Starting phenix.real_space_refine on Thu Jun 19 02:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x81_38132/06_2025/8x81_38132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x81_38132/06_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_38132/06_2025/8x81_38132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x81_38132/06_2025/8x81_38132.map" model { file = "/net/cci-nas-00/data/ceres_data/8x81_38132/06_2025/8x81_38132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x81_38132/06_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-5710/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: 15.15, per 1000 atoms: 0.69 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: 5.26 Conformation dependent library (CDL) restraints added in 3.3 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: 3.90 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: 9.38 Time building geometry restraints manager: 6.35 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: 51.530 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: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.180 Process input model: 56.890 Find NCS groups from input model: 1.150 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 22513 Z= 0.165 Angle : 0.737 13.297 30722 Z= 0.391 Chirality : 0.046 0.465 3524 Planarity : 0.005 0.125 3793 Dihedral : 16.023 117.089 8569 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.78 % Favored : 96.00 % Rotamer: Outliers : 0.40 % Allowed : 25.17 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2672 helix: 0.24 (0.31), residues: 316 sheet: 0.62 (0.20), residues: 700 loop : -0.63 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 625 HIS 0.012 0.001 HIS A 467 PHE 0.029 0.001 PHE C 703 TYR 0.032 0.001 TYR B 769 ARG 0.010 0.000 ARG B 573 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 20) link_NAG-ASN : angle 2.94543 ( 60) link_BETA1-4 : bond 0.00502 ( 1) link_BETA1-4 : angle 0.83709 ( 3) hydrogen bonds : bond 0.16568 ( 587) hydrogen bonds : angle 6.98667 ( 1581) link_BETA1-6 : bond 0.00687 ( 1) link_BETA1-6 : angle 1.28231 ( 3) SS BOND : bond 0.00185 ( 39) SS BOND : angle 1.52230 ( 78) covalent geometry : bond 0.00369 (22452) covalent geometry : angle 0.72308 (30578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 421 time to evaluate : 4.385 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: 0.5146 time to fit residues: 336.6240 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 : 4.566 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166525 restraints weight = 50049.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171025 restraints weight = 24867.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.173842 restraints weight = 15561.282| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22513 Z= 0.218 Angle : 0.687 10.968 30722 Z= 0.344 Chirality : 0.047 0.288 3524 Planarity : 0.005 0.075 3793 Dihedral : 7.390 96.156 3353 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 3.62 % Allowed : 21.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2672 helix: 1.10 (0.30), residues: 303 sheet: 0.51 (0.19), residues: 745 loop : -0.66 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 512 HIS 0.010 0.001 HIS B 467 PHE 0.032 0.002 PHE B 500 TYR 0.026 0.002 TYR A 335 ARG 0.012 0.001 ARG B 573 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 20) link_NAG-ASN : angle 2.90030 ( 60) link_BETA1-4 : bond 0.00127 ( 1) link_BETA1-4 : angle 0.29926 ( 3) hydrogen bonds : bond 0.05661 ( 587) hydrogen bonds : angle 5.49322 ( 1581) link_BETA1-6 : bond 0.01461 ( 1) link_BETA1-6 : angle 3.10031 ( 3) SS BOND : bond 0.00444 ( 39) SS BOND : angle 1.59846 ( 78) covalent geometry : bond 0.00481 (22452) covalent geometry : angle 0.67107 (30578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 456 time to evaluate : 3.146 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: 0.7603 (pm20) cc_final: 0.7232 (pm20) REVERT: A 422 TYR cc_start: 0.8458 (p90) cc_final: 0.7501 (p90) REVERT: A 449 TRP cc_start: 0.7856 (p-90) cc_final: 0.7537 (p-90) REVERT: A 506 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7272 (tp) REVERT: A 694 ASP cc_start: 0.6639 (t0) cc_final: 0.6421 (t0) REVERT: A 707 GLU cc_start: 0.7593 (pp20) cc_final: 0.7285 (pp20) REVERT: B 439 ASP cc_start: 0.8070 (t0) cc_final: 0.7740 (t0) REVERT: B 444 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8204 (ptpp) REVERT: B 544 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7456 (mtmm) REVERT: B 550 ASN cc_start: 0.7851 (t0) cc_final: 0.7426 (t0) REVERT: B 558 TRP cc_start: 0.8618 (p90) cc_final: 0.7880 (p90) REVERT: B 559 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 573 ARG cc_start: 0.7462 (ptt90) cc_final: 0.6593 (ptm-80) REVERT: B 787 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7192 (tpp80) REVERT: B 788 ILE cc_start: 0.7968 (tp) cc_final: 0.7754 (tp) REVERT: F 26 LYS cc_start: 0.7559 (tptp) cc_final: 0.7262 (tptp) REVERT: F 43 ASN cc_start: 0.8222 (m-40) cc_final: 0.7805 (m-40) REVERT: F 89 MET cc_start: 0.7792 (mtt) cc_final: 0.7525 (mtt) REVERT: E 74 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7214 (ttmt) REVERT: E 83 GLN cc_start: 0.8170 (tp40) cc_final: 0.7963 (tp-100) REVERT: E 89 MET cc_start: 0.8153 (mpp) cc_final: 0.7498 (mtm) REVERT: E 159 TRP cc_start: 0.7719 (t60) cc_final: 0.7246 (t60) REVERT: E 160 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7784 (mm-40) REVERT: C 307 GLN cc_start: 0.7269 (mp-120) cc_final: 0.6978 (mp10) REVERT: C 387 HIS cc_start: 0.8973 (m-70) cc_final: 0.8752 (m-70) REVERT: C 457 LEU cc_start: 0.2661 (OUTLIER) cc_final: 0.1781 (mm) REVERT: C 544 LYS cc_start: 0.8184 (tptt) cc_final: 0.7821 (tptt) REVERT: C 615 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.8044 (mtp85) REVERT: C 625 TRP cc_start: 0.7343 (m100) cc_final: 0.7086 (m100) REVERT: C 662 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7125 (mm) outliers start: 91 outliers final: 53 residues processed: 505 average time/residue: 0.4021 time to fit residues: 315.3336 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 : 4.909 ------------------------------------------------------------------------------- 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: 0.9990 chunk 100 optimal weight: 5.9990 chunk 190 optimal weight: 80.0000 chunk 196 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 F 47 HIS E 96 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 = 0.4619 r_free = 0.4619 target = 0.215822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.167457 restraints weight = 49530.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171976 restraints weight = 24662.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174737 restraints weight = 15486.089| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22513 Z= 0.162 Angle : 0.618 10.634 30722 Z= 0.309 Chirality : 0.045 0.227 3524 Planarity : 0.004 0.064 3793 Dihedral : 6.412 95.468 3338 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 3.90 % Allowed : 22.58 % Favored : 73.52 % 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: -0.13 (0.16), residues: 2672 helix: 1.33 (0.30), residues: 310 sheet: 0.49 (0.19), residues: 746 loop : -0.64 (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 0.020 0.001 PHE B 500 TYR 0.017 0.001 TYR B 422 ARG 0.006 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 20) link_NAG-ASN : angle 2.37063 ( 60) link_BETA1-4 : bond 0.00629 ( 1) link_BETA1-4 : angle 0.39747 ( 3) hydrogen bonds : bond 0.04968 ( 587) hydrogen bonds : angle 5.26304 ( 1581) link_BETA1-6 : bond 0.01913 ( 1) link_BETA1-6 : angle 2.72952 ( 3) SS BOND : bond 0.00252 ( 39) SS BOND : angle 1.49253 ( 78) covalent geometry : bond 0.00368 (22452) covalent geometry : angle 0.60504 (30578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 444 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7666 (mmtt) REVERT: A 422 TYR cc_start: 0.8483 (p90) cc_final: 0.8152 (p90) REVERT: A 424 GLU cc_start: 0.7992 (pt0) cc_final: 0.7768 (pt0) REVERT: A 449 TRP cc_start: 0.7852 (p-90) cc_final: 0.7421 (p-90) REVERT: A 463 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 469 SER cc_start: 0.7795 (m) cc_final: 0.7435 (t) REVERT: A 787 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8172 (ttp80) REVERT: A 823 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7249 (tttp) REVERT: B 272 LYS cc_start: 0.7666 (mptt) cc_final: 0.7360 (mmtt) REVERT: B 375 LYS cc_start: 0.7426 (tptm) cc_final: 0.7160 (tptm) REVERT: B 407 TYR cc_start: 0.8104 (p90) cc_final: 0.7822 (p90) REVERT: B 439 ASP cc_start: 0.8077 (t0) cc_final: 0.7717 (t0) REVERT: B 444 LYS cc_start: 0.8470 (ptpt) cc_final: 0.8199 (ptpp) REVERT: B 448 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6699 (mtp85) REVERT: B 544 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7400 (mtmm) REVERT: B 550 ASN cc_start: 0.7868 (t0) cc_final: 0.7420 (t0) REVERT: B 558 TRP cc_start: 0.8622 (p90) cc_final: 0.7823 (p90) REVERT: B 787 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7321 (tpp80) REVERT: B 788 ILE cc_start: 0.7995 (tp) cc_final: 0.7744 (tp) REVERT: D 89 MET cc_start: 0.7501 (tpp) cc_final: 0.7259 (tpp) REVERT: F 26 LYS cc_start: 0.7499 (tptp) cc_final: 0.7189 (tptp) REVERT: F 43 ASN cc_start: 0.8193 (m-40) cc_final: 0.7730 (m-40) REVERT: F 47 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7161 (m170) REVERT: F 89 MET cc_start: 0.7880 (mtt) cc_final: 0.7646 (mtt) REVERT: E 89 MET cc_start: 0.8336 (mpp) cc_final: 0.7958 (mtm) REVERT: E 159 TRP cc_start: 0.7750 (t60) cc_final: 0.7374 (t60) REVERT: E 160 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7825 (mm-40) REVERT: C 307 GLN cc_start: 0.7335 (mp-120) cc_final: 0.7025 (mp10) REVERT: C 387 HIS cc_start: 0.8932 (m-70) cc_final: 0.8714 (m-70) REVERT: C 544 LYS cc_start: 0.8233 (tptt) cc_final: 0.8000 (tptt) REVERT: C 584 LYS cc_start: 0.8823 (tptm) cc_final: 0.8560 (tppt) REVERT: C 615 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.8043 (mtp85) REVERT: C 662 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7098 (mm) outliers start: 98 outliers final: 66 residues processed: 502 average time/residue: 0.3940 time to fit residues: 307.9798 Evaluate side-chains 502 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 430 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 TYR 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 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 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 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 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 51 VAL 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 480 HIS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 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: 40.0000 chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 chunk 184 optimal weight: 0.5980 chunk 254 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 C 798 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.206820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157682 restraints weight = 48473.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163740 restraints weight = 25582.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164844 restraints weight = 13471.140| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 22513 Z= 0.312 Angle : 0.732 10.961 30722 Z= 0.374 Chirality : 0.049 0.284 3524 Planarity : 0.005 0.072 3793 Dihedral : 6.536 91.549 3336 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.50 % Favored : 94.35 % Rotamer: Outliers : 5.25 % Allowed : 22.11 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2672 helix: 0.90 (0.29), residues: 301 sheet: 0.05 (0.18), residues: 770 loop : -0.80 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 774 HIS 0.015 0.002 HIS B 710 PHE 0.036 0.002 PHE B 500 TYR 0.029 0.002 TYR B 422 ARG 0.009 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.01124 ( 20) link_NAG-ASN : angle 2.88788 ( 60) link_BETA1-4 : bond 0.00763 ( 1) link_BETA1-4 : angle 0.86622 ( 3) hydrogen bonds : bond 0.06462 ( 587) hydrogen bonds : angle 5.70042 ( 1581) link_BETA1-6 : bond 0.01343 ( 1) link_BETA1-6 : angle 0.73733 ( 3) SS BOND : bond 0.00452 ( 39) SS BOND : angle 1.75260 ( 78) covalent geometry : bond 0.00689 (22452) covalent geometry : angle 0.71746 (30578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 460 time to evaluate : 2.563 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: 0.7193 (tp30) cc_final: 0.6859 (tp30) REVERT: A 254 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7674 (mmtm) REVERT: A 293 LEU cc_start: 0.8105 (tp) cc_final: 0.7877 (tp) REVERT: A 469 SER cc_start: 0.7724 (m) cc_final: 0.7407 (t) REVERT: A 506 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7482 (tp) REVERT: A 521 SER cc_start: 0.8081 (p) cc_final: 0.7828 (m) REVERT: A 574 TYR cc_start: 0.8009 (p90) cc_final: 0.7721 (p90) REVERT: A 584 LYS cc_start: 0.8806 (pptt) cc_final: 0.8373 (pttp) REVERT: A 587 GLU cc_start: 0.7680 (mp0) cc_final: 0.7372 (mp0) REVERT: A 707 GLU cc_start: 0.7513 (pp20) cc_final: 0.7064 (pp20) REVERT: A 729 LEU cc_start: 0.6275 (tp) cc_final: 0.6054 (tp) REVERT: A 731 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: A 769 TYR cc_start: 0.7360 (p90) cc_final: 0.7136 (p90) REVERT: A 823 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7319 (tttm) REVERT: B 355 LYS cc_start: 0.7606 (tppp) cc_final: 0.7358 (tptm) REVERT: B 375 LYS cc_start: 0.7633 (tptm) cc_final: 0.7320 (tptm) REVERT: B 390 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8302 (tttt) REVERT: B 392 THR cc_start: 0.8431 (t) cc_final: 0.8153 (p) REVERT: B 407 TYR cc_start: 0.8124 (p90) cc_final: 0.7810 (p90) REVERT: B 439 ASP cc_start: 0.8115 (t0) cc_final: 0.7653 (t70) REVERT: B 448 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7461 (ptp-170) REVERT: B 486 LYS cc_start: 0.8351 (tppt) cc_final: 0.7719 (tptp) REVERT: B 517 HIS cc_start: 0.8198 (t-90) cc_final: 0.7954 (t-90) REVERT: B 544 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7458 (mtmm) REVERT: B 550 ASN cc_start: 0.7923 (t0) cc_final: 0.7506 (t0) REVERT: B 700 LYS cc_start: 0.8368 (tttt) cc_final: 0.8147 (tttt) REVERT: B 787 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7148 (tpp80) REVERT: B 788 ILE cc_start: 0.8118 (tp) cc_final: 0.7852 (tp) REVERT: B 795 TYR cc_start: 0.7677 (t80) cc_final: 0.7368 (t80) REVERT: D 89 MET cc_start: 0.7691 (tpp) cc_final: 0.7427 (tpp) REVERT: D 149 ARG cc_start: 0.7321 (ptp-170) cc_final: 0.7083 (ptp-170) REVERT: F 26 LYS cc_start: 0.7771 (tptp) cc_final: 0.7387 (tptp) REVERT: F 43 ASN cc_start: 0.8354 (m-40) cc_final: 0.7913 (m-40) REVERT: F 44 ASP cc_start: 0.7657 (t0) cc_final: 0.7329 (t70) REVERT: F 89 MET cc_start: 0.8158 (mtt) cc_final: 0.7888 (mtt) REVERT: F 156 ASP cc_start: 0.7877 (m-30) cc_final: 0.7629 (m-30) REVERT: E 89 MET cc_start: 0.8535 (mpp) cc_final: 0.7864 (mtm) REVERT: E 96 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7867 (tm-30) REVERT: E 143 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 307 GLN cc_start: 0.7255 (mp-120) cc_final: 0.6948 (mp10) REVERT: C 387 HIS cc_start: 0.8954 (m-70) cc_final: 0.8748 (m-70) REVERT: C 428 ILE cc_start: 0.4021 (OUTLIER) cc_final: 0.3759 (mp) REVERT: C 457 LEU cc_start: 0.2692 (OUTLIER) cc_final: 0.1611 (mm) REVERT: C 506 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.7910 (tp) REVERT: C 523 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7286 (t70) REVERT: C 544 LYS cc_start: 0.8207 (tptt) cc_final: 0.7889 (tptt) REVERT: C 563 PHE cc_start: 0.8610 (m-80) cc_final: 0.8403 (m-80) REVERT: C 583 TRP cc_start: 0.6339 (m100) cc_final: 0.6086 (m100) REVERT: C 615 ARG cc_start: 0.8509 (ttt-90) cc_final: 0.8235 (ttt-90) REVERT: C 662 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7085 (mm) outliers start: 132 outliers final: 87 residues processed: 539 average time/residue: 0.3328 time to fit residues: 276.8734 Evaluate side-chains 545 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 448 time to evaluate : 2.445 ------------------------------------------------------------------------------- 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 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 497 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 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 436 CYS Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 645 PHE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 51 VAL 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 24 ILE Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 85 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 410 VAL 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 20 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 172 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 726 ASN C 798 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.212134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163989 restraints weight = 49899.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169458 restraints weight = 26049.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171335 restraints weight = 13954.576| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22513 Z= 0.132 Angle : 0.637 11.280 30722 Z= 0.316 Chirality : 0.046 0.425 3524 Planarity : 0.004 0.066 3793 Dihedral : 6.125 90.520 3336 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 4.57 % Allowed : 23.18 % Favored : 72.25 % 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: -0.32 (0.16), residues: 2672 helix: 1.37 (0.30), residues: 302 sheet: 0.13 (0.19), residues: 763 loop : -0.68 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 449 HIS 0.007 0.001 HIS A 710 PHE 0.015 0.001 PHE A 336 TYR 0.014 0.001 TYR B 807 ARG 0.008 0.001 ARG A 787 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 20) link_NAG-ASN : angle 2.61933 ( 60) link_BETA1-4 : bond 0.00655 ( 1) link_BETA1-4 : angle 0.64837 ( 3) hydrogen bonds : bond 0.04791 ( 587) hydrogen bonds : angle 5.31522 ( 1581) link_BETA1-6 : bond 0.01543 ( 1) link_BETA1-6 : angle 1.04550 ( 3) SS BOND : bond 0.00284 ( 39) SS BOND : angle 1.60282 ( 78) covalent geometry : bond 0.00299 (22452) covalent geometry : angle 0.62293 (30578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 449 time to evaluate : 2.261 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: 0.7181 (tp30) cc_final: 0.6884 (tp30) REVERT: A 270 GLN cc_start: 0.7790 (pm20) cc_final: 0.7283 (pm20) REVERT: A 395 ASN cc_start: 0.7144 (p0) cc_final: 0.6836 (p0) REVERT: A 434 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7316 (mt) REVERT: A 449 TRP cc_start: 0.8151 (p-90) cc_final: 0.7944 (p-90) REVERT: A 463 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: A 469 SER cc_start: 0.7739 (m) cc_final: 0.7408 (t) REVERT: A 521 SER cc_start: 0.7887 (p) cc_final: 0.7551 (m) REVERT: A 574 TYR cc_start: 0.7798 (p90) cc_final: 0.7593 (p90) REVERT: A 584 LYS cc_start: 0.8819 (pptt) cc_final: 0.8333 (pttp) REVERT: A 707 GLU cc_start: 0.7492 (pp20) cc_final: 0.7068 (pp20) REVERT: A 729 LEU cc_start: 0.6149 (tp) cc_final: 0.5935 (tp) REVERT: A 769 TYR cc_start: 0.7326 (p90) cc_final: 0.6977 (p90) REVERT: A 771 ILE cc_start: 0.8746 (mm) cc_final: 0.8453 (mm) REVERT: B 355 LYS cc_start: 0.7380 (tppp) cc_final: 0.7092 (tptm) REVERT: B 375 LYS cc_start: 0.7468 (tptm) cc_final: 0.7167 (tptm) REVERT: B 390 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8081 (tttt) REVERT: B 407 TYR cc_start: 0.8156 (p90) cc_final: 0.7901 (p90) REVERT: B 439 ASP cc_start: 0.8081 (t0) cc_final: 0.7650 (t70) REVERT: B 486 LYS cc_start: 0.8190 (tppt) cc_final: 0.7634 (tptp) REVERT: B 544 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7388 (mtmm) REVERT: B 550 ASN cc_start: 0.7877 (t0) cc_final: 0.7457 (t0) REVERT: B 669 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: B 682 ASN cc_start: 0.7230 (OUTLIER) cc_final: 0.6592 (t0) REVERT: B 700 LYS cc_start: 0.8310 (tttt) cc_final: 0.8093 (tttt) REVERT: B 787 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7094 (tpp80) REVERT: B 788 ILE cc_start: 0.8083 (tp) cc_final: 0.7747 (tp) REVERT: D 26 LYS cc_start: 0.8082 (pttp) cc_final: 0.7828 (pttp) REVERT: D 149 ARG cc_start: 0.7355 (ptp-170) cc_final: 0.6994 (ptp-170) REVERT: F 26 LYS cc_start: 0.7534 (tptp) cc_final: 0.7194 (tptp) REVERT: F 43 ASN cc_start: 0.8194 (m-40) cc_final: 0.7803 (m-40) REVERT: F 75 MET cc_start: 0.8139 (ttt) cc_final: 0.7240 (mtp) REVERT: F 89 MET cc_start: 0.8006 (mtt) cc_final: 0.7742 (mtt) REVERT: E 77 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: E 89 MET cc_start: 0.8447 (mpp) cc_final: 0.7862 (mtm) REVERT: E 96 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7866 (tm-30) REVERT: C 243 LEU cc_start: 0.0345 (OUTLIER) cc_final: -0.0961 (tt) REVERT: C 307 GLN cc_start: 0.7313 (mp-120) cc_final: 0.7040 (mp10) REVERT: C 394 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.4846 (m-10) REVERT: C 428 ILE cc_start: 0.3961 (OUTLIER) cc_final: 0.3733 (mp) REVERT: C 457 LEU cc_start: 0.2631 (OUTLIER) cc_final: 0.1555 (mm) REVERT: C 472 TYR cc_start: 0.7198 (m-80) cc_final: 0.6902 (m-80) REVERT: C 544 LYS cc_start: 0.8188 (tptt) cc_final: 0.7775 (tptt) REVERT: C 583 TRP cc_start: 0.6290 (m100) cc_final: 0.6005 (m100) REVERT: C 587 GLU cc_start: 0.7599 (mp0) cc_final: 0.7388 (mp0) REVERT: C 592 LYS cc_start: 0.8658 (ptpp) cc_final: 0.7961 (ptpp) REVERT: C 615 ARG cc_start: 0.8473 (ttt-90) cc_final: 0.8216 (ttt-90) REVERT: C 646 TRP cc_start: 0.8205 (t-100) cc_final: 0.7705 (t-100) REVERT: C 662 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7114 (mm) REVERT: C 675 SER cc_start: 0.7779 (t) cc_final: 0.7557 (p) outliers start: 115 outliers final: 81 residues processed: 520 average time/residue: 0.3335 time to fit residues: 267.6901 Evaluate side-chains 528 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 436 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 463 GLN 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 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 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 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 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 640 MET Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 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 787 ARG Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 51 VAL 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 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 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 490 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 203 optimal weight: 30.0000 chunk 198 optimal weight: 30.0000 chunk 219 optimal weight: 0.0980 chunk 31 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 243 optimal weight: 0.0020 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.0350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 683 HIS B 710 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.207242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157714 restraints weight = 48303.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.163640 restraints weight = 25478.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165181 restraints weight = 13481.559| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22513 Z= 0.229 Angle : 0.681 12.874 30722 Z= 0.341 Chirality : 0.048 0.496 3524 Planarity : 0.005 0.068 3793 Dihedral : 6.198 87.979 3336 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.39 % Favored : 94.42 % Rotamer: Outliers : 5.25 % Allowed : 22.90 % Favored : 71.85 % 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: -0.51 (0.16), residues: 2672 helix: 1.13 (0.30), residues: 302 sheet: 0.03 (0.19), residues: 753 loop : -0.80 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 449 HIS 0.009 0.001 HIS B 467 PHE 0.028 0.001 PHE B 500 TYR 0.021 0.002 TYR B 422 ARG 0.010 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00765 ( 20) link_NAG-ASN : angle 2.50602 ( 60) link_BETA1-4 : bond 0.00641 ( 1) link_BETA1-4 : angle 0.69143 ( 3) hydrogen bonds : bond 0.05637 ( 587) hydrogen bonds : angle 5.40673 ( 1581) link_BETA1-6 : bond 0.01359 ( 1) link_BETA1-6 : angle 1.18684 ( 3) SS BOND : bond 0.00317 ( 39) SS BOND : angle 1.68912 ( 78) covalent geometry : bond 0.00512 (22452) covalent geometry : angle 0.66820 (30578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 448 time to evaluate : 2.355 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: 0.7253 (tp30) cc_final: 0.6968 (tp30) REVERT: A 270 GLN cc_start: 0.7777 (pm20) cc_final: 0.7304 (pm20) REVERT: A 434 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7447 (mt) REVERT: A 469 SER cc_start: 0.7772 (m) cc_final: 0.7439 (t) REVERT: A 497 GLU cc_start: 0.6858 (tt0) cc_final: 0.6609 (tp30) REVERT: A 506 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7264 (mm) REVERT: A 521 SER cc_start: 0.7905 (p) cc_final: 0.7590 (m) REVERT: A 584 LYS cc_start: 0.8770 (pptt) cc_final: 0.8371 (pttp) REVERT: A 669 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8741 (mmmm) REVERT: A 729 LEU cc_start: 0.6146 (tp) cc_final: 0.5893 (tp) REVERT: A 731 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: A 770 PHE cc_start: 0.6557 (m-80) cc_final: 0.6312 (m-10) REVERT: B 355 LYS cc_start: 0.7488 (tppp) cc_final: 0.7250 (tptm) REVERT: B 375 LYS cc_start: 0.7579 (tptm) cc_final: 0.7266 (tptm) REVERT: B 390 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8247 (tttt) REVERT: B 407 TYR cc_start: 0.8137 (p90) cc_final: 0.7815 (p90) REVERT: B 439 ASP cc_start: 0.8082 (t0) cc_final: 0.7642 (t70) REVERT: B 448 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6821 (mtp85) REVERT: B 486 LYS cc_start: 0.8262 (tppt) cc_final: 0.7629 (tptp) REVERT: B 544 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7440 (mtmm) REVERT: B 550 ASN cc_start: 0.7922 (t0) cc_final: 0.7497 (t0) REVERT: B 682 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.6937 (t0) REVERT: B 700 LYS cc_start: 0.8384 (tttt) cc_final: 0.8155 (tttt) REVERT: B 787 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7039 (tpt90) REVERT: B 788 ILE cc_start: 0.8140 (tp) cc_final: 0.7927 (tp) REVERT: D 149 ARG cc_start: 0.7403 (ptp-170) cc_final: 0.7044 (ptp-170) REVERT: F 26 LYS cc_start: 0.7619 (tptp) cc_final: 0.7280 (tptp) REVERT: F 43 ASN cc_start: 0.8252 (m-40) cc_final: 0.7849 (m-40) REVERT: F 75 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (ttt) REVERT: F 89 MET cc_start: 0.8088 (mtt) cc_final: 0.7831 (mtt) REVERT: E 89 MET cc_start: 0.8555 (mpp) cc_final: 0.7953 (mtm) REVERT: E 96 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7746 (tm-30) REVERT: E 131 LEU cc_start: 0.7669 (tp) cc_final: 0.7421 (tt) REVERT: C 243 LEU cc_start: 0.0593 (OUTLIER) cc_final: -0.0723 (tt) REVERT: C 307 GLN cc_start: 0.7407 (mp-120) cc_final: 0.7113 (mp10) REVERT: C 394 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: C 428 ILE cc_start: 0.4003 (OUTLIER) cc_final: 0.3751 (mp) REVERT: C 457 LEU cc_start: 0.2733 (OUTLIER) cc_final: 0.1681 (mm) REVERT: C 472 TYR cc_start: 0.7365 (m-80) cc_final: 0.7080 (m-80) REVERT: C 506 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.7869 (tp) REVERT: C 544 LYS cc_start: 0.8219 (tptt) cc_final: 0.7812 (tptt) REVERT: C 583 TRP cc_start: 0.6398 (m100) cc_final: 0.6116 (m100) REVERT: C 615 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.8274 (ttt-90) REVERT: C 662 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7008 (mm) REVERT: C 675 SER cc_start: 0.7624 (t) cc_final: 0.7421 (p) REVERT: C 754 VAL cc_start: 0.5220 (OUTLIER) cc_final: 0.4999 (t) REVERT: C 771 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7212 (tt) outliers start: 132 outliers final: 98 residues processed: 530 average time/residue: 0.3526 time to fit residues: 290.6038 Evaluate side-chains 555 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 442 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 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 434 ILE Chi-restraints excluded: chain A residue 473 CYS 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 735 MET Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 815 PHE 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 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 524 SER 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 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 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 B residue 792 VAL Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 51 VAL 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 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 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 480 HIS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain C residue 771 ILE Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 221 optimal weight: 0.0000 chunk 128 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 12 optimal weight: 30.0000 chunk 144 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 682 ASN B 683 HIS B 710 HIS F 160 GLN E 43 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.210600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161660 restraints weight = 49274.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.166157 restraints weight = 24286.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168958 restraints weight = 15023.411| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22513 Z= 0.140 Angle : 0.660 13.673 30722 Z= 0.326 Chirality : 0.046 0.379 3524 Planarity : 0.004 0.066 3793 Dihedral : 5.890 86.233 3336 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.64 % Favored : 95.17 % Rotamer: Outliers : 4.77 % Allowed : 24.57 % Favored : 70.66 % 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: -0.44 (0.16), residues: 2672 helix: 1.18 (0.30), residues: 313 sheet: 0.06 (0.19), residues: 762 loop : -0.76 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 449 HIS 0.005 0.001 HIS E 47 PHE 0.025 0.001 PHE C 703 TYR 0.022 0.001 TYR A 795 ARG 0.007 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 20) link_NAG-ASN : angle 2.17763 ( 60) link_BETA1-4 : bond 0.00694 ( 1) link_BETA1-4 : angle 0.75719 ( 3) hydrogen bonds : bond 0.04751 ( 587) hydrogen bonds : angle 5.23374 ( 1581) link_BETA1-6 : bond 0.01314 ( 1) link_BETA1-6 : angle 0.96919 ( 3) SS BOND : bond 0.00329 ( 39) SS BOND : angle 1.68169 ( 78) covalent geometry : bond 0.00322 (22452) covalent geometry : angle 0.64926 (30578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 445 time to evaluate : 2.115 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: 0.7200 (tp30) cc_final: 0.6898 (tp30) REVERT: A 252 ASN cc_start: 0.7491 (p0) cc_final: 0.7122 (p0) REVERT: A 270 GLN cc_start: 0.7647 (pm20) cc_final: 0.7240 (pm20) REVERT: A 374 GLU cc_start: 0.6612 (mp0) cc_final: 0.6168 (mp0) REVERT: A 434 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7380 (mt) REVERT: A 459 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5783 (pp20) REVERT: A 469 SER cc_start: 0.7845 (m) cc_final: 0.7479 (t) REVERT: A 497 GLU cc_start: 0.6740 (tt0) cc_final: 0.6524 (tp30) REVERT: A 521 SER cc_start: 0.7774 (p) cc_final: 0.7462 (m) REVERT: A 574 TYR cc_start: 0.8053 (p90) cc_final: 0.7835 (p90) REVERT: A 584 LYS cc_start: 0.8819 (pptt) cc_final: 0.8515 (pttp) REVERT: A 667 LEU cc_start: 0.7869 (mm) cc_final: 0.7601 (mp) REVERT: A 707 GLU cc_start: 0.7418 (pp20) cc_final: 0.6973 (pp20) REVERT: A 729 LEU cc_start: 0.6029 (tp) cc_final: 0.5794 (tp) REVERT: A 770 PHE cc_start: 0.6332 (m-80) cc_final: 0.6130 (m-10) REVERT: B 355 LYS cc_start: 0.7358 (tppp) cc_final: 0.7120 (tptm) REVERT: B 375 LYS cc_start: 0.7445 (tptm) cc_final: 0.7177 (tptm) REVERT: B 407 TYR cc_start: 0.8155 (p90) cc_final: 0.7884 (p90) REVERT: B 439 ASP cc_start: 0.8070 (t0) cc_final: 0.7643 (t70) REVERT: B 486 LYS cc_start: 0.8267 (tppt) cc_final: 0.7734 (tptp) REVERT: B 544 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7368 (mtmm) REVERT: B 644 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6619 (mm-30) REVERT: B 682 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6925 (t0) REVERT: B 727 PHE cc_start: 0.7941 (m-80) cc_final: 0.7700 (m-80) REVERT: D 149 ARG cc_start: 0.7233 (ptp-170) cc_final: 0.6869 (ptp-170) REVERT: F 26 LYS cc_start: 0.7534 (tptp) cc_final: 0.7271 (tptp) REVERT: F 43 ASN cc_start: 0.8251 (m-40) cc_final: 0.7868 (m-40) REVERT: F 89 MET cc_start: 0.7954 (mtt) cc_final: 0.7726 (mtt) REVERT: E 83 GLN cc_start: 0.7931 (tp40) cc_final: 0.7572 (tp40) REVERT: E 89 MET cc_start: 0.8524 (mpp) cc_final: 0.7905 (mtm) REVERT: E 96 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7827 (tm-30) REVERT: E 131 LEU cc_start: 0.7692 (tp) cc_final: 0.7458 (tt) REVERT: C 243 LEU cc_start: 0.0266 (OUTLIER) cc_final: -0.1333 (tt) REVERT: C 307 GLN cc_start: 0.7260 (mp-120) cc_final: 0.7001 (mp10) REVERT: C 394 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.4891 (m-10) REVERT: C 428 ILE cc_start: 0.3971 (OUTLIER) cc_final: 0.3731 (mp) REVERT: C 457 LEU cc_start: 0.2666 (OUTLIER) cc_final: 0.1559 (mm) REVERT: C 472 TYR cc_start: 0.7200 (m-80) cc_final: 0.6788 (m-80) REVERT: C 544 LYS cc_start: 0.8177 (tptt) cc_final: 0.7760 (tptt) REVERT: C 583 TRP cc_start: 0.6398 (m100) cc_final: 0.6102 (m100) REVERT: C 587 GLU cc_start: 0.7665 (mp0) cc_final: 0.7403 (mp0) REVERT: C 615 ARG cc_start: 0.8481 (ttt-90) cc_final: 0.8262 (ttt-90) REVERT: C 662 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6739 (mm) REVERT: C 675 SER cc_start: 0.7449 (t) cc_final: 0.7191 (p) outliers start: 120 outliers final: 90 residues processed: 522 average time/residue: 0.3079 time to fit residues: 247.8850 Evaluate side-chains 537 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 439 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 387 HIS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 473 CYS 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 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 815 PHE 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 640 MET Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN 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 755 ILE 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 F residue 51 VAL Chi-restraints excluded: chain F residue 69 ILE 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 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 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 490 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 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 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 796 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 207 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 197 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 248 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 HIS A 798 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 683 HIS B 710 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN C 670 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.209192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.160152 restraints weight = 49345.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166391 restraints weight = 26673.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167942 restraints weight = 13858.737| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22513 Z= 0.190 Angle : 0.697 13.779 30722 Z= 0.345 Chirality : 0.047 0.327 3524 Planarity : 0.004 0.067 3793 Dihedral : 5.899 84.374 3336 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.39 % Rotamer: Outliers : 4.89 % Allowed : 25.01 % Favored : 70.10 % 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: -0.50 (0.16), residues: 2672 helix: 1.09 (0.30), residues: 313 sheet: 0.03 (0.19), residues: 757 loop : -0.79 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 449 HIS 0.006 0.001 HIS B 467 PHE 0.024 0.001 PHE B 500 TYR 0.019 0.001 TYR A 795 ARG 0.011 0.001 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 20) link_NAG-ASN : angle 2.19483 ( 60) link_BETA1-4 : bond 0.00591 ( 1) link_BETA1-4 : angle 0.72486 ( 3) hydrogen bonds : bond 0.05192 ( 587) hydrogen bonds : angle 5.30213 ( 1581) link_BETA1-6 : bond 0.01368 ( 1) link_BETA1-6 : angle 1.07157 ( 3) SS BOND : bond 0.00383 ( 39) SS BOND : angle 1.80309 ( 78) covalent geometry : bond 0.00431 (22452) covalent geometry : angle 0.68583 (30578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 452 time to evaluate : 2.207 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: 0.7246 (tp30) cc_final: 0.6962 (tp30) REVERT: A 252 ASN cc_start: 0.7555 (p0) cc_final: 0.7172 (p0) REVERT: A 270 GLN cc_start: 0.7755 (pm20) cc_final: 0.7307 (pm20) REVERT: A 374 GLU cc_start: 0.6657 (mp0) cc_final: 0.6186 (mp0) REVERT: A 459 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5872 (pp20) REVERT: A 469 SER cc_start: 0.7754 (m) cc_final: 0.7424 (t) REVERT: A 521 SER cc_start: 0.7919 (p) cc_final: 0.7559 (m) REVERT: A 667 LEU cc_start: 0.7888 (mm) cc_final: 0.7672 (mp) REVERT: A 669 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8771 (mmmt) REVERT: A 729 LEU cc_start: 0.6145 (tp) cc_final: 0.5791 (tp) REVERT: A 731 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: A 771 ILE cc_start: 0.8729 (mm) cc_final: 0.8526 (mm) REVERT: A 787 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8144 (ttp80) REVERT: B 355 LYS cc_start: 0.7448 (tppp) cc_final: 0.7197 (tptm) REVERT: B 375 LYS cc_start: 0.7552 (tptm) cc_final: 0.7242 (tptm) REVERT: B 407 TYR cc_start: 0.8132 (p90) cc_final: 0.7862 (p90) REVERT: B 439 ASP cc_start: 0.8065 (t0) cc_final: 0.7643 (t70) REVERT: B 486 LYS cc_start: 0.8359 (tppt) cc_final: 0.7719 (tptp) REVERT: B 544 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7409 (mtmm) REVERT: B 682 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.6982 (t0) REVERT: D 149 ARG cc_start: 0.7311 (ptp-170) cc_final: 0.6942 (ptp-170) REVERT: F 26 LYS cc_start: 0.7566 (tptp) cc_final: 0.7259 (tptp) REVERT: F 43 ASN cc_start: 0.8200 (m-40) cc_final: 0.7942 (m-40) REVERT: F 89 MET cc_start: 0.8021 (mtt) cc_final: 0.7799 (mtt) REVERT: E 83 GLN cc_start: 0.8010 (tp40) cc_final: 0.7707 (tp40) REVERT: E 89 MET cc_start: 0.8522 (mpp) cc_final: 0.7833 (mtm) REVERT: E 96 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7742 (tm-30) REVERT: E 131 LEU cc_start: 0.7641 (tp) cc_final: 0.7413 (tt) REVERT: E 159 TRP cc_start: 0.8098 (t60) cc_final: 0.7620 (t60) REVERT: C 243 LEU cc_start: 0.0338 (OUTLIER) cc_final: -0.1274 (tt) REVERT: C 307 GLN cc_start: 0.7320 (mp-120) cc_final: 0.7052 (mp10) REVERT: C 394 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: C 428 ILE cc_start: 0.3948 (OUTLIER) cc_final: 0.3714 (mp) REVERT: C 457 LEU cc_start: 0.2653 (OUTLIER) cc_final: 0.1619 (mm) REVERT: C 472 TYR cc_start: 0.7329 (m-80) cc_final: 0.7005 (m-80) REVERT: C 506 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 523 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7309 (t70) REVERT: C 544 LYS cc_start: 0.8169 (tptt) cc_final: 0.7768 (tptt) REVERT: C 583 TRP cc_start: 0.6471 (m100) cc_final: 0.6140 (m100) REVERT: C 612 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5861 (mtp85) REVERT: C 615 ARG cc_start: 0.8464 (ttt-90) cc_final: 0.8243 (ttt-90) REVERT: C 662 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.6850 (mm) REVERT: C 665 LYS cc_start: 0.7875 (tptp) cc_final: 0.7552 (mptp) REVERT: C 675 SER cc_start: 0.7348 (t) cc_final: 0.7073 (p) REVERT: C 754 VAL cc_start: 0.5235 (OUTLIER) cc_final: 0.5017 (t) REVERT: C 771 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7203 (tt) outliers start: 123 outliers final: 95 residues processed: 533 average time/residue: 0.3322 time to fit residues: 274.3486 Evaluate side-chains 558 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 450 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 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 815 PHE 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 372 LEU 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 682 ASN Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 710 HIS Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 51 VAL 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 55 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 109 HIS Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 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 679 TYR 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: 0.0170 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 173 optimal weight: 0.5980 chunk 166 optimal weight: 0.0980 chunk 128 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS B 351 HIS B 682 ASN B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.213942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166085 restraints weight = 48745.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170568 restraints weight = 24017.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173353 restraints weight = 14834.211| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22513 Z= 0.127 Angle : 0.690 13.858 30722 Z= 0.339 Chirality : 0.046 0.281 3524 Planarity : 0.004 0.066 3793 Dihedral : 5.703 82.639 3334 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 4.49 % Allowed : 25.33 % 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: -0.39 (0.16), residues: 2672 helix: 1.27 (0.30), residues: 313 sheet: 0.08 (0.19), residues: 757 loop : -0.73 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 449 HIS 0.016 0.001 HIS A 798 PHE 0.026 0.001 PHE C 703 TYR 0.016 0.001 TYR A 795 ARG 0.008 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 20) link_NAG-ASN : angle 2.10073 ( 60) link_BETA1-4 : bond 0.00667 ( 1) link_BETA1-4 : angle 0.69478 ( 3) hydrogen bonds : bond 0.04458 ( 587) hydrogen bonds : angle 5.19008 ( 1581) link_BETA1-6 : bond 0.01421 ( 1) link_BETA1-6 : angle 0.95132 ( 3) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.73969 ( 78) covalent geometry : bond 0.00297 (22452) covalent geometry : angle 0.67983 (30578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 454 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: A 246 GLU cc_start: 0.7198 (tp30) cc_final: 0.6909 (tp30) REVERT: A 252 ASN cc_start: 0.7475 (p0) cc_final: 0.7112 (p0) REVERT: A 270 GLN cc_start: 0.7635 (pm20) cc_final: 0.7279 (pm20) REVERT: A 335 TYR cc_start: 0.7729 (m-10) cc_final: 0.7129 (m-10) REVERT: A 424 GLU cc_start: 0.8038 (pt0) cc_final: 0.7791 (pt0) REVERT: A 459 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5809 (pp20) REVERT: A 463 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6202 (tm-30) REVERT: A 469 SER cc_start: 0.7753 (m) cc_final: 0.7409 (t) REVERT: A 521 SER cc_start: 0.7800 (p) cc_final: 0.7403 (m) REVERT: A 548 THR cc_start: 0.7433 (p) cc_final: 0.5871 (m) REVERT: A 667 LEU cc_start: 0.7840 (mm) cc_final: 0.7639 (mp) REVERT: A 669 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8747 (mmmt) REVERT: A 729 LEU cc_start: 0.5982 (tp) cc_final: 0.5637 (tp) REVERT: A 731 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: B 355 LYS cc_start: 0.7362 (tppp) cc_final: 0.7104 (tptm) REVERT: B 390 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8120 (tttt) REVERT: B 407 TYR cc_start: 0.8141 (p90) cc_final: 0.7868 (p90) REVERT: B 439 ASP cc_start: 0.8069 (t0) cc_final: 0.7633 (t70) REVERT: B 486 LYS cc_start: 0.8329 (tppt) cc_final: 0.7720 (tptp) REVERT: B 544 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7354 (mtmm) REVERT: B 558 TRP cc_start: 0.8470 (p90) cc_final: 0.7951 (p90) REVERT: B 668 MET cc_start: 0.7408 (tpt) cc_final: 0.7186 (tpt) REVERT: B 700 LYS cc_start: 0.8404 (pttt) cc_final: 0.8202 (pttt) REVERT: D 149 ARG cc_start: 0.7246 (ptp-170) cc_final: 0.6876 (ptp-170) REVERT: F 26 LYS cc_start: 0.7479 (tptp) cc_final: 0.7208 (tptp) REVERT: F 43 ASN cc_start: 0.8197 (m-40) cc_final: 0.7792 (m-40) REVERT: F 89 MET cc_start: 0.7871 (mtt) cc_final: 0.7668 (mtt) REVERT: F 141 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7700 (m) REVERT: F 156 ASP cc_start: 0.7556 (m-30) cc_final: 0.7256 (m-30) REVERT: E 83 GLN cc_start: 0.7916 (tp40) cc_final: 0.7564 (tp40) REVERT: E 89 MET cc_start: 0.8494 (mpp) cc_final: 0.7759 (mtm) REVERT: E 96 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7807 (tm-30) REVERT: E 159 TRP cc_start: 0.8086 (t60) cc_final: 0.7616 (t60) REVERT: C 243 LEU cc_start: 0.0212 (OUTLIER) cc_final: -0.1377 (tt) REVERT: C 307 GLN cc_start: 0.7220 (mp-120) cc_final: 0.6967 (mp10) REVERT: C 394 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.5128 (m-80) REVERT: C 457 LEU cc_start: 0.2592 (OUTLIER) cc_final: 0.1485 (mm) REVERT: C 472 TYR cc_start: 0.7198 (m-80) cc_final: 0.6774 (m-80) REVERT: C 506 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.7354 (tt) REVERT: C 523 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7223 (t70) REVERT: C 544 LYS cc_start: 0.8241 (tptt) cc_final: 0.7817 (tptt) REVERT: C 583 TRP cc_start: 0.6402 (m100) cc_final: 0.6127 (m100) REVERT: C 615 ARG cc_start: 0.8472 (ttt-90) cc_final: 0.8194 (ttt-90) REVERT: C 662 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6664 (mm) REVERT: C 675 SER cc_start: 0.7389 (t) cc_final: 0.7108 (p) REVERT: C 754 VAL cc_start: 0.5226 (OUTLIER) cc_final: 0.5001 (t) REVERT: C 771 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7014 (tt) outliers start: 113 outliers final: 92 residues processed: 530 average time/residue: 0.3414 time to fit residues: 281.0221 Evaluate side-chains 549 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 445 time to evaluate : 2.523 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS 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 604 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 TRP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 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 778 ASN Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 51 VAL 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 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 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 679 TYR 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 186 optimal weight: 0.6980 chunk 151 optimal weight: 0.0670 chunk 168 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 212 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 223 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 B 682 ASN B 683 HIS B 710 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.213340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163660 restraints weight = 49557.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.168183 restraints weight = 24601.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.171023 restraints weight = 15313.395| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22513 Z= 0.142 Angle : 0.701 14.402 30722 Z= 0.344 Chirality : 0.046 0.278 3524 Planarity : 0.004 0.066 3793 Dihedral : 5.632 80.810 3334 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.94 % Favored : 94.91 % Rotamer: Outliers : 4.57 % Allowed : 25.13 % Favored : 70.30 % 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: -0.38 (0.16), residues: 2672 helix: 1.25 (0.30), residues: 313 sheet: 0.09 (0.19), residues: 757 loop : -0.72 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 449 HIS 0.016 0.001 HIS A 798 PHE 0.021 0.001 PHE C 645 TYR 0.017 0.001 TYR B 807 ARG 0.012 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 20) link_NAG-ASN : angle 2.10480 ( 60) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 0.74650 ( 3) hydrogen bonds : bond 0.04548 ( 587) hydrogen bonds : angle 5.15009 ( 1581) link_BETA1-6 : bond 0.01305 ( 1) link_BETA1-6 : angle 0.94294 ( 3) SS BOND : bond 0.00451 ( 39) SS BOND : angle 1.81851 ( 78) covalent geometry : bond 0.00332 (22452) covalent geometry : angle 0.68998 (30578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 449 time to evaluate : 2.297 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: 0.7233 (tp30) cc_final: 0.6941 (tp30) REVERT: A 252 ASN cc_start: 0.7521 (p0) cc_final: 0.7147 (p0) REVERT: A 270 GLN cc_start: 0.7639 (pm20) cc_final: 0.7284 (pm20) REVERT: A 331 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8437 (mm-40) REVERT: A 335 TYR cc_start: 0.7746 (m-10) cc_final: 0.7252 (m-80) REVERT: A 424 GLU cc_start: 0.8053 (pt0) cc_final: 0.7829 (pt0) REVERT: A 459 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5840 (pp20) REVERT: A 463 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: A 469 SER cc_start: 0.7813 (m) cc_final: 0.7473 (t) REVERT: A 497 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6457 (tp30) REVERT: A 521 SER cc_start: 0.7817 (p) cc_final: 0.7432 (m) REVERT: A 548 THR cc_start: 0.7439 (p) cc_final: 0.5899 (m) REVERT: A 669 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8748 (mmmt) REVERT: A 729 LEU cc_start: 0.5997 (tp) cc_final: 0.5648 (tp) REVERT: A 731 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: B 355 LYS cc_start: 0.7361 (tppp) cc_final: 0.7108 (tptm) REVERT: B 390 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8043 (tttt) REVERT: B 407 TYR cc_start: 0.8118 (p90) cc_final: 0.7860 (p90) REVERT: B 439 ASP cc_start: 0.8067 (t0) cc_final: 0.7652 (t70) REVERT: B 486 LYS cc_start: 0.8341 (tppt) cc_final: 0.8025 (tptp) REVERT: B 544 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7370 (mtmm) REVERT: B 635 ASP cc_start: 0.8037 (p0) cc_final: 0.7833 (p0) REVERT: B 668 MET cc_start: 0.7429 (tpt) cc_final: 0.7223 (tpt) REVERT: B 700 LYS cc_start: 0.8404 (pttt) cc_final: 0.8190 (pttt) REVERT: D 149 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.6951 (ptp-170) REVERT: F 26 LYS cc_start: 0.7476 (tptp) cc_final: 0.7169 (tptp) REVERT: F 43 ASN cc_start: 0.8218 (m-40) cc_final: 0.7933 (m-40) REVERT: F 156 ASP cc_start: 0.7559 (m-30) cc_final: 0.7260 (m-30) REVERT: E 77 GLN cc_start: 0.7186 (pm20) cc_final: 0.6634 (pm20) REVERT: E 83 GLN cc_start: 0.7942 (tp40) cc_final: 0.7595 (tp40) REVERT: E 89 MET cc_start: 0.8499 (mpp) cc_final: 0.8230 (mtm) REVERT: E 96 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7778 (tm-30) REVERT: E 159 TRP cc_start: 0.8081 (t60) cc_final: 0.7630 (t60) REVERT: C 243 LEU cc_start: 0.0221 (OUTLIER) cc_final: -0.1365 (tt) REVERT: C 307 GLN cc_start: 0.7313 (mp-120) cc_final: 0.7043 (mp10) REVERT: C 394 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: C 457 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1294 (mm) REVERT: C 506 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.7799 (tp) REVERT: C 523 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7223 (t70) REVERT: C 544 LYS cc_start: 0.8231 (tptt) cc_final: 0.7840 (tptt) REVERT: C 615 ARG cc_start: 0.8460 (ttt-90) cc_final: 0.8258 (ttt-90) REVERT: C 625 TRP cc_start: 0.7601 (m100) cc_final: 0.7372 (m100) REVERT: C 662 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6635 (mm) REVERT: C 675 SER cc_start: 0.7469 (t) cc_final: 0.7193 (p) REVERT: C 754 VAL cc_start: 0.5255 (OUTLIER) cc_final: 0.5035 (t) REVERT: C 771 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7062 (tt) outliers start: 115 outliers final: 92 residues processed: 526 average time/residue: 0.3231 time to fit residues: 263.0696 Evaluate side-chains 552 residues out of total 2515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 447 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 331 GLN 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 454 ILE Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 449 TRP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 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 778 ASN 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 147 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 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 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 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 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: 0.9980 chunk 91 optimal weight: 50.0000 chunk 225 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 139 optimal weight: 0.0770 chunk 116 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 107 optimal weight: 0.0770 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 682 ASN B 683 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.213361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.163675 restraints weight = 49109.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168188 restraints weight = 24276.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.171039 restraints weight = 15119.698| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 22513 Z= 0.227 Angle : 0.857 59.197 30722 Z= 0.451 Chirality : 0.046 0.306 3524 Planarity : 0.005 0.092 3793 Dihedral : 5.632 80.801 3334 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 4.41 % Allowed : 25.53 % Favored : 70.06 % Cbeta Deviations : 0.04 % 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: -0.38 (0.16), residues: 2672 helix: 1.26 (0.30), residues: 313 sheet: 0.09 (0.19), residues: 757 loop : -0.72 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 449 HIS 0.097 0.002 HIS B 710 PHE 0.019 0.001 PHE C 645 TYR 0.015 0.001 TYR B 807 ARG 0.017 0.000 ARG C 647 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 20) link_NAG-ASN : angle 2.10579 ( 60) link_BETA1-4 : bond 0.00569 ( 1) link_BETA1-4 : angle 0.78751 ( 3) hydrogen bonds : bond 0.04564 ( 587) hydrogen bonds : angle 5.15190 ( 1581) link_BETA1-6 : bond 0.01315 ( 1) link_BETA1-6 : angle 1.05019 ( 3) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.76173 ( 78) covalent geometry : bond 0.00479 (22452) covalent geometry : angle 0.84890 (30578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11334.97 seconds wall clock time: 199 minutes 45.85 seconds (11985.85 seconds total)