Starting phenix.real_space_refine on Fri Jan 24 14:37:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x81_38132/01_2025/8x81_38132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x81_38132/01_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_38132/01_2025/8x81_38132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x81_38132/01_2025/8x81_38132.map" model { file = "/net/cci-nas-00/data/ceres_data/8x81_38132/01_2025/8x81_38132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x81_38132/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 14.54, per 1000 atoms: 0.66 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: 5.05 Conformation dependent library (CDL) restraints added in 2.6 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: 3.27 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: 8.66 Time building geometry restraints manager: 5.93 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: 10.490 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: 0.940 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 50.420 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.850 ------------------------------------------------------------------------------- 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 22452 Z= 0.252 Angle : 0.723 13.297 30578 Z= 0.388 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 *********************** 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 : 2.203 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: 0.3664 time to fit residues: 237.0384 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 : 2.426 ------------------------------------------------------------------------------- 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 22452 Z= 0.315 Angle : 0.671 10.507 30578 Z= 0.340 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 *********************** 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 : 2.343 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: 0.3727 time to fit residues: 292.8786 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 : 2.795 ------------------------------------------------------------------------------- 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: 0.3980 chunk 58 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 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 = 45)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168593 restraints weight = 49490.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173056 restraints weight = 24914.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175916 restraints weight = 15688.575| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 22452 Z= 0.209 Angle : 0.591 10.831 30578 Z= 0.297 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 *********************** 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 : 2.284 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: 0.8077 (mmtt) cc_final: 0.7726 (mmtt) REVERT: A 422 TYR cc_start: 0.8468 (p90) cc_final: 0.8152 (p90) REVERT: A 424 GLU cc_start: 0.7965 (pt0) cc_final: 0.7745 (pt0) REVERT: A 449 TRP cc_start: 0.7820 (p-90) cc_final: 0.7378 (p-90) REVERT: A 463 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: A 469 SER cc_start: 0.7782 (m) cc_final: 0.7264 (p) REVERT: A 787 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8166 (ttp80) REVERT: A 823 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7291 (tttp) REVERT: B 272 LYS cc_start: 0.7718 (mptt) cc_final: 0.7385 (mmtt) REVERT: B 375 LYS cc_start: 0.7352 (tptm) cc_final: 0.7097 (tptm) REVERT: B 407 TYR cc_start: 0.8094 (p90) cc_final: 0.7850 (p90) REVERT: B 439 ASP cc_start: 0.8051 (t0) cc_final: 0.7703 (t0) REVERT: B 444 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8227 (ptpp) REVERT: B 448 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6632 (mtp85) REVERT: B 544 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7345 (mtmm) REVERT: B 550 ASN cc_start: 0.7860 (t0) cc_final: 0.7412 (t0) REVERT: B 788 ILE cc_start: 0.8033 (tp) cc_final: 0.7725 (tp) REVERT: B 795 TYR cc_start: 0.7163 (t80) cc_final: 0.6927 (t80) REVERT: D 89 MET cc_start: 0.7492 (tpp) cc_final: 0.7258 (tpp) REVERT: F 26 LYS cc_start: 0.7453 (tptp) cc_final: 0.7154 (tptp) REVERT: F 43 ASN cc_start: 0.8182 (m-40) cc_final: 0.7744 (m-40) REVERT: F 47 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7253 (m170) REVERT: F 89 MET cc_start: 0.7772 (mtt) cc_final: 0.7525 (mtt) REVERT: E 89 MET cc_start: 0.8299 (mpp) cc_final: 0.7901 (mtm) REVERT: E 159 TRP cc_start: 0.7713 (t60) cc_final: 0.7334 (t60) REVERT: E 160 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7814 (mm-40) REVERT: C 307 GLN cc_start: 0.7382 (mp-120) cc_final: 0.7071 (mp10) REVERT: C 387 HIS cc_start: 0.8928 (m-70) cc_final: 0.8713 (m-70) REVERT: C 544 LYS cc_start: 0.8229 (tptt) cc_final: 0.7953 (tptt) REVERT: C 584 LYS cc_start: 0.8817 (tptm) cc_final: 0.8548 (tppt) REVERT: C 615 ARG cc_start: 0.8375 (ttt-90) cc_final: 0.8045 (mtp85) REVERT: C 625 TRP cc_start: 0.7410 (m100) cc_final: 0.7146 (m100) REVERT: C 662 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7044 (mm) REVERT: C 826 ASN cc_start: 0.7629 (m-40) cc_final: 0.7428 (m-40) outliers start: 90 outliers final: 63 residues processed: 495 average time/residue: 0.3544 time to fit residues: 269.6096 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 : 2.213 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 40.0000 chunk 184 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 395 ASN ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS F 47 HIS E 55 GLN C 726 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.208958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160025 restraints weight = 49162.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166441 restraints weight = 25927.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167458 restraints weight = 13309.127| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 22452 Z= 0.383 Angle : 0.677 11.325 30578 Z= 0.347 Chirality : 0.048 0.454 3524 Planarity : 0.005 0.067 3793 Dihedral : 6.287 91.500 3336 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.20 % Favored : 94.65 % Rotamer: Outliers : 4.93 % Allowed : 22.03 % 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: -0.36 (0.16), residues: 2672 helix: 1.14 (0.29), residues: 301 sheet: 0.20 (0.19), residues: 755 loop : -0.71 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 368 HIS 0.024 0.001 HIS B 710 PHE 0.033 0.002 PHE B 500 TYR 0.026 0.002 TYR B 422 ARG 0.010 0.001 ARG E 41 *********************** 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 581 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 457 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7130 (tp30) cc_final: 0.6814 (tp30) REVERT: A 254 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7495 (mmtm) REVERT: A 424 GLU cc_start: 0.8119 (pt0) cc_final: 0.7790 (pt0) REVERT: A 449 TRP cc_start: 0.7857 (p-90) cc_final: 0.7652 (p-90) REVERT: A 469 SER cc_start: 0.7716 (m) cc_final: 0.7382 (t) REVERT: A 506 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7478 (tp) REVERT: A 521 SER cc_start: 0.8086 (p) cc_final: 0.7825 (m) REVERT: A 587 GLU cc_start: 0.7602 (mp0) cc_final: 0.7302 (mp0) REVERT: A 707 GLU cc_start: 0.7517 (pp20) cc_final: 0.7077 (pp20) REVERT: A 731 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: A 823 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7321 (tttm) REVERT: B 375 LYS cc_start: 0.7595 (tptm) cc_final: 0.7285 (tptm) REVERT: B 390 LYS cc_start: 0.8480 (ttpt) cc_final: 0.8251 (tttt) REVERT: B 407 TYR cc_start: 0.8115 (p90) cc_final: 0.7831 (p90) REVERT: B 439 ASP cc_start: 0.8094 (t0) cc_final: 0.7630 (t70) REVERT: B 448 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6885 (mtp85) REVERT: B 544 LYS cc_start: 0.7766 (mtmm) cc_final: 0.7420 (mtmm) REVERT: B 550 ASN cc_start: 0.7893 (t0) cc_final: 0.7480 (t0) REVERT: B 700 LYS cc_start: 0.8352 (tttt) cc_final: 0.8125 (tttt) REVERT: B 787 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7152 (tpp80) REVERT: B 788 ILE cc_start: 0.8107 (tp) cc_final: 0.7782 (tp) REVERT: B 795 TYR cc_start: 0.7669 (t80) cc_final: 0.7319 (t80) REVERT: D 89 MET cc_start: 0.7660 (tpp) cc_final: 0.7401 (tpp) REVERT: D 149 ARG cc_start: 0.7322 (ptp-170) cc_final: 0.7037 (ptp-170) REVERT: F 26 LYS cc_start: 0.7681 (tptp) cc_final: 0.7319 (tptp) REVERT: F 43 ASN cc_start: 0.8308 (m-40) cc_final: 0.7847 (m-40) REVERT: F 47 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7415 (m90) REVERT: F 89 MET cc_start: 0.8108 (mtt) cc_final: 0.7787 (mtt) REVERT: F 156 ASP cc_start: 0.7814 (m-30) cc_final: 0.7552 (m-30) REVERT: E 74 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7311 (ttmt) REVERT: E 89 MET cc_start: 0.8465 (mpp) cc_final: 0.8184 (mtm) REVERT: E 96 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7712 (tm-30) REVERT: E 159 TRP cc_start: 0.7926 (t60) cc_final: 0.7415 (t60) REVERT: E 160 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7776 (mm-40) REVERT: C 307 GLN cc_start: 0.7167 (mp-120) cc_final: 0.6883 (mp10) REVERT: C 387 HIS cc_start: 0.8928 (m-70) cc_final: 0.8722 (m-70) REVERT: C 428 ILE cc_start: 0.4016 (OUTLIER) cc_final: 0.3759 (mp) REVERT: C 457 LEU cc_start: 0.2704 (OUTLIER) cc_final: 0.1651 (mm) REVERT: C 506 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.7881 (tp) REVERT: C 544 LYS cc_start: 0.8202 (tptt) cc_final: 0.7816 (tptt) REVERT: C 583 TRP cc_start: 0.6297 (m100) cc_final: 0.6050 (m100) REVERT: C 615 ARG cc_start: 0.8460 (ttt-90) cc_final: 0.8120 (ttt-90) REVERT: C 662 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7042 (mm) REVERT: C 735 MET cc_start: 0.7923 (mmm) cc_final: 0.7679 (mmm) outliers start: 124 outliers final: 80 residues processed: 531 average time/residue: 0.3493 time to fit residues: 286.6446 Evaluate side-chains 529 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 439 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 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 327 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 416 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 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 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 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 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 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 677 GLN Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 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 58 THR 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 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 567 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 630 TYR Chi-restraints excluded: chain C residue 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: 0.4980 chunk 41 optimal weight: 0.6980 chunk 135 optimal weight: 0.0670 chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 86 optimal weight: 40.0000 chunk 105 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 682 ASN B 683 HIS B 710 HIS F 155 GLN F 160 GLN E 43 ASN C 268 GLN C 798 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.214950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166222 restraints weight = 49835.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.170800 restraints weight = 24792.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173663 restraints weight = 15419.072| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22452 Z= 0.181 Angle : 0.612 10.957 30578 Z= 0.307 Chirality : 0.046 0.535 3524 Planarity : 0.004 0.063 3793 Dihedral : 5.968 90.135 3336 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 4.25 % Allowed : 23.46 % Favored : 72.29 % 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 (0.17), residues: 2672 helix: 1.52 (0.30), residues: 302 sheet: 0.26 (0.19), residues: 762 loop : -0.62 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 646 HIS 0.007 0.001 HIS A 710 PHE 0.014 0.001 PHE A 336 TYR 0.021 0.001 TYR A 769 ARG 0.007 0.000 ARG C 678 *********************** 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 554 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 447 time to evaluate : 3.633 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: 0.7101 (tp30) cc_final: 0.6776 (tp30) REVERT: A 395 ASN cc_start: 0.7022 (p0) cc_final: 0.6704 (p0) REVERT: A 422 TYR cc_start: 0.8555 (p90) cc_final: 0.8217 (p90) REVERT: A 424 GLU cc_start: 0.8097 (pt0) cc_final: 0.7818 (pt0) REVERT: A 434 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7282 (mt) REVERT: A 449 TRP cc_start: 0.7853 (p-90) cc_final: 0.7585 (p-90) REVERT: A 463 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 469 SER cc_start: 0.7833 (m) cc_final: 0.7451 (t) REVERT: A 521 SER cc_start: 0.7910 (p) cc_final: 0.7537 (m) REVERT: A 584 LYS cc_start: 0.8736 (pptt) cc_final: 0.8407 (pttp) REVERT: A 669 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8860 (mmmt) REVERT: A 707 GLU cc_start: 0.7499 (pp20) cc_final: 0.7078 (pp20) REVERT: A 787 ARG cc_start: 0.8313 (ttp80) cc_final: 0.8111 (ttp80) REVERT: A 823 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: B 272 LYS cc_start: 0.7728 (mptt) cc_final: 0.7373 (mmtt) REVERT: B 375 LYS cc_start: 0.7436 (tptm) cc_final: 0.7135 (tptm) REVERT: B 407 TYR cc_start: 0.8155 (p90) cc_final: 0.7882 (p90) REVERT: B 544 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7380 (mtmm) REVERT: B 550 ASN cc_start: 0.7910 (t0) cc_final: 0.7479 (t0) REVERT: B 558 TRP cc_start: 0.8516 (p90) cc_final: 0.7946 (p90) REVERT: B 682 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6549 (t0) REVERT: B 787 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7109 (tpp80) REVERT: B 788 ILE cc_start: 0.8069 (tp) cc_final: 0.7745 (tp) REVERT: D 89 MET cc_start: 0.7467 (tpp) cc_final: 0.7216 (tpp) REVERT: D 149 ARG cc_start: 0.7308 (ptp-170) cc_final: 0.6931 (ptp-170) REVERT: F 26 LYS cc_start: 0.7506 (tptp) cc_final: 0.7200 (tptp) REVERT: F 43 ASN cc_start: 0.8243 (m-40) cc_final: 0.7841 (m-40) REVERT: F 75 MET cc_start: 0.8142 (ttt) cc_final: 0.7337 (mtp) REVERT: F 89 MET cc_start: 0.7922 (mtt) cc_final: 0.7648 (mtt) REVERT: E 89 MET cc_start: 0.8409 (mpp) cc_final: 0.8095 (mtm) REVERT: E 96 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7816 (tp40) REVERT: E 131 LEU cc_start: 0.7607 (tp) cc_final: 0.7393 (tt) REVERT: E 159 TRP cc_start: 0.7914 (t60) cc_final: 0.7408 (t60) REVERT: E 160 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7753 (mm-40) REVERT: C 243 LEU cc_start: 0.0309 (OUTLIER) cc_final: -0.1329 (tt) REVERT: C 307 GLN cc_start: 0.7318 (mp-120) cc_final: 0.7049 (mp10) REVERT: C 387 HIS cc_start: 0.8877 (m-70) cc_final: 0.8667 (m-70) REVERT: C 394 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.4871 (m-10) REVERT: C 428 ILE cc_start: 0.3922 (OUTLIER) cc_final: 0.3679 (mp) REVERT: C 457 LEU cc_start: 0.2600 (OUTLIER) cc_final: 0.1542 (mm) REVERT: C 523 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7293 (t70) REVERT: C 544 LYS cc_start: 0.8215 (tptt) cc_final: 0.7434 (tptt) REVERT: C 546 GLU cc_start: 0.7594 (pm20) cc_final: 0.6459 (pm20) REVERT: C 583 TRP cc_start: 0.6231 (m100) cc_final: 0.5963 (m100) REVERT: C 587 GLU cc_start: 0.7656 (mp0) cc_final: 0.7436 (mp0) REVERT: C 615 ARG cc_start: 0.8452 (ttt-90) cc_final: 0.8149 (ttt-90) REVERT: C 662 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6948 (mm) outliers start: 107 outliers final: 70 residues processed: 514 average time/residue: 0.3617 time to fit residues: 287.6800 Evaluate side-chains 513 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 432 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 ILE 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 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 400 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG 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 562 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 695 VAL 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 84 GLN Chi-restraints excluded: chain D residue 147 LEU 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 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 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 796 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 203 optimal weight: 0.3980 chunk 198 optimal weight: 40.0000 chunk 219 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 517 HIS ** A 683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 683 HIS F 47 HIS F 49 GLN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN C 726 ASN C 742 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.204756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155312 restraints weight = 48105.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160929 restraints weight = 25153.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162066 restraints weight = 13471.681| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 22452 Z= 0.440 Angle : 0.711 12.413 30578 Z= 0.366 Chirality : 0.049 0.427 3524 Planarity : 0.005 0.068 3793 Dihedral : 6.267 87.266 3334 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.16 % Rotamer: Outliers : 5.13 % Allowed : 23.54 % Favored : 71.33 % 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: -0.66 (0.16), residues: 2672 helix: 0.72 (0.28), residues: 313 sheet: -0.07 (0.18), residues: 759 loop : -0.85 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 368 HIS 0.016 0.001 HIS B 710 PHE 0.036 0.002 PHE B 500 TYR 0.029 0.002 TYR B 422 ARG 0.016 0.001 ARG C 647 *********************** 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 584 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 455 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7265 (tp30) cc_final: 0.6969 (tp30) REVERT: A 270 GLN cc_start: 0.7773 (pm20) cc_final: 0.7342 (pm20) REVERT: A 469 SER cc_start: 0.7734 (m) cc_final: 0.7393 (t) REVERT: A 506 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7482 (tp) REVERT: A 521 SER cc_start: 0.8043 (p) cc_final: 0.7755 (m) REVERT: A 584 LYS cc_start: 0.8785 (pptt) cc_final: 0.8511 (pttp) REVERT: A 587 GLU cc_start: 0.7774 (mp0) cc_final: 0.7502 (mp0) REVERT: A 669 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8757 (mmmm) REVERT: A 731 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: A 770 PHE cc_start: 0.6732 (m-80) cc_final: 0.6329 (m-10) REVERT: A 787 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7902 (ttp80) REVERT: A 794 LYS cc_start: 0.8101 (tppt) cc_final: 0.7814 (tptt) REVERT: A 823 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7534 (tttm) REVERT: B 355 LYS cc_start: 0.7569 (tppp) cc_final: 0.7309 (tptm) REVERT: B 375 LYS cc_start: 0.7640 (tptm) cc_final: 0.7320 (tptm) REVERT: B 392 THR cc_start: 0.8400 (t) cc_final: 0.8118 (p) REVERT: B 407 TYR cc_start: 0.8119 (p90) cc_final: 0.7792 (p90) REVERT: B 439 ASP cc_start: 0.8082 (t0) cc_final: 0.7648 (t70) REVERT: B 448 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6774 (mtp85) REVERT: B 486 LYS cc_start: 0.8205 (tppt) cc_final: 0.7668 (tptp) REVERT: B 544 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7470 (mtmm) REVERT: B 550 ASN cc_start: 0.7971 (t0) cc_final: 0.7556 (t0) REVERT: B 669 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8486 (mtpp) REVERT: B 788 ILE cc_start: 0.8155 (tp) cc_final: 0.7923 (tp) REVERT: B 821 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7158 (tptt) REVERT: D 149 ARG cc_start: 0.7394 (ptp-170) cc_final: 0.7045 (ptp-170) REVERT: F 26 LYS cc_start: 0.7776 (tptp) cc_final: 0.7383 (tptp) REVERT: F 43 ASN cc_start: 0.8304 (m-40) cc_final: 0.7857 (m-40) REVERT: F 75 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7600 (ttt) REVERT: F 89 MET cc_start: 0.8150 (mtt) cc_final: 0.7865 (mtt) REVERT: E 89 MET cc_start: 0.8590 (mpp) cc_final: 0.7978 (mtm) REVERT: E 96 GLN cc_start: 0.8374 (tp-100) cc_final: 0.8148 (tp40) REVERT: E 159 TRP cc_start: 0.8091 (t60) cc_final: 0.7531 (t60) REVERT: E 160 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7846 (mm-40) REVERT: C 243 LEU cc_start: 0.0749 (OUTLIER) cc_final: -0.0613 (tt) REVERT: C 307 GLN cc_start: 0.7430 (mp-120) cc_final: 0.7135 (mp10) REVERT: C 394 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: C 428 ILE cc_start: 0.4034 (OUTLIER) cc_final: 0.3813 (mp) REVERT: C 506 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.7910 (tp) REVERT: C 523 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7325 (t70) REVERT: C 544 LYS cc_start: 0.8214 (tptt) cc_final: 0.7819 (tptt) REVERT: C 583 TRP cc_start: 0.6383 (m100) cc_final: 0.6095 (m100) REVERT: C 587 GLU cc_start: 0.7603 (mp0) cc_final: 0.7388 (mp0) REVERT: C 615 ARG cc_start: 0.8518 (ttt-90) cc_final: 0.8244 (ttt-90) REVERT: C 662 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.6953 (mm) REVERT: C 754 VAL cc_start: 0.5253 (OUTLIER) cc_final: 0.4979 (t) outliers start: 129 outliers final: 93 residues processed: 537 average time/residue: 0.3631 time to fit residues: 301.9896 Evaluate side-chains 540 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 434 time to evaluate : 3.119 ------------------------------------------------------------------------------- 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 327 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 416 HIS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 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 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 430 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 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 676 VAL 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 757 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 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 410 VAL 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 461 THR Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 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 567 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 630 TYR Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 796 TYR 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: 3.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 148 optimal weight: 0.0370 chunk 257 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 12 optimal weight: 40.0000 chunk 144 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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 B 710 HIS F 47 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.209467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160906 restraints weight = 49106.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166968 restraints weight = 26113.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168178 restraints weight = 13217.279| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22452 Z= 0.259 Angle : 0.662 12.773 30578 Z= 0.333 Chirality : 0.047 0.328 3524 Planarity : 0.005 0.066 3793 Dihedral : 6.026 85.850 3334 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.90 % Favored : 94.91 % Rotamer: Outliers : 4.69 % Allowed : 24.53 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.16), residues: 2672 helix: 1.00 (0.30), residues: 313 sheet: -0.06 (0.18), residues: 770 loop : -0.81 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 449 HIS 0.020 0.001 HIS F 47 PHE 0.026 0.001 PHE C 703 TYR 0.017 0.001 TYR B 466 ARG 0.009 0.001 ARG C 647 *********************** 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 569 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 451 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7258 (tp30) cc_final: 0.6984 (tp30) REVERT: A 254 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7601 (mmtm) REVERT: A 270 GLN cc_start: 0.7788 (pm20) cc_final: 0.7319 (pm20) REVERT: A 374 GLU cc_start: 0.6644 (mp0) cc_final: 0.6149 (mp0) REVERT: A 469 SER cc_start: 0.7827 (m) cc_final: 0.7480 (t) REVERT: A 497 GLU cc_start: 0.6894 (tt0) cc_final: 0.6595 (tp30) REVERT: A 521 SER cc_start: 0.8034 (p) cc_final: 0.7748 (m) REVERT: A 574 TYR cc_start: 0.8289 (p90) cc_final: 0.8068 (p90) REVERT: A 587 GLU cc_start: 0.7716 (mp0) cc_final: 0.7430 (mp0) REVERT: A 607 TYR cc_start: 0.6604 (m-10) cc_final: 0.6400 (m-10) REVERT: A 669 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8766 (mmmm) REVERT: A 823 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7516 (tttm) REVERT: B 355 LYS cc_start: 0.7401 (tppp) cc_final: 0.7168 (tptm) REVERT: B 375 LYS cc_start: 0.7562 (tptm) cc_final: 0.7260 (tptm) REVERT: B 407 TYR cc_start: 0.8161 (p90) cc_final: 0.7872 (p90) REVERT: B 439 ASP cc_start: 0.8042 (t0) cc_final: 0.7617 (t70) REVERT: B 486 LYS cc_start: 0.8208 (tppt) cc_final: 0.7852 (tptp) REVERT: B 544 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7400 (mtmm) REVERT: B 669 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8431 (mtpp) REVERT: B 700 LYS cc_start: 0.8456 (pttt) cc_final: 0.8236 (pttt) REVERT: B 788 ILE cc_start: 0.8133 (tp) cc_final: 0.7910 (tp) REVERT: D 149 ARG cc_start: 0.7398 (ptp-170) cc_final: 0.7004 (ptp-170) REVERT: F 26 LYS cc_start: 0.7571 (tptp) cc_final: 0.7203 (tptp) REVERT: F 43 ASN cc_start: 0.8267 (m-40) cc_final: 0.7850 (m-40) REVERT: F 89 MET cc_start: 0.8034 (mtt) cc_final: 0.7775 (mtt) REVERT: F 161 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8035 (mp) REVERT: E 74 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7508 (ttmt) REVERT: E 83 GLN cc_start: 0.8017 (tp40) cc_final: 0.7697 (tp40) REVERT: E 89 MET cc_start: 0.8523 (mpp) cc_final: 0.7942 (mtm) REVERT: E 96 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7732 (tm-30) REVERT: E 159 TRP cc_start: 0.8096 (t60) cc_final: 0.7572 (t60) REVERT: E 160 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7872 (mm-40) REVERT: C 243 LEU cc_start: 0.0492 (OUTLIER) cc_final: -0.1138 (tt) REVERT: C 307 GLN cc_start: 0.7295 (mp-120) cc_final: 0.7030 (mp10) REVERT: C 394 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5031 (m-10) REVERT: C 523 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7304 (t70) REVERT: C 544 LYS cc_start: 0.8192 (tptt) cc_final: 0.7810 (tptt) REVERT: C 583 TRP cc_start: 0.6420 (m100) cc_final: 0.6091 (m100) REVERT: C 615 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8261 (ttt-90) REVERT: C 662 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.6894 (mm) REVERT: C 771 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7057 (tt) REVERT: C 774 TRP cc_start: 0.6356 (p90) cc_final: 0.5799 (p90) outliers start: 118 outliers final: 92 residues processed: 528 average time/residue: 0.3406 time to fit residues: 277.2690 Evaluate side-chains 539 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 440 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 384 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 400 LYS 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 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 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 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 430 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 548 THR 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 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 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN 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 F residue 161 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 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 447 CYS 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 609 VAL Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 675 SER Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 771 ILE 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: 8.9990 chunk 192 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 197 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 139 optimal weight: 0.0050 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.206324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156965 restraints weight = 48466.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162953 restraints weight = 25479.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.164316 restraints weight = 13391.526| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 22452 Z= 0.355 Angle : 0.709 14.026 30578 Z= 0.357 Chirality : 0.048 0.320 3524 Planarity : 0.005 0.068 3793 Dihedral : 6.085 83.529 3334 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.82 % Rotamer: Outliers : 5.05 % Allowed : 24.81 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.16), residues: 2672 helix: 0.75 (0.29), residues: 315 sheet: -0.13 (0.18), residues: 768 loop : -0.86 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 449 HIS 0.007 0.001 HIS B 467 PHE 0.027 0.001 PHE B 500 TYR 0.024 0.002 TYR B 422 ARG 0.012 0.001 ARG C 647 *********************** 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 574 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 447 time to evaluate : 2.394 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: 0.7327 (tp30) cc_final: 0.7066 (tp30) REVERT: A 254 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7667 (mmtm) REVERT: A 270 GLN cc_start: 0.7735 (pm20) cc_final: 0.7351 (pm20) REVERT: A 459 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5945 (pp20) REVERT: A 469 SER cc_start: 0.7763 (m) cc_final: 0.7436 (t) REVERT: A 497 GLU cc_start: 0.6881 (tt0) cc_final: 0.6584 (tp30) REVERT: A 521 SER cc_start: 0.8047 (p) cc_final: 0.7743 (m) REVERT: A 587 GLU cc_start: 0.7859 (mp0) cc_final: 0.7552 (mp0) REVERT: A 731 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: A 768 MET cc_start: 0.6048 (pmm) cc_final: 0.5833 (pmm) REVERT: A 770 PHE cc_start: 0.6543 (m-80) cc_final: 0.6219 (m-10) REVERT: A 823 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7451 (tttm) REVERT: B 355 LYS cc_start: 0.7499 (tppp) cc_final: 0.7267 (tptm) REVERT: B 407 TYR cc_start: 0.8152 (p90) cc_final: 0.7838 (p90) REVERT: B 439 ASP cc_start: 0.8076 (t0) cc_final: 0.7753 (t70) REVERT: B 448 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6749 (mtp85) REVERT: B 486 LYS cc_start: 0.8351 (tppt) cc_final: 0.7597 (tptp) REVERT: B 544 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7442 (mtmm) REVERT: B 700 LYS cc_start: 0.8477 (pttt) cc_final: 0.8271 (pttt) REVERT: B 788 ILE cc_start: 0.8183 (tp) cc_final: 0.7905 (tp) REVERT: D 149 ARG cc_start: 0.7430 (ptp-170) cc_final: 0.7046 (ptp-170) REVERT: F 26 LYS cc_start: 0.7660 (tptp) cc_final: 0.7336 (tptp) REVERT: F 43 ASN cc_start: 0.8285 (m-40) cc_final: 0.8038 (m-40) REVERT: F 89 MET cc_start: 0.8096 (mtt) cc_final: 0.7857 (mtt) REVERT: E 74 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7701 (ttmt) REVERT: E 89 MET cc_start: 0.8559 (mpp) cc_final: 0.7938 (mtm) REVERT: E 96 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8122 (tp40) REVERT: E 159 TRP cc_start: 0.8184 (t60) cc_final: 0.7683 (t60) REVERT: E 160 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7886 (mm-40) REVERT: C 243 LEU cc_start: 0.0674 (OUTLIER) cc_final: -0.0970 (tt) REVERT: C 307 GLN cc_start: 0.7427 (mp-120) cc_final: 0.7145 (mp10) REVERT: C 394 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5618 (m-80) REVERT: C 523 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7355 (t70) REVERT: C 544 LYS cc_start: 0.8232 (tptt) cc_final: 0.7859 (tptt) REVERT: C 583 TRP cc_start: 0.6406 (m100) cc_final: 0.6095 (m100) REVERT: C 615 ARG cc_start: 0.8563 (ttt-90) cc_final: 0.8250 (ttt-90) REVERT: C 662 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.6926 (mm) REVERT: C 754 VAL cc_start: 0.5037 (OUTLIER) cc_final: 0.4805 (t) REVERT: C 771 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7240 (tt) outliers start: 127 outliers final: 95 residues processed: 529 average time/residue: 0.3384 time to fit residues: 277.9114 Evaluate side-chains 545 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 440 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 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 332 ASP Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 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 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 816 MET 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 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 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 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 40 THR 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 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 109 HIS 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 447 CYS 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 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 754 VAL Chi-restraints excluded: chain C residue 771 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 118 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 166 optimal weight: 0.3980 chunk 128 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 220 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.210831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161832 restraints weight = 49032.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.166312 restraints weight = 24187.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169129 restraints weight = 14951.456| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22452 Z= 0.215 Angle : 0.693 14.347 30578 Z= 0.343 Chirality : 0.047 0.283 3524 Planarity : 0.005 0.069 3793 Dihedral : 5.841 81.747 3334 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.98 % Favored : 94.87 % Rotamer: Outliers : 4.21 % Allowed : 25.65 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (0.16), residues: 2672 helix: 0.98 (0.30), residues: 315 sheet: -0.04 (0.19), residues: 764 loop : -0.78 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 449 HIS 0.018 0.001 HIS A 798 PHE 0.028 0.001 PHE C 703 TYR 0.017 0.001 TYR B 807 ARG 0.010 0.001 ARG C 647 *********************** 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 539 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 433 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7270 (tp30) cc_final: 0.7000 (tp30) REVERT: A 252 ASN cc_start: 0.7562 (p0) cc_final: 0.7109 (p0) REVERT: A 270 GLN cc_start: 0.7637 (pm20) cc_final: 0.7279 (pm20) REVERT: A 469 SER cc_start: 0.7740 (m) cc_final: 0.7419 (t) REVERT: A 521 SER cc_start: 0.7904 (p) cc_final: 0.7567 (m) REVERT: A 587 GLU cc_start: 0.7757 (mp0) cc_final: 0.7474 (mp0) REVERT: A 694 ASP cc_start: 0.7126 (t0) cc_final: 0.6841 (t0) REVERT: A 769 TYR cc_start: 0.7412 (p90) cc_final: 0.7076 (p90) REVERT: A 771 ILE cc_start: 0.8730 (mm) cc_final: 0.8530 (mm) REVERT: A 823 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7482 (tttm) REVERT: B 355 LYS cc_start: 0.7361 (tppp) cc_final: 0.7117 (tptm) REVERT: B 407 TYR cc_start: 0.8174 (p90) cc_final: 0.7930 (p90) REVERT: B 439 ASP cc_start: 0.8068 (t0) cc_final: 0.7743 (t70) REVERT: B 486 LYS cc_start: 0.8369 (tppt) cc_final: 0.7642 (tptp) REVERT: B 544 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7371 (mtmm) REVERT: B 700 LYS cc_start: 0.8413 (pttt) cc_final: 0.8205 (pttt) REVERT: D 149 ARG cc_start: 0.7286 (ptp-170) cc_final: 0.6886 (ptp-170) REVERT: F 26 LYS cc_start: 0.7533 (tptp) cc_final: 0.7229 (tptp) REVERT: F 43 ASN cc_start: 0.8251 (m-40) cc_final: 0.7817 (m-40) REVERT: F 89 MET cc_start: 0.7930 (mtt) cc_final: 0.7709 (mtt) REVERT: E 74 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7390 (ttmt) REVERT: E 83 GLN cc_start: 0.7945 (tp40) cc_final: 0.7572 (tp40) REVERT: E 89 MET cc_start: 0.8556 (mpp) cc_final: 0.7893 (mtm) REVERT: E 96 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7832 (tp40) REVERT: E 159 TRP cc_start: 0.8139 (t60) cc_final: 0.7652 (t60) REVERT: E 160 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7882 (mm-40) REVERT: C 243 LEU cc_start: 0.0294 (OUTLIER) cc_final: -0.2650 (pt) REVERT: C 307 GLN cc_start: 0.7273 (mp-120) cc_final: 0.7034 (mp10) REVERT: C 394 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.5716 (m-80) REVERT: C 495 PHE cc_start: 0.8391 (m-80) cc_final: 0.8150 (m-80) REVERT: C 523 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7276 (t70) REVERT: C 544 LYS cc_start: 0.8232 (tptt) cc_final: 0.7842 (tptt) REVERT: C 583 TRP cc_start: 0.6384 (m100) cc_final: 0.6122 (m100) REVERT: C 615 ARG cc_start: 0.8536 (ttt-90) cc_final: 0.8273 (ttt-90) REVERT: C 647 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8118 (ttp80) REVERT: C 662 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6659 (mm) REVERT: C 754 VAL cc_start: 0.5227 (OUTLIER) cc_final: 0.4984 (t) REVERT: C 771 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7059 (tt) outliers start: 106 outliers final: 92 residues processed: 502 average time/residue: 0.3336 time to fit residues: 258.8622 Evaluate side-chains 534 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 435 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 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 332 ASP Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 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 685 THR 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 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 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 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 548 THR 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 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 119 LEU 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 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 109 HIS 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 447 CYS 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 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 754 VAL Chi-restraints excluded: chain C residue 771 ILE 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: 6.9990 chunk 151 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 223 optimal weight: 8.9990 chunk 134 optimal weight: 0.0980 chunk 238 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 123 optimal weight: 0.0050 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.210656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161735 restraints weight = 49620.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166221 restraints weight = 24473.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169067 restraints weight = 15167.452| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22452 Z= 0.204 Angle : 0.688 14.581 30578 Z= 0.339 Chirality : 0.046 0.293 3524 Planarity : 0.004 0.068 3793 Dihedral : 5.631 79.081 3334 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 3.94 % Allowed : 25.88 % Favored : 70.18 % 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: -0.47 (0.16), residues: 2672 helix: 1.08 (0.30), residues: 315 sheet: 0.01 (0.19), residues: 762 loop : -0.74 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 449 HIS 0.006 0.001 HIS E 47 PHE 0.027 0.001 PHE C 703 TYR 0.022 0.001 TYR A 795 ARG 0.011 0.000 ARG C 647 ********************** 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 550 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 451 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7242 (tp30) cc_final: 0.6967 (tp30) REVERT: A 252 ASN cc_start: 0.7571 (p0) cc_final: 0.7105 (p0) REVERT: A 270 GLN cc_start: 0.7650 (pm20) cc_final: 0.7322 (pm20) REVERT: A 395 ASN cc_start: 0.7645 (p0) cc_final: 0.7271 (p0) REVERT: A 422 TYR cc_start: 0.8580 (p90) cc_final: 0.8315 (p90) REVERT: A 469 SER cc_start: 0.7773 (m) cc_final: 0.7471 (t) REVERT: A 521 SER cc_start: 0.7894 (p) cc_final: 0.7557 (m) REVERT: A 548 THR cc_start: 0.7460 (p) cc_final: 0.5917 (m) REVERT: A 587 GLU cc_start: 0.7723 (mp0) cc_final: 0.7433 (mp0) REVERT: A 731 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: A 771 ILE cc_start: 0.8671 (mm) cc_final: 0.8464 (mm) REVERT: B 355 LYS cc_start: 0.7338 (tppp) cc_final: 0.7083 (tptm) REVERT: B 407 TYR cc_start: 0.8132 (p90) cc_final: 0.7897 (p90) REVERT: B 439 ASP cc_start: 0.8077 (t0) cc_final: 0.7713 (t70) REVERT: B 486 LYS cc_start: 0.8385 (tppt) cc_final: 0.7648 (tptp) REVERT: B 544 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7363 (mtmm) REVERT: B 700 LYS cc_start: 0.8418 (pttt) cc_final: 0.8203 (pttt) REVERT: D 149 ARG cc_start: 0.7254 (ptp-170) cc_final: 0.6950 (ptp-170) REVERT: F 26 LYS cc_start: 0.7484 (tptp) cc_final: 0.7174 (tptp) REVERT: F 43 ASN cc_start: 0.8198 (m-40) cc_final: 0.7920 (m-40) REVERT: F 156 ASP cc_start: 0.7594 (m-30) cc_final: 0.7317 (m-30) REVERT: E 74 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7456 (ttmt) REVERT: E 83 GLN cc_start: 0.7926 (tp40) cc_final: 0.7563 (tp40) REVERT: E 89 MET cc_start: 0.8511 (mpp) cc_final: 0.7789 (mtm) REVERT: E 96 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7802 (tp40) REVERT: E 159 TRP cc_start: 0.8092 (t60) cc_final: 0.7638 (t60) REVERT: E 160 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7918 (mm-40) REVERT: C 243 LEU cc_start: 0.0102 (OUTLIER) cc_final: -0.2804 (pt) REVERT: C 307 GLN cc_start: 0.7262 (mp-120) cc_final: 0.7026 (mp10) REVERT: C 394 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5613 (m-80) REVERT: C 484 GLU cc_start: 0.8090 (mp0) cc_final: 0.7804 (mp0) REVERT: C 495 PHE cc_start: 0.8422 (m-80) cc_final: 0.8119 (m-80) REVERT: C 544 LYS cc_start: 0.8203 (tptt) cc_final: 0.7919 (tptt) REVERT: C 546 GLU cc_start: 0.7624 (pm20) cc_final: 0.7381 (pm20) REVERT: C 583 TRP cc_start: 0.6462 (m100) cc_final: 0.6241 (m100) REVERT: C 615 ARG cc_start: 0.8500 (ttt-90) cc_final: 0.8230 (ttt-90) REVERT: C 647 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8114 (ttp80) REVERT: C 662 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6560 (mm) REVERT: C 754 VAL cc_start: 0.5108 (OUTLIER) cc_final: 0.4877 (t) REVERT: C 771 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7059 (tt) outliers start: 99 outliers final: 85 residues processed: 512 average time/residue: 0.3412 time to fit residues: 269.8283 Evaluate side-chains 531 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 440 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 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 332 ASP Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 454 ILE 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 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS 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 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 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 119 LEU 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 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 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 447 CYS Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 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 754 VAL Chi-restraints excluded: chain C residue 771 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 218 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS B 710 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.205930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155898 restraints weight = 48214.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160217 restraints weight = 23899.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162906 restraints weight = 14856.559| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 22452 Z= 0.424 Angle : 0.777 15.879 30578 Z= 0.394 Chirality : 0.049 0.375 3524 Planarity : 0.005 0.069 3793 Dihedral : 5.996 76.690 3334 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.15 % Rotamer: Outliers : 4.25 % Allowed : 25.92 % Favored : 69.82 % 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: -0.78 (0.16), residues: 2672 helix: 0.58 (0.29), residues: 315 sheet: -0.20 (0.19), residues: 758 loop : -0.89 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A 449 HIS 0.029 0.002 HIS A 798 PHE 0.034 0.002 PHE B 500 TYR 0.030 0.002 TYR B 422 ARG 0.031 0.001 ARG B 787 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9969.19 seconds wall clock time: 180 minutes 24.55 seconds (10824.55 seconds total)