89 MET cc_start: 0.7545 (tpp) cc_final: 0.7319 (tpp) REVERT: D 149 ARG cc_start: 0.7119 (ptp-170) cc_final: 0.6861 (ptp-170) REVERT: F 26 LYS cc_start: 0.7579 (tptp) cc_final: 0.7218 (tptp) REVERT: F 43 ASN cc_start: 0.8261 (m-40) cc_final: 0.7777 (m-40) REVERT: F 47 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7113 (m170) REVERT: F 89 MET cc_start: 0.8025 (mtt) cc_final: 0.7716 (mtt) REVERT: E 89 MET cc_start: 0.8412 (mpp) cc_final: 0.8083 (mtm) REVERT: E 159 TRP cc_start: 0.7857 (t60) cc_final: 0.7379 (t60) REVERT: E 160 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7747 (mm-40) REVERT: C 307 GLN cc_start: 0.7178 (mp-120) cc_final: 0.6895 (mp10) REVERT: C 428 ILE cc_start: 0.4037 (OUTLIER) cc_final: 0.3783 (mp) REVERT: C 457 LEU cc_start: 0.2587 (OUTLIER) cc_final: 0.1514 (mm) REVERT: C 544 LYS cc_start: 0.8191 (tptt) cc_final: 0.7804 (tptt) REVERT: C 615 ARG cc_start: 0.8437 (ttt-90) cc_final: 0.7905 (ttt90) REVERT: C 662 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7010 (mm) outliers start: 116 outliers final: 80 residues processed: 515 average time/residue: 0.3217 time to fit residues: 254.6798 Evaluate side-chains 521 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 431 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 434 ILE 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 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 CYS 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 699 THR Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE 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 298 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 400 LYS 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 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 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 649 ILE Chi-restraints excluded: chain B residue 660 VAL 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 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 MET 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 114 SER 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 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 522 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 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 800 HIS Chi-restraints excluded: chain C residue 809 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 20 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 105 optimal weight: 0.5980 chunk 245 optimal weight: 0.7980 chunk 172 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 683 HIS F 155 GLN E 55 GLN E 96 GLN C 268 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 = 0.4602 r_free = 0.4602 target = 0.213075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164145 restraints weight = 49743.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170438 restraints weight = 26275.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.171466 restraints weight = 13951.927| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2304 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= 0.141 Angle : 0.619 10.722 30722 Z= 0.309 Chirality : 0.046 0.516 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.942 89.968 3336 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 4.17 % Allowed : 22.90 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2672 helix: 1.56 (0.30), residues: 302 sheet: 0.31 (0.19), residues: 762 loop : -0.61 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 368 HIS 0.006 0.001 HIS B 467 PHE 0.017 0.001 PHE B 500 TYR 0.014 0.001 TYR B 466 ARG 0.006 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 20) link_NAG-ASN : angle 2.36890 ( 60) link_BETA1-4 : bond 0.00641 ( 1) link_BETA1-4 : angle 0.61978 ( 3) hydrogen bonds : bond 0.04630 ( 587) hydrogen bonds : angle 5.08535 ( 1581) link_BETA1-6 : bond 0.01423 ( 1) link_BETA1-6 : angle 1.10249 ( 3) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.59729 ( 78) covalent geometry : bond 0.00321 (22452) covalent geometry : angle 0.60632 (30578) *********************** 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 544 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 439 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7104 (tp30) cc_final: 0.6844 (tp30) REVERT: A 449 TRP cc_start: 0.7798 (p-90) cc_final: 0.7482 (p-90) REVERT: A 463 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: A 469 SER cc_start: 0.7819 (m) cc_final: 0.7435 (t) REVERT: A 521 SER cc_start: 0.7948 (p) cc_final: 0.7593 (m) REVERT: A 584 LYS cc_start: 0.8677 (pptt) cc_final: 0.8227 (pttp) REVERT: A 707 GLU cc_start: 0.7475 (pp20) cc_final: 0.7073 (pp20) REVERT: A 787 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7933 (ttp80) REVERT: A 823 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7385 (tttm) REVERT: B 375 LYS cc_start: 0.7492 (tptm) cc_final: 0.7189 (tptm) REVERT: B 407 TYR cc_start: 0.8108 (p90) cc_final: 0.7855 (p90) REVERT: B 544 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7376 (mtmm) REVERT: B 550 ASN cc_start: 0.7885 (t0) cc_final: 0.7455 (t0) REVERT: B 558 TRP cc_start: 0.8525 (p90) cc_final: 0.7956 (p90) REVERT: B 700 LYS cc_start: 0.8283 (tttt) cc_final: 0.8077 (tttt) REVERT: B 787 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7104 (tpp80) REVERT: B 788 ILE cc_start: 0.8046 (tp) cc_final: 0.7751 (tp) REVERT: D 26 LYS cc_start: 0.8019 (pttp) cc_final: 0.7780 (pttp) REVERT: D 89 MET cc_start: 0.7505 (tpp) cc_final: 0.7254 (tpp) REVERT: D 149 ARG cc_start: 0.7265 (ptp-170) cc_final: 0.6897 (ptp-170) REVERT: F 26 LYS cc_start: 0.7509 (tptp) cc_final: 0.7203 (tptp) REVERT: F 43 ASN cc_start: 0.8231 (m-40) cc_final: 0.7846 (m-40) REVERT: F 75 MET cc_start: 0.8120 (ttt) cc_final: 0.7143 (ttt) REVERT: F 89 MET cc_start: 0.7957 (mtt) cc_final: 0.7673 (mtt) REVERT: E 89 MET cc_start: 0.8387 (mpp) cc_final: 0.8076 (mtm) REVERT: E 131 LEU cc_start: 0.7633 (tp) cc_final: 0.7411 (tt) REVERT: E 159 TRP cc_start: 0.7871 (t60) cc_final: 0.7361 (t60) REVERT: E 160 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7736 (mm-40) REVERT: C 243 LEU cc_start: 0.0347 (OUTLIER) cc_final: -0.1282 (tt) REVERT: C 307 GLN cc_start: 0.7211 (mp-120) cc_final: 0.6941 (mp10) REVERT: C 394 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.4861 (m-10) REVERT: C 428 ILE cc_start: 0.3968 (OUTLIER) cc_final: 0.3725 (mp) REVERT: C 457 LEU cc_start: 0.2605 (OUTLIER) cc_final: 0.1552 (mm) REVERT: C 484 GLU cc_start: 0.8105 (mp0) cc_final: 0.7852 (mp0) REVERT: C 506 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.7842 (tp) REVERT: C 544 LYS cc_start: 0.8214 (tptt) cc_final: 0.7442 (tptt) REVERT: C 546 GLU cc_start: 0.7597 (pm20) cc_final: 0.6569 (pm20) REVERT: C 583 TRP cc_start: 0.6248 (m100) cc_final: 0.5988 (m100) REVERT: C 587 GLU cc_start: 0.7582 (mp0) cc_final: 0.7359 (mp0) REVERT: C 615 ARG cc_start: 0.8377 (ttt-90) cc_final: 0.8050 (mtp85) REVERT: C 662 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7090 (mm) outliers start: 105 outliers final: 77 residues processed: 503 average time/residue: 0.3281 time to fit residues: 253.9180 Evaluate side-chains 507 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 421 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 273 TYR 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 387 HIS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 505 LEU 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 588 VAL 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 711 THR 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 298 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS 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 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 TRP 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 562 VAL Chi-restraints excluded: chain B residue 572 ILE 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 660 VAL 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 695 VAL Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 154 LEU 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 115 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU 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 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 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 522 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 631 THR 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 798 HIS Chi-restraints excluded: chain C residue 809 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 0.0030 chunk 220 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 203 optimal weight: 40.0000 chunk 198 optimal weight: 40.0000 chunk 219 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.0370 chunk 243 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 683 HIS B 710 HIS E 55 GLN E 96 GLN C 798 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.216301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167261 restraints weight = 49330.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171740 restraints weight = 24682.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174585 restraints weight = 15429.790| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22513 Z= 0.123 Angle : 0.621 12.506 30722 Z= 0.306 Chirality : 0.047 0.674 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.888 87.894 3336 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 4.37 % Allowed : 23.18 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2672 helix: 1.63 (0.30), residues: 302 sheet: 0.32 (0.19), residues: 757 loop : -0.59 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 368 HIS 0.007 0.001 HIS C 800 PHE 0.022 0.001 PHE C 703 TYR 0.019 0.001 TYR A 769 ARG 0.010 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 20) link_NAG-ASN : angle 2.73291 ( 60) link_BETA1-4 : bond 0.00701 ( 1) link_BETA1-4 : angle 0.71615 ( 3) hydrogen bonds : bond 0.04379 ( 587) hydrogen bonds : angle 4.99054 ( 1581) link_BETA1-6 : bond 0.01478 ( 1) link_BETA1-6 : angle 0.99773 ( 3) SS BOND : bond 0.00243 ( 39) SS BOND : angle 1.53510 ( 78) covalent geometry : bond 0.00282 (22452) covalent geometry : angle 0.60570 (30578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 442 time to evaluate : 2.103 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: 0.7104 (tp30) cc_final: 0.6791 (tp30) REVERT: A 254 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7633 (mmtm) REVERT: A 422 TYR cc_start: 0.8503 (p90) cc_final: 0.8199 (p90) REVERT: A 434 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7216 (mt) REVERT: A 449 TRP cc_start: 0.7716 (p-90) cc_final: 0.7469 (p-90) REVERT: A 463 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6644 (tm-30) REVERT: A 469 SER cc_start: 0.7880 (m) cc_final: 0.7468 (t) REVERT: A 521 SER cc_start: 0.7865 (p) cc_final: 0.7509 (m) REVERT: A 584 LYS cc_start: 0.8672 (pptt) cc_final: 0.8411 (pttp) REVERT: A 587 GLU cc_start: 0.7418 (mp0) cc_final: 0.7149 (mp0) REVERT: A 707 GLU cc_start: 0.7460 (pp20) cc_final: 0.7041 (pp20) REVERT: A 823 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7445 (tttm) REVERT: B 375 LYS cc_start: 0.7485 (tptm) cc_final: 0.7161 (tptm) REVERT: B 407 TYR cc_start: 0.8126 (p90) cc_final: 0.7844 (p90) REVERT: B 544 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7346 (mtmm) REVERT: B 550 ASN cc_start: 0.7923 (t0) cc_final: 0.7503 (t0) REVERT: B 558 TRP cc_start: 0.8522 (p90) cc_final: 0.7949 (p90) REVERT: B 644 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6611 (mm-30) REVERT: B 669 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8374 (mtmm) REVERT: B 727 PHE cc_start: 0.7937 (m-80) cc_final: 0.7706 (m-80) REVERT: B 787 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7154 (tpp80) REVERT: B 788 ILE cc_start: 0.8043 (tp) cc_final: 0.7748 (tp) REVERT: D 89 MET cc_start: 0.7418 (tpp) cc_final: 0.7181 (tpp) REVERT: D 149 ARG cc_start: 0.7298 (ptp-170) cc_final: 0.6888 (ptp-170) REVERT: F 26 LYS cc_start: 0.7458 (tptp) cc_final: 0.7146 (tptp) REVERT: F 43 ASN cc_start: 0.8210 (m-40) cc_final: 0.7811 (m-40) REVERT: F 89 MET cc_start: 0.7816 (mtt) cc_final: 0.7594 (mtt) REVERT: F 156 ASP cc_start: 0.7600 (m-30) cc_final: 0.7297 (m-30) REVERT: E 89 MET cc_start: 0.8389 (mpp) cc_final: 0.8037 (mtm) REVERT: E 96 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7877 (tp40) REVERT: E 159 TRP cc_start: 0.7914 (t60) cc_final: 0.7396 (t60) REVERT: E 160 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7740 (mm-40) REVERT: C 307 GLN cc_start: 0.7322 (mp-120) cc_final: 0.7045 (mp10) REVERT: C 394 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.4786 (m-10) REVERT: C 428 ILE cc_start: 0.3933 (OUTLIER) cc_final: 0.3694 (mp) REVERT: C 457 LEU cc_start: 0.2518 (OUTLIER) cc_final: 0.1461 (mm) REVERT: C 484 GLU cc_start: 0.8013 (mp0) cc_final: 0.7677 (mp0) REVERT: C 506 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.7807 (tp) REVERT: C 544 LYS cc_start: 0.8247 (tptt) cc_final: 0.7812 (tptt) REVERT: C 583 TRP cc_start: 0.6263 (m100) cc_final: 0.6013 (m100) REVERT: C 615 ARG cc_start: 0.8423 (ttt-90) cc_final: 0.8066 (mtp85) REVERT: C 662 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6891 (mm) outliers start: 110 outliers final: 83 residues processed: 508 average time/residue: 0.3173 time to fit residues: 250.9888 Evaluate side-chains 527 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 434 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 613 CYS 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 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 298 ILE 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 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN 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 448 ARG Chi-restraints excluded: chain B residue 449 TRP 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 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 640 MET 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 669 LYS Chi-restraints excluded: chain B residue 681 ILE 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 D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU 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 115 LYS 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 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 505 LEU Chi-restraints excluded: chain C residue 506 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 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 810 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 221 optimal weight: 0.0040 chunk 128 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 257 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 E 55 GLN C 798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.212253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164449 restraints weight = 48824.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.168874 restraints weight = 24298.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.171645 restraints weight = 15059.750| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2478 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= 0.136 Angle : 0.635 11.375 30722 Z= 0.313 Chirality : 0.047 0.748 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.731 85.641 3336 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 4.45 % Allowed : 23.82 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2672 helix: 1.41 (0.30), residues: 313 sheet: 0.30 (0.19), residues: 755 loop : -0.59 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 368 HIS 0.024 0.001 HIS B 710 PHE 0.017 0.001 PHE B 500 TYR 0.016 0.001 TYR A 769 ARG 0.011 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 20) link_NAG-ASN : angle 2.88840 ( 60) link_BETA1-4 : bond 0.00581 ( 1) link_BETA1-4 : angle 0.63147 ( 3) hydrogen bonds : bond 0.04421 ( 587) hydrogen bonds : angle 4.97064 ( 1581) link_BETA1-6 : bond 0.01311 ( 1) link_BETA1-6 : angle 1.03059 ( 3) SS BOND : bond 0.00294 ( 39) SS BOND : angle 1.59308 ( 78) covalent geometry : bond 0.00312 (22452) covalent geometry : angle 0.61857 (30578) *********************** 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 558 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 446 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7069 (tp30) cc_final: 0.6797 (tp30) REVERT: A 254 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7600 (mmtm) REVERT: A 270 GLN cc_start: 0.7685 (pm20) cc_final: 0.7219 (pm20) REVERT: A 395 ASN cc_start: 0.7101 (p0) cc_final: 0.6660 (p0) REVERT: A 449 TRP cc_start: 0.7697 (p-90) cc_final: 0.7456 (p-90) REVERT: A 463 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: A 469 SER cc_start: 0.7858 (m) cc_final: 0.7458 (t) REVERT: A 521 SER cc_start: 0.7853 (p) cc_final: 0.7524 (m) REVERT: A 584 LYS cc_start: 0.8805 (pptt) cc_final: 0.8425 (pttp) REVERT: A 707 GLU cc_start: 0.7434 (pp20) cc_final: 0.7013 (pp20) REVERT: A 731 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: A 823 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7569 (tttm) REVERT: B 375 LYS cc_start: 0.7456 (tptm) cc_final: 0.7144 (tptm) REVERT: B 407 TYR cc_start: 0.8118 (p90) cc_final: 0.7819 (p90) REVERT: B 439 ASP cc_start: 0.8086 (t0) cc_final: 0.7605 (t70) REVERT: B 497 GLU cc_start: 0.7905 (tp30) cc_final: 0.7663 (tp30) REVERT: B 544 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7358 (mtmm) REVERT: B 550 ASN cc_start: 0.7930 (t0) cc_final: 0.7519 (t0) REVERT: B 558 TRP cc_start: 0.8508 (p90) cc_final: 0.7921 (p90) REVERT: B 669 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8367 (mtmm) REVERT: D 89 MET cc_start: 0.7420 (tpp) cc_final: 0.7186 (tpp) REVERT: D 149 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6788 (ptp-170) REVERT: F 26 LYS cc_start: 0.7468 (tptp) cc_final: 0.7200 (tptp) REVERT: F 43 ASN cc_start: 0.8207 (m-40) cc_final: 0.7807 (m-40) REVERT: F 89 MET cc_start: 0.7825 (mtt) cc_final: 0.7551 (mtt) REVERT: F 156 ASP cc_start: 0.7531 (m-30) cc_final: 0.7209 (m-30) REVERT: E 89 MET cc_start: 0.8404 (mpp) cc_final: 0.8050 (mtm) REVERT: E 159 TRP cc_start: 0.7946 (t60) cc_final: 0.7415 (t60) REVERT: E 160 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7773 (mm-40) REVERT: C 243 LEU cc_start: 0.0163 (OUTLIER) cc_final: -0.1416 (tt) REVERT: C 307 GLN cc_start: 0.7267 (mp-120) cc_final: 0.7007 (mp10) REVERT: C 394 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.4755 (m-10) REVERT: C 428 ILE cc_start: 0.4005 (OUTLIER) cc_final: 0.3760 (mp) REVERT: C 457 LEU cc_start: 0.2574 (OUTLIER) cc_final: 0.1485 (mm) REVERT: C 506 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.7790 (tp) REVERT: C 523 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7199 (t70) REVERT: C 544 LYS cc_start: 0.8194 (tptt) cc_final: 0.7477 (tptt) REVERT: C 546 GLU cc_start: 0.7630 (pm20) cc_final: 0.6447 (pm20) REVERT: C 583 TRP cc_start: 0.6249 (m100) cc_final: 0.5995 (m100) REVERT: C 587 GLU cc_start: 0.7685 (mp0) cc_final: 0.7450 (mp0) REVERT: C 615 ARG cc_start: 0.8416 (ttt-90) cc_final: 0.8176 (ttt-90) REVERT: C 662 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6763 (mm) outliers start: 112 outliers final: 86 residues processed: 519 average time/residue: 0.3341 time to fit residues: 268.4788 Evaluate side-chains 527 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 430 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL 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 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 298 ILE 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 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS 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 449 TRP 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 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE 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 660 VAL 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 710 HIS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU 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 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU 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 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 505 LEU Chi-restraints excluded: chain C residue 506 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 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 796 TYR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 30.0000 chunk 192 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 207 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 31 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS E 43 ASN E 96 GLN C 798 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.210318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161190 restraints weight = 49487.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165679 restraints weight = 24499.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168506 restraints weight = 15183.107| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2776 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= 0.185 Angle : 0.681 12.923 30722 Z= 0.338 Chirality : 0.048 0.786 3524 Planarity : 0.004 0.065 3793 Dihedral : 5.786 83.076 3336 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.87 % Favored : 94.99 % Rotamer: Outliers : 4.65 % Allowed : 24.21 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2672 helix: 1.23 (0.30), residues: 313 sheet: 0.22 (0.19), residues: 755 loop : -0.65 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 368 HIS 0.009 0.001 HIS A 517 PHE 0.026 0.001 PHE C 703 TYR 0.022 0.001 TYR A 426 ARG 0.010 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 20) link_NAG-ASN : angle 2.94964 ( 60) link_BETA1-4 : bond 0.00498 ( 1) link_BETA1-4 : angle 0.60810 ( 3) hydrogen bonds : bond 0.05000 ( 587) hydrogen bonds : angle 5.12092 ( 1581) link_BETA1-6 : bond 0.01150 ( 1) link_BETA1-6 : angle 1.07097 ( 3) SS BOND : bond 0.00391 ( 39) SS BOND : angle 1.78328 ( 78) covalent geometry : bond 0.00420 (22452) covalent geometry : angle 0.66371 (30578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 449 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7148 (tp30) cc_final: 0.6870 (tp30) REVERT: A 254 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7650 (mmtt) REVERT: A 270 GLN cc_start: 0.7640 (pm20) cc_final: 0.7234 (pm20) REVERT: A 374 GLU cc_start: 0.6664 (mp0) cc_final: 0.6193 (mp0) REVERT: A 463 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: A 469 SER cc_start: 0.7813 (m) cc_final: 0.7434 (t) REVERT: A 521 SER cc_start: 0.7901 (p) cc_final: 0.7605 (m) REVERT: A 584 LYS cc_start: 0.8814 (pptt) cc_final: 0.8498 (pttp) REVERT: A 624 ASN cc_start: 0.5930 (p0) cc_final: 0.5708 (p0) REVERT: A 731 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: A 771 ILE cc_start: 0.8657 (mm) cc_final: 0.8436 (mm) REVERT: A 787 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8078 (ttp80) REVERT: A 823 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7263 (ttmm) REVERT: B 375 LYS cc_start: 0.7489 (tptm) cc_final: 0.7200 (tptm) REVERT: B 407 TYR cc_start: 0.8117 (p90) cc_final: 0.7812 (p90) REVERT: B 439 ASP cc_start: 0.7993 (t0) cc_final: 0.7639 (t70) REVERT: B 544 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7394 (mtmm) REVERT: B 550 ASN cc_start: 0.7920 (t0) cc_final: 0.7497 (t0) REVERT: B 558 TRP cc_start: 0.8519 (p90) cc_final: 0.7978 (p90) REVERT: B 669 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8382 (mtmm) REVERT: B 700 LYS cc_start: 0.8340 (tttt) cc_final: 0.8140 (tttt) REVERT: B 787 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6922 (tpt90) REVERT: B 795 TYR cc_start: 0.7657 (t80) cc_final: 0.7435 (t80) REVERT: D 89 MET cc_start: 0.7490 (tpp) cc_final: 0.7249 (tpp) REVERT: D 149 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6803 (ptp-170) REVERT: F 26 LYS cc_start: 0.7534 (tptp) cc_final: 0.7222 (tptp) REVERT: F 43 ASN cc_start: 0.8235 (m-40) cc_final: 0.7840 (m-40) REVERT: F 89 MET cc_start: 0.7966 (mtt) cc_final: 0.7684 (mtt) REVERT: F 156 ASP cc_start: 0.7559 (m-30) cc_final: 0.7277 (m-30) REVERT: E 30 ASP cc_start: 0.7246 (m-30) cc_final: 0.7024 (m-30) REVERT: E 89 MET cc_start: 0.8488 (mpp) cc_final: 0.8176 (mtm) REVERT: E 96 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7904 (tp40) REVERT: C 243 LEU cc_start: 0.0348 (OUTLIER) cc_final: -0.1248 (tt) REVERT: C 307 GLN cc_start: 0.7210 (mp-120) cc_final: 0.6955 (mp10) REVERT: C 394 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.4727 (m-10) REVERT: C 428 ILE cc_start: 0.4033 (OUTLIER) cc_final: 0.3786 (mp) REVERT: C 457 LEU cc_start: 0.2660 (OUTLIER) cc_final: 0.1555 (mm) REVERT: C 506 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.7794 (tp) REVERT: C 523 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7257 (t70) REVERT: C 544 LYS cc_start: 0.8185 (tptt) cc_final: 0.7807 (tptt) REVERT: C 583 TRP cc_start: 0.6341 (m100) cc_final: 0.6092 (m100) REVERT: C 615 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8201 (ttt-90) REVERT: C 662 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6670 (mm) outliers start: 117 outliers final: 88 residues processed: 524 average time/residue: 0.3294 time to fit residues: 267.0608 Evaluate side-chains 542 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 442 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 483 SER 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 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 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 298 ILE 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 366 ILE 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 422 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 TRP 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 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 640 MET 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 669 LYS Chi-restraints excluded: chain B residue 681 ILE 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 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 58 THR 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 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 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU 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 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 505 LEU Chi-restraints excluded: chain C residue 506 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 572 ILE Chi-restraints excluded: chain C residue 609 VAL 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 796 TYR Chi-restraints excluded: chain C residue 798 HIS Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 118 optimal weight: 0.5980 chunk 255 optimal weight: 0.0010 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 173 optimal weight: 0.4980 chunk 166 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 151 optimal weight: 0.0270 chunk 131 optimal weight: 0.0770 chunk 59 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 overall best weight: 0.2402 ------------------------------------------------------------------------------- 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 B 683 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.214094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.165478 restraints weight = 49657.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170057 restraints weight = 24662.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172897 restraints weight = 15256.480| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22513 Z= 0.119 Angle : 0.676 12.881 30722 Z= 0.331 Chirality : 0.047 0.619 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.606 81.584 3336 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 3.78 % Allowed : 25.49 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2672 helix: 1.41 (0.30), residues: 313 sheet: 0.31 (0.19), residues: 765 loop : -0.60 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A 449 HIS 0.031 0.001 HIS C 798 PHE 0.019 0.001 PHE C 495 TYR 0.018 0.001 TYR A 769 ARG 0.012 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 20) link_NAG-ASN : angle 2.75172 ( 60) link_BETA1-4 : bond 0.00611 ( 1) link_BETA1-4 : angle 0.67051 ( 3) hydrogen bonds : bond 0.04200 ( 587) hydrogen bonds : angle 4.99446 ( 1581) link_BETA1-6 : bond 0.01194 ( 1) link_BETA1-6 : angle 0.96508 ( 3) SS BOND : bond 0.00346 ( 39) SS BOND : angle 1.72275 ( 78) covalent geometry : bond 0.00277 (22452) covalent geometry : angle 0.66096 (30578) *********************** 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 541 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 446 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7105 (tp30) cc_final: 0.6831 (tp30) REVERT: A 270 GLN cc_start: 0.7631 (pm20) cc_final: 0.7256 (pm20) REVERT: A 421 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7762 (mmm-85) REVERT: A 463 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: A 469 SER cc_start: 0.7839 (m) cc_final: 0.7447 (t) REVERT: A 521 SER cc_start: 0.7832 (p) cc_final: 0.7505 (m) REVERT: A 548 THR cc_start: 0.7435 (p) cc_final: 0.5812 (m) REVERT: A 584 LYS cc_start: 0.8724 (pptt) cc_final: 0.8369 (pttp) REVERT: A 624 ASN cc_start: 0.5832 (p0) cc_final: 0.5630 (p0) REVERT: A 693 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 771 ILE cc_start: 0.8667 (mm) cc_final: 0.8451 (mm) REVERT: A 823 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7481 (tttm) REVERT: B 375 LYS cc_start: 0.7385 (tptm) cc_final: 0.7130 (tptm) REVERT: B 398 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7627 (mt-10) REVERT: B 407 TYR cc_start: 0.8139 (p90) cc_final: 0.7851 (p90) REVERT: B 439 ASP cc_start: 0.7993 (t0) cc_final: 0.7595 (t70) REVERT: B 544 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7336 (mtmm) REVERT: B 550 ASN cc_start: 0.7921 (t0) cc_final: 0.7493 (t0) REVERT: B 558 TRP cc_start: 0.8478 (p90) cc_final: 0.7913 (p90) REVERT: D 149 ARG cc_start: 0.7231 (ptp-170) cc_final: 0.6844 (ptp-170) REVERT: F 26 LYS cc_start: 0.7437 (tptp) cc_final: 0.7193 (tptp) REVERT: F 43 ASN cc_start: 0.8198 (m-40) cc_final: 0.7809 (m-40) REVERT: F 89 MET cc_start: 0.7794 (mtt) cc_final: 0.7548 (mtt) REVERT: F 156 ASP cc_start: 0.7398 (m-30) cc_final: 0.7126 (m-30) REVERT: E 83 GLN cc_start: 0.7893 (tp40) cc_final: 0.7675 (tp40) REVERT: E 89 MET cc_start: 0.8418 (mpp) cc_final: 0.8124 (mtm) REVERT: E 96 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7885 (tp40) REVERT: C 243 LEU cc_start: 0.0111 (OUTLIER) cc_final: -0.1469 (tt) REVERT: C 307 GLN cc_start: 0.7284 (mp-120) cc_final: 0.7027 (mp10) REVERT: C 394 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.4733 (m-10) REVERT: C 428 ILE cc_start: 0.3925 (OUTLIER) cc_final: 0.3692 (mp) REVERT: C 457 LEU cc_start: 0.2631 (OUTLIER) cc_final: 0.1552 (mm) REVERT: C 523 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7218 (t70) REVERT: C 544 LYS cc_start: 0.8227 (tptt) cc_final: 0.7819 (tptt) REVERT: C 583 TRP cc_start: 0.6335 (m100) cc_final: 0.6068 (m100) REVERT: C 615 ARG cc_start: 0.8452 (ttt-90) cc_final: 0.8190 (ttt-90) REVERT: C 662 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6630 (mm) outliers start: 95 outliers final: 80 residues processed: 504 average time/residue: 0.3339 time to fit residues: 262.9501 Evaluate side-chains 523 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 435 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR 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 387 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 523 ASP 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 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 744 LEU 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 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 TRP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 476 ILE 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 640 MET 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 669 LYS Chi-restraints excluded: chain B residue 681 ILE 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 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER 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 154 LEU 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 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE 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 491 GLN Chi-restraints excluded: chain C residue 505 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 572 ILE Chi-restraints excluded: chain C residue 609 VAL 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 796 TYR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 186 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 212 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 123 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS B 683 HIS E 43 ASN C 798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.212932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163401 restraints weight = 49332.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167919 restraints weight = 24615.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170683 restraints weight = 15327.594| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22513 Z= 0.171 Angle : 0.706 12.889 30722 Z= 0.348 Chirality : 0.047 0.572 3524 Planarity : 0.005 0.065 3793 Dihedral : 5.646 78.709 3336 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 3.90 % Allowed : 25.41 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2672 helix: 1.25 (0.30), residues: 313 sheet: 0.23 (0.19), residues: 743 loop : -0.65 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 449 HIS 0.007 0.001 HIS B 467 PHE 0.023 0.001 PHE B 500 TYR 0.018 0.001 TYR B 422 ARG 0.014 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 20) link_NAG-ASN : angle 2.74950 ( 60) link_BETA1-4 : bond 0.00692 ( 1) link_BETA1-4 : angle 0.67717 ( 3) hydrogen bonds : bond 0.04790 ( 587) hydrogen bonds : angle 5.08826 ( 1581) link_BETA1-6 : bond 0.01307 ( 1) link_BETA1-6 : angle 1.08902 ( 3) SS BOND : bond 0.00347 ( 39) SS BOND : angle 1.83366 ( 78) covalent geometry : bond 0.00393 (22452) covalent geometry : angle 0.69098 (30578) ********************** 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 543 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 445 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7174 (tp30) cc_final: 0.6924 (tp30) REVERT: A 270 GLN cc_start: 0.7623 (pm20) cc_final: 0.7286 (pm20) REVERT: A 463 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: A 469 SER cc_start: 0.7800 (m) cc_final: 0.7427 (t) REVERT: A 521 SER cc_start: 0.7848 (p) cc_final: 0.7527 (m) REVERT: A 584 LYS cc_start: 0.8731 (pptt) cc_final: 0.8405 (pttp) REVERT: A 731 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: A 823 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7096 (ttmm) REVERT: B 343 SER cc_start: 0.8140 (m) cc_final: 0.7846 (p) REVERT: B 375 LYS cc_start: 0.7500 (tptm) cc_final: 0.7225 (tptm) REVERT: B 407 TYR cc_start: 0.8114 (p90) cc_final: 0.7794 (p90) REVERT: B 439 ASP cc_start: 0.8049 (t0) cc_final: 0.7685 (t70) REVERT: B 544 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7398 (mtmm) REVERT: B 550 ASN cc_start: 0.7918 (t0) cc_final: 0.7498 (t0) REVERT: B 558 TRP cc_start: 0.8480 (p90) cc_final: 0.7985 (p90) REVERT: D 149 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.6947 (ptp-170) REVERT: F 26 LYS cc_start: 0.7508 (tptp) cc_final: 0.7191 (tptp) REVERT: F 43 ASN cc_start: 0.8220 (m-40) cc_final: 0.7901 (m-40) REVERT: F 89 MET cc_start: 0.7899 (mtt) cc_final: 0.7637 (mtt) REVERT: F 156 ASP cc_start: 0.7522 (m-30) cc_final: 0.7275 (m-30) REVERT: E 89 MET cc_start: 0.8467 (mpp) cc_final: 0.8150 (mtm) REVERT: E 159 TRP cc_start: 0.8038 (t60) cc_final: 0.7507 (t60) REVERT: C 243 LEU cc_start: 0.0302 (OUTLIER) cc_final: -0.2663 (pt) REVERT: C 307 GLN cc_start: 0.7274 (mp-120) cc_final: 0.7034 (mp10) REVERT: C 394 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5000 (m-10) REVERT: C 428 ILE cc_start: 0.4030 (OUTLIER) cc_final: 0.3781 (mp) REVERT: C 457 LEU cc_start: 0.2649 (OUTLIER) cc_final: 0.1549 (mm) REVERT: C 506 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.7763 (tp) REVERT: C 523 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7201 (t70) REVERT: C 544 LYS cc_start: 0.8217 (tptt) cc_final: 0.7807 (tptt) REVERT: C 583 TRP cc_start: 0.6331 (m100) cc_final: 0.6089 (m100) REVERT: C 615 ARG cc_start: 0.8455 (ttt-90) cc_final: 0.8255 (mtp85) REVERT: C 631 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.7799 (p) REVERT: C 662 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6599 (mm) outliers start: 98 outliers final: 83 residues processed: 507 average time/residue: 0.3204 time to fit residues: 249.6132 Evaluate side-chains 534 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 440 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 299 LEU 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 430 VAL 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 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 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE 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 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 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 TRP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 ILE 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 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE 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 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU 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 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE 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 491 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 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 572 ILE Chi-restraints excluded: chain C residue 609 VAL 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 796 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 225 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 258 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 798 HIS B 683 HIS E 96 GLN C 670 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.212182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164647 restraints weight = 48417.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169040 restraints weight = 23947.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171772 restraints weight = 14851.348| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22513 Z= 0.149 Angle : 0.708 14.250 30722 Z= 0.348 Chirality : 0.048 0.861 3524 Planarity : 0.004 0.065 3793 Dihedral : 5.625 77.151 3336 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Rotamer: Outliers : 4.14 % Allowed : 25.21 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2672 helix: 1.31 (0.30), residues: 313 sheet: 0.26 (0.19), residues: 736 loop : -0.67 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 449 HIS 0.007 0.001 HIS A 798 PHE 0.032 0.001 PHE C 828 TYR 0.016 0.001 TYR B 807 ARG 0.013 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 20) link_NAG-ASN : angle 2.93695 ( 60) link_BETA1-4 : bond 0.00474 ( 1) link_BETA1-4 : angle 0.64944 ( 3) hydrogen bonds : bond 0.04572 ( 587) hydrogen bonds : angle 5.05344 ( 1581) link_BETA1-6 : bond 0.01223 ( 1) link_BETA1-6 : angle 0.97794 ( 3) SS BOND : bond 0.00388 ( 39) SS BOND : angle 1.80092 ( 78) covalent geometry : bond 0.00347 (22452) covalent geometry : angle 0.69186 (30578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10151.70 seconds wall clock time: 177 minutes 38.20 seconds (10658.20 seconds total)