Starting phenix.real_space_refine on Sun Sep 29 09:19:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x81_38132/09_2024/8x81_38132.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x81_38132/09_2024/8x81_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x81_38132/09_2024/8x81_38132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x81_38132/09_2024/8x81_38132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x81_38132/09_2024/8x81_38132.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x81_38132/09_2024/8x81_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-5461/modules/chem_data/mon_lib" Total number of atoms: 21875 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 715} Chain breaks: 1 Chain: "B" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 715} Chain breaks: 1 Chain: "D" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 819 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 2 Chain: "F" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "E" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1124 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "C" Number of atoms: 6168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6168 Classifications: {'peptide': 766} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 715} Chain breaks: 1 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.02, per 1000 atoms: 0.64 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: 5.46 Conformation dependent library (CDL) restraints added in 2.7 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: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.570A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.581A pdb=" N MET A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 235 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 451 through 457 removed outlier: 4.095A pdb=" N GLN A 455 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.927A pdb=" N LYS A 737 " --> pdb=" O PRO A 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.637A pdb=" N ASN B 206 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 233 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.206A pdb=" N GLN B 380 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 381 " --> pdb=" O GLN B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.766A pdb=" N SER B 456 " --> pdb=" O THR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.831A pdb=" N VAL B 535 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 733 through 737 removed outlier: 3.927A pdb=" N LYS B 737 " --> pdb=" O TRP B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 733 through 737' Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 30 through 46 removed outlier: 4.234A pdb=" N LEU D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR D 40 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 4.022A pdb=" N MET D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 144 through 159 removed outlier: 4.146A pdb=" N SER D 148 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'F' and resid 23 through 44 Processing helix chain 'F' and resid 71 through 88 removed outlier: 3.931A pdb=" N SER F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 115 Processing helix chain 'F' and resid 128 through 161 removed outlier: 3.959A pdb=" N GLY F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER F 141 " --> pdb=" O ALA F 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 44 Processing helix chain 'E' and resid 71 through 87 Processing helix chain 'E' and resid 91 through 115 removed outlier: 3.650A pdb=" N LYS E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.998A pdb=" N LEU E 128 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 129 " --> pdb=" O GLU E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 125 through 129' Processing helix chain 'E' and resid 130 through 162 removed outlier: 4.474A pdb=" N GLU E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.728A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 230 through 235 removed outlier: 3.853A pdb=" N VAL C 235 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.641A pdb=" N LEU C 457 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 673 Processing helix chain 'C' and resid 734 through 738 removed outlier: 3.639A pdb=" N VAL C 738 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.573A pdb=" N PHE A 91 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A 98 " --> pdb=" O PHE A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 133 removed outlier: 4.087A pdb=" N ASN A 128 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 4.776A pdb=" N LYS A 158 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR A 216 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS A 160 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS A 214 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.858A pdb=" N VAL A 164 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 210 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET A 211 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET A 227 " --> pdb=" O MET A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 248 removed outlier: 3.719A pdb=" N ASN A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 253 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 295 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 255 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 293 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 288 removed outlier: 3.540A pdb=" N TYR A 273 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 286 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 271 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN A 268 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS A 311 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 270 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 309 " --> pdb=" O GLN A 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AB1, first strand: chain 'A' and resid 333 through 336 removed outlier: 3.609A pdb=" N VAL A 348 " --> pdb=" O PHE A 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 339 through 343 removed outlier: 6.382A pdb=" N ILE A 340 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 428 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 342 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AB4, first strand: chain 'A' and resid 461 through 469 Processing sheet with id=AB5, first strand: chain 'A' and resid 461 through 469 removed outlier: 3.912A pdb=" N TYR A 509 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 529 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 544 through 547 removed outlier: 3.668A pdb=" N LEU A 598 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 584 through 588 removed outlier: 3.788A pdb=" N LYS A 584 " --> pdb=" O TYR A 574 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 574 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 645 through 649 removed outlier: 3.602A pdb=" N PHE A 701 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 693 through 694 removed outlier: 3.678A pdb=" N THR A 711 " --> pdb=" O HIS A 684 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS A 710 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 731 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 743 through 748 removed outlier: 3.740A pdb=" N VAL A 756 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR A 795 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 784 through 789 removed outlier: 3.525A pdb=" N LYS A 784 " --> pdb=" O TRP A 774 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.518A pdb=" N PHE B 87 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 223 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.736A pdb=" N PHE B 91 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 128 through 129 removed outlier: 4.128A pdb=" N ASN B 128 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 145 " --> pdb=" O ASN B 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 133 through 134 removed outlier: 7.113A pdb=" N LEU B 133 " --> pdb=" O LYS B 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.785A pdb=" N LEU B 161 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 184 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AC9, first strand: chain 'B' and resid 267 through 268 removed outlier: 4.096A pdb=" N GLN B 268 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS B 311 " --> pdb=" O GLN B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 339 through 343 removed outlier: 3.877A pdb=" N ILE B 428 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 374 through 375 removed outlier: 3.602A pdb=" N MET B 370 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 382 through 383 removed outlier: 3.631A pdb=" N ASP B 382 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 390 " --> pdb=" O ASP B 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AD5, first strand: chain 'B' and resid 435 through 438 removed outlier: 3.886A pdb=" N ARG B 448 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 437 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.305A pdb=" N LEU B 464 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.305A pdb=" N LEU B 464 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 541 through 547 removed outlier: 5.961A pdb=" N SER B 542 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU B 559 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 584 through 588 removed outlier: 3.503A pdb=" N VAL B 609 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 645 through 650 Processing sheet with id=AE2, first strand: chain 'B' and resid 693 through 696 removed outlier: 5.983A pdb=" N TYR B 679 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 745 through 748 removed outlier: 3.674A pdb=" N VAL B 756 " --> pdb=" O TYR B 795 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 795 " --> pdb=" O VAL B 756 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 784 through 789 removed outlier: 3.936A pdb=" N LYS B 784 " --> pdb=" O TRP B 774 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR B 769 " --> pdb=" O ILE B 814 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 814 " --> pdb=" O TYR B 769 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 771 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 35 through 36 removed outlier: 4.808A pdb=" N SER C 36 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS C 90 " --> pdb=" O SER C 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 85 through 88 removed outlier: 6.824A pdb=" N THR C 85 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN C 223 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE C 87 " --> pdb=" O GLN C 223 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 214 " --> pdb=" O HIS C 160 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 158 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 128 through 133 removed outlier: 4.196A pdb=" N ASN C 128 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 145 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 141 " --> pdb=" O TRP C 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AE9, first strand: chain 'C' and resid 241 through 247 removed outlier: 5.567A pdb=" N GLY C 242 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 258 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 268 through 271 removed outlier: 4.116A pdb=" N GLN C 268 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 275 through 276 removed outlier: 3.952A pdb=" N GLU C 275 " --> pdb=" O ARG C 282 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 282 " --> pdb=" O GLU C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 334 through 335 removed outlier: 4.342A pdb=" N ILE C 334 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 353 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 348 " --> pdb=" O PHE C 393 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 341 through 343 removed outlier: 3.729A pdb=" N THR C 342 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 428 " --> pdb=" O THR C 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 355 through 356 Processing sheet with id=AF6, first strand: chain 'C' and resid 366 through 370 Processing sheet with id=AF7, first strand: chain 'C' and resid 437 through 438 Processing sheet with id=AF8, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AF9, first strand: chain 'C' and resid 461 through 469 removed outlier: 3.611A pdb=" N TYR C 509 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 527 " --> pdb=" O MET C 511 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 544 through 547 Processing sheet with id=AG2, first strand: chain 'C' and resid 583 through 588 Processing sheet with id=AG3, first strand: chain 'C' and resid 645 through 650 removed outlier: 3.687A pdb=" N THR C 661 " --> pdb=" O ILE C 648 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN C 650 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 659 " --> pdb=" O ASN C 650 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 691 through 694 removed outlier: 4.053A pdb=" N TRP C 691 " --> pdb=" O HIS C 683 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 741 through 748 Processing sheet with id=AG6, first strand: chain 'C' and resid 785 through 789 612 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 6.39 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: 0.010 Normalize map: mean=0, sd=1: 16.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 51.570 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 22452 Z= 0.252 Angle : 0.723 13.297 30578 Z= 0.388 Chirality : 0.046 0.465 3524 Planarity : 0.005 0.125 3793 Dihedral : 16.023 117.089 8569 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.78 % Favored : 96.00 % Rotamer: Outliers : 0.40 % Allowed : 25.17 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2672 helix: 0.24 (0.31), residues: 316 sheet: 0.62 (0.20), residues: 700 loop : -0.63 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 625 HIS 0.012 0.001 HIS A 467 PHE 0.029 0.001 PHE C 703 TYR 0.032 0.001 TYR B 769 ARG 0.010 0.000 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 421 time to evaluate : 2.315 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: 0.3542 time to fit residues: 228.9529 Evaluate side-chains 422 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 412 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22452 Z= 0.315 Angle : 0.671 10.507 30578 Z= 0.340 Chirality : 0.047 0.288 3524 Planarity : 0.005 0.075 3793 Dihedral : 7.390 96.156 3353 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 3.62 % Allowed : 21.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2672 helix: 1.10 (0.30), residues: 303 sheet: 0.51 (0.19), residues: 745 loop : -0.66 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 512 HIS 0.010 0.001 HIS B 467 PHE 0.032 0.002 PHE B 500 TYR 0.026 0.002 TYR A 335 ARG 0.012 0.001 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 456 time to evaluate : 2.773 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: 0.7650 (pm20) cc_final: 0.7233 (pm20) REVERT: A 422 TYR cc_start: 0.8427 (p90) cc_final: 0.7435 (p90) REVERT: A 449 TRP cc_start: 0.7799 (p-90) cc_final: 0.7453 (p-90) REVERT: A 506 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7138 (tp) REVERT: A 694 ASP cc_start: 0.6689 (t0) cc_final: 0.6468 (t0) REVERT: A 707 GLU cc_start: 0.7637 (pp20) cc_final: 0.7314 (pp20) REVERT: B 417 GLU cc_start: 0.7688 (mp0) cc_final: 0.7474 (mp0) REVERT: B 439 ASP cc_start: 0.8066 (t0) cc_final: 0.7719 (t0) REVERT: B 444 LYS cc_start: 0.8474 (ptpt) cc_final: 0.8199 (ptpp) REVERT: B 544 LYS cc_start: 0.7723 (mtmm) cc_final: 0.7463 (mtmm) REVERT: B 550 ASN cc_start: 0.7822 (t0) cc_final: 0.7400 (t0) REVERT: B 558 TRP cc_start: 0.8610 (p90) cc_final: 0.7880 (p90) REVERT: B 559 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7373 (mm-30) REVERT: B 573 ARG cc_start: 0.7475 (ptt90) cc_final: 0.6616 (ptm-80) REVERT: B 787 ARG cc_start: 0.7370 (ttt180) cc_final: 0.7150 (tpp80) REVERT: B 788 ILE cc_start: 0.7945 (tp) cc_final: 0.7733 (tp) REVERT: F 26 LYS cc_start: 0.7537 (tptp) cc_final: 0.7275 (tptp) REVERT: F 43 ASN cc_start: 0.8328 (m-40) cc_final: 0.7909 (m-40) REVERT: F 89 MET cc_start: 0.7873 (mtt) cc_final: 0.7621 (mtt) REVERT: E 74 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7262 (ttmt) REVERT: E 83 GLN cc_start: 0.8195 (tp40) cc_final: 0.7979 (tp-100) REVERT: E 89 MET cc_start: 0.8149 (mpp) cc_final: 0.7557 (mtm) REVERT: E 159 TRP cc_start: 0.7670 (t60) cc_final: 0.7233 (t60) REVERT: E 160 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7801 (mm-40) REVERT: C 307 GLN cc_start: 0.7781 (mp-120) cc_final: 0.7530 (mp10) REVERT: C 387 HIS cc_start: 0.8985 (m-70) cc_final: 0.8758 (m-70) REVERT: C 457 LEU cc_start: 0.2597 (OUTLIER) cc_final: 0.1745 (mm) REVERT: C 544 LYS cc_start: 0.8150 (tptt) cc_final: 0.7796 (tptt) REVERT: C 615 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.8012 (mtp85) REVERT: C 625 TRP cc_start: 0.7342 (m100) cc_final: 0.7038 (m100) REVERT: C 662 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7097 (mm) outliers start: 91 outliers final: 53 residues processed: 505 average time/residue: 0.3349 time to fit residues: 259.3814 Evaluate side-chains 495 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 439 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 134 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 40.0000 chunk 164 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 239 optimal weight: 0.4980 chunk 82 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 395 ASN B 358 ASN B 610 GLN B 683 HIS B 710 HIS E 55 GLN E 96 GLN C 798 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22452 Z= 0.241 Angle : 0.600 10.656 30578 Z= 0.303 Chirality : 0.045 0.229 3524 Planarity : 0.004 0.064 3793 Dihedral : 6.490 95.554 3338 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.51 % Rotamer: Outliers : 4.02 % Allowed : 22.54 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2672 helix: 1.42 (0.31), residues: 303 sheet: 0.48 (0.19), residues: 771 loop : -0.64 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 369 HIS 0.006 0.001 HIS B 467 PHE 0.023 0.001 PHE C 828 TYR 0.016 0.001 TYR B 422 ARG 0.006 0.000 ARG C 647 *********************** 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 550 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 449 time to evaluate : 2.455 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 424 GLU cc_start: 0.8047 (pt0) cc_final: 0.7768 (pt0) REVERT: A 449 TRP cc_start: 0.7775 (p-90) cc_final: 0.7335 (p-90) REVERT: A 463 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: A 469 SER cc_start: 0.7718 (m) cc_final: 0.7217 (p) REVERT: A 823 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7234 (tttp) REVERT: B 375 LYS cc_start: 0.7520 (tptm) cc_final: 0.7224 (tptm) REVERT: B 407 TYR cc_start: 0.8115 (p90) cc_final: 0.7801 (p90) REVERT: B 417 GLU cc_start: 0.7637 (mp0) cc_final: 0.7423 (mp0) REVERT: B 439 ASP cc_start: 0.8077 (t0) cc_final: 0.7699 (t0) REVERT: B 444 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8191 (ptpp) REVERT: B 448 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6710 (mtp85) REVERT: B 544 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7373 (mtmm) REVERT: B 550 ASN cc_start: 0.7833 (t0) cc_final: 0.7390 (t0) REVERT: B 788 ILE cc_start: 0.7953 (tp) cc_final: 0.7678 (tp) REVERT: B 795 TYR cc_start: 0.7222 (t80) cc_final: 0.6952 (t80) REVERT: D 89 MET cc_start: 0.7578 (tpp) cc_final: 0.7272 (tpp) REVERT: F 26 LYS cc_start: 0.7486 (tptp) cc_final: 0.7215 (tptp) REVERT: F 43 ASN cc_start: 0.8327 (m-40) cc_final: 0.7870 (m-40) REVERT: F 47 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7109 (m170) REVERT: F 89 MET cc_start: 0.7910 (mtt) cc_final: 0.7682 (mtt) REVERT: E 89 MET cc_start: 0.8261 (mpp) cc_final: 0.7944 (mtm) REVERT: E 159 TRP cc_start: 0.7699 (t60) cc_final: 0.7306 (t60) REVERT: E 160 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7812 (mm-40) REVERT: C 307 GLN cc_start: 0.7877 (mp-120) cc_final: 0.7597 (mp10) REVERT: C 387 HIS cc_start: 0.8940 (m-70) cc_final: 0.8725 (m-70) REVERT: C 544 LYS cc_start: 0.8194 (tptt) cc_final: 0.7882 (tptt) REVERT: C 584 LYS cc_start: 0.8879 (tptm) cc_final: 0.8583 (tppt) REVERT: C 615 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.8014 (mtp85) REVERT: C 625 TRP cc_start: 0.7435 (m100) cc_final: 0.7198 (m100) REVERT: C 662 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7066 (mm) outliers start: 101 outliers final: 69 residues processed: 510 average time/residue: 0.3529 time to fit residues: 276.3807 Evaluate side-chains 508 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 434 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 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 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 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 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 792 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 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 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 660 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 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 239 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 115 optimal weight: 0.0000 chunk 162 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 257 optimal weight: 0.0040 chunk 126 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 HIS B 682 ASN B 683 HIS F 155 GLN E 55 GLN C 798 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22452 Z= 0.154 Angle : 0.584 11.742 30578 Z= 0.291 Chirality : 0.045 0.195 3524 Planarity : 0.004 0.059 3793 Dihedral : 5.893 92.357 3336 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 3.86 % Allowed : 22.78 % Favored : 73.36 % 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: -0.02 (0.16), residues: 2672 helix: 1.58 (0.30), residues: 305 sheet: 0.51 (0.19), residues: 755 loop : -0.57 (0.16), residues: 1612 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 0.018 0.001 PHE C 703 TYR 0.016 0.001 TYR B 574 ARG 0.005 0.000 ARG C 465 *********************** 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 543 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 446 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.7602 (pm20) cc_final: 0.7140 (pm20) REVERT: A 422 TYR cc_start: 0.8629 (p90) cc_final: 0.8095 (p90) REVERT: A 424 GLU cc_start: 0.8015 (pt0) cc_final: 0.7703 (pt0) REVERT: A 449 TRP cc_start: 0.7703 (p-90) cc_final: 0.7201 (p-90) REVERT: A 463 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: A 469 SER cc_start: 0.7738 (m) cc_final: 0.7202 (p) REVERT: A 521 SER cc_start: 0.8011 (p) cc_final: 0.7645 (m) REVERT: A 707 GLU cc_start: 0.7514 (pp20) cc_final: 0.7128 (pp20) REVERT: A 823 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7114 (tttp) REVERT: B 272 LYS cc_start: 0.7698 (mptt) cc_final: 0.7334 (mmtt) REVERT: B 375 LYS cc_start: 0.7410 (tptm) cc_final: 0.7098 (tptm) REVERT: B 407 TYR cc_start: 0.8107 (p90) cc_final: 0.7822 (p90) REVERT: B 417 GLU cc_start: 0.7629 (mp0) cc_final: 0.7420 (mp0) REVERT: B 439 ASP cc_start: 0.8039 (t0) cc_final: 0.7650 (t0) REVERT: B 544 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7315 (mtmm) REVERT: B 550 ASN cc_start: 0.7815 (t0) cc_final: 0.7370 (t0) REVERT: B 558 TRP cc_start: 0.8575 (p90) cc_final: 0.7907 (p90) REVERT: B 682 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6947 (p0) REVERT: B 735 MET cc_start: 0.8149 (tmm) cc_final: 0.7620 (tmm) REVERT: B 787 ARG cc_start: 0.6952 (tpp80) cc_final: 0.6703 (tpt170) REVERT: B 788 ILE cc_start: 0.7917 (tp) cc_final: 0.7620 (tp) REVERT: D 89 MET cc_start: 0.7467 (tpp) cc_final: 0.7163 (tpp) REVERT: D 149 ARG cc_start: 0.7916 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: F 26 LYS cc_start: 0.7324 (tptp) cc_final: 0.7062 (tptp) REVERT: F 43 ASN cc_start: 0.8252 (m-40) cc_final: 0.7922 (m-40) REVERT: F 75 MET cc_start: 0.7936 (ttt) cc_final: 0.6888 (ttt) REVERT: F 156 ASP cc_start: 0.7397 (m-30) cc_final: 0.7181 (m-30) REVERT: E 89 MET cc_start: 0.8236 (mpp) cc_final: 0.7869 (mtm) REVERT: E 96 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7787 (tp40) REVERT: E 141 SER cc_start: 0.7671 (m) cc_final: 0.7468 (p) REVERT: E 159 TRP cc_start: 0.7696 (t60) cc_final: 0.7334 (t60) REVERT: E 160 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7825 (mm-40) REVERT: C 307 GLN cc_start: 0.7744 (mp-120) cc_final: 0.7503 (mp10) REVERT: C 544 LYS cc_start: 0.8150 (tptt) cc_final: 0.7766 (tptt) REVERT: C 584 LYS cc_start: 0.8788 (tptm) cc_final: 0.8514 (tppt) REVERT: C 615 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.8008 (mtp85) REVERT: C 662 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7079 (mm) outliers start: 97 outliers final: 70 residues processed: 501 average time/residue: 0.3246 time to fit residues: 250.4393 Evaluate side-chains 511 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 437 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 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 699 THR Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 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 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 786 LEU Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 97 ILE 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 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 613 CYS 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 800 HIS Chi-restraints excluded: chain C residue 809 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 0 optimal weight: 90.0000 chunk 131 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 517 HIS B 683 HIS B 710 HIS F 47 HIS E 55 GLN C 268 GLN C 798 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 22452 Z= 0.320 Angle : 0.653 10.948 30578 Z= 0.332 Chirality : 0.048 0.628 3524 Planarity : 0.005 0.064 3793 Dihedral : 6.180 89.688 3336 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.87 % Rotamer: Outliers : 4.53 % Allowed : 22.58 % Favored : 72.88 % 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: -0.20 (0.16), residues: 2672 helix: 1.32 (0.29), residues: 302 sheet: 0.34 (0.19), residues: 751 loop : -0.64 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 583 HIS 0.010 0.001 HIS B 467 PHE 0.030 0.001 PHE B 500 TYR 0.023 0.002 TYR B 422 ARG 0.011 0.001 ARG C 647 *********************** 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 567 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 453 time to evaluate : 2.403 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 252 ASN cc_start: 0.7308 (p0) cc_final: 0.7068 (p0) REVERT: A 254 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7670 (mmtm) REVERT: A 422 TYR cc_start: 0.8747 (p90) cc_final: 0.8114 (p90) REVERT: A 424 GLU cc_start: 0.8109 (pt0) cc_final: 0.7832 (pt0) REVERT: A 449 TRP cc_start: 0.7755 (p-90) cc_final: 0.7393 (p-90) REVERT: A 463 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: A 469 SER cc_start: 0.7711 (m) cc_final: 0.7346 (t) REVERT: A 497 GLU cc_start: 0.6974 (tt0) cc_final: 0.6648 (tp30) REVERT: A 506 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7393 (tp) REVERT: A 521 SER cc_start: 0.7964 (p) cc_final: 0.7654 (m) REVERT: A 584 LYS cc_start: 0.8802 (pptt) cc_final: 0.8345 (pttp) REVERT: A 707 GLU cc_start: 0.7517 (pp20) cc_final: 0.7104 (pp20) REVERT: A 731 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 823 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6869 (ttmm) REVERT: B 375 LYS cc_start: 0.7623 (tptm) cc_final: 0.7279 (tptm) REVERT: B 407 TYR cc_start: 0.8128 (p90) cc_final: 0.7768 (p90) REVERT: B 417 GLU cc_start: 0.7657 (mp0) cc_final: 0.7395 (mp0) REVERT: B 439 ASP cc_start: 0.8084 (t0) cc_final: 0.7671 (t70) REVERT: B 448 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6789 (mtp85) REVERT: B 486 LYS cc_start: 0.8198 (tppt) cc_final: 0.7680 (tttm) REVERT: B 544 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7405 (mtmm) REVERT: B 550 ASN cc_start: 0.7872 (t0) cc_final: 0.7451 (t0) REVERT: B 787 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7079 (tpp80) REVERT: B 788 ILE cc_start: 0.8039 (tp) cc_final: 0.7764 (tp) REVERT: B 795 TYR cc_start: 0.7534 (t80) cc_final: 0.7176 (t80) REVERT: D 89 MET cc_start: 0.7588 (tpp) cc_final: 0.7264 (tpp) REVERT: D 149 ARG cc_start: 0.8019 (ptp-170) cc_final: 0.7432 (ptp-170) REVERT: F 26 LYS cc_start: 0.7605 (tptp) cc_final: 0.7262 (tptp) REVERT: F 43 ASN cc_start: 0.8328 (m-40) cc_final: 0.7996 (m-40) REVERT: F 47 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.6985 (m170) REVERT: F 89 MET cc_start: 0.8050 (mtt) cc_final: 0.7831 (mtt) REVERT: E 30 ASP cc_start: 0.7263 (m-30) cc_final: 0.7060 (m-30) REVERT: E 74 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7316 (ttmt) REVERT: E 89 MET cc_start: 0.8409 (mpp) cc_final: 0.8158 (mtm) REVERT: E 96 GLN cc_start: 0.8390 (tp-100) cc_final: 0.7701 (tm-30) REVERT: E 131 LEU cc_start: 0.7629 (tp) cc_final: 0.7416 (tt) REVERT: E 159 TRP cc_start: 0.7893 (t60) cc_final: 0.7415 (t60) REVERT: E 160 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7777 (mm-40) REVERT: C 307 GLN cc_start: 0.7699 (mp-120) cc_final: 0.7455 (mp10) REVERT: C 387 HIS cc_start: 0.8954 (m-70) cc_final: 0.8740 (m-70) REVERT: C 394 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5112 (m-10) REVERT: C 428 ILE cc_start: 0.3882 (OUTLIER) cc_final: 0.3623 (mp) REVERT: C 457 LEU cc_start: 0.2501 (OUTLIER) cc_final: 0.1462 (mm) REVERT: C 506 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 544 LYS cc_start: 0.8226 (tptt) cc_final: 0.7797 (tptt) REVERT: C 615 ARG cc_start: 0.8352 (ttt-90) cc_final: 0.7837 (ttt90) REVERT: C 662 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7002 (mm) REVERT: C 675 SER cc_start: 0.7782 (t) cc_final: 0.7552 (p) outliers start: 114 outliers final: 82 residues processed: 523 average time/residue: 0.3292 time to fit residues: 265.1702 Evaluate side-chains 533 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 440 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 463 GLN 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 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 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 383 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain 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 108 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 538 LEU 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 796 TYR Chi-restraints excluded: chain C residue 798 HIS Chi-restraints excluded: chain C residue 809 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 257 optimal weight: 0.0980 chunk 213 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 682 ASN B 683 HIS B 710 HIS F 155 GLN F 160 GLN E 55 GLN C 798 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22452 Z= 0.256 Angle : 0.630 11.401 30578 Z= 0.318 Chirality : 0.047 0.476 3524 Planarity : 0.004 0.065 3793 Dihedral : 6.073 88.226 3336 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.45 % Favored : 95.36 % Rotamer: Outliers : 4.41 % Allowed : 23.82 % Favored : 71.77 % 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: -0.25 (0.16), residues: 2672 helix: 1.36 (0.30), residues: 302 sheet: 0.22 (0.19), residues: 755 loop : -0.63 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 583 HIS 0.008 0.001 HIS C 798 PHE 0.023 0.001 PHE C 703 TYR 0.017 0.001 TYR B 466 ARG 0.011 0.001 ARG C 647 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 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: A 395 ASN cc_start: 0.7124 (p0) cc_final: 0.6847 (p0) REVERT: A 434 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7200 (mt) REVERT: A 449 TRP cc_start: 0.7737 (p-90) cc_final: 0.7445 (p-90) REVERT: A 463 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: A 469 SER cc_start: 0.7788 (m) cc_final: 0.7388 (t) REVERT: A 506 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7440 (tp) REVERT: A 521 SER cc_start: 0.7772 (p) cc_final: 0.7444 (m) REVERT: A 584 LYS cc_start: 0.8817 (pptt) cc_final: 0.8381 (pttp) REVERT: A 631 THR cc_start: 0.8317 (p) cc_final: 0.8016 (t) REVERT: A 636 ILE cc_start: 0.7573 (mm) cc_final: 0.7317 (tt) REVERT: A 669 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8670 (mmmm) REVERT: A 693 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 707 GLU cc_start: 0.7507 (pp20) cc_final: 0.7085 (pp20) REVERT: A 823 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7332 (tttm) REVERT: B 375 LYS cc_start: 0.7572 (tptm) cc_final: 0.7235 (tptm) REVERT: B 407 TYR cc_start: 0.8140 (p90) cc_final: 0.7800 (p90) REVERT: B 439 ASP cc_start: 0.8090 (t0) cc_final: 0.7662 (t70) REVERT: B 486 LYS cc_start: 0.8214 (tppt) cc_final: 0.7609 (tptp) REVERT: B 544 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7421 (mtmm) REVERT: B 550 ASN cc_start: 0.7871 (t0) cc_final: 0.7449 (t0) REVERT: B 558 TRP cc_start: 0.8519 (p90) cc_final: 0.7952 (p90) REVERT: B 682 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6631 (t0) REVERT: B 787 ARG cc_start: 0.7426 (tpp80) cc_final: 0.7200 (tpp80) REVERT: B 788 ILE cc_start: 0.8066 (tp) cc_final: 0.7802 (tp) REVERT: D 89 MET cc_start: 0.7571 (tpp) cc_final: 0.7223 (tpp) REVERT: D 149 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7435 (ptp-170) REVERT: F 26 LYS cc_start: 0.7540 (tptp) cc_final: 0.7227 (tptp) REVERT: F 43 ASN cc_start: 0.8368 (m-40) cc_final: 0.8012 (m-40) REVERT: E 89 MET cc_start: 0.8452 (mpp) cc_final: 0.8207 (mtm) REVERT: E 96 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8171 (tp40) REVERT: E 131 LEU cc_start: 0.7605 (tp) cc_final: 0.7405 (tt) REVERT: E 159 TRP cc_start: 0.7925 (t60) cc_final: 0.7400 (t60) REVERT: E 160 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7823 (mm-40) REVERT: C 243 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.0600 (tt) REVERT: C 307 GLN cc_start: 0.7747 (mp-120) cc_final: 0.7535 (mp10) REVERT: C 387 HIS cc_start: 0.8903 (m-70) cc_final: 0.8693 (m-70) REVERT: C 394 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.4965 (m-10) REVERT: C 428 ILE cc_start: 0.3898 (OUTLIER) cc_final: 0.3632 (mp) REVERT: C 457 LEU cc_start: 0.2512 (OUTLIER) cc_final: 0.1460 (mm) REVERT: C 544 LYS cc_start: 0.8226 (tptt) cc_final: 0.7835 (tptt) REVERT: C 615 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.8157 (ttt-90) REVERT: C 662 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6936 (mm) REVERT: C 675 SER cc_start: 0.7791 (t) cc_final: 0.7550 (p) outliers start: 111 outliers final: 80 residues processed: 517 average time/residue: 0.3400 time to fit residues: 273.2557 Evaluate side-chains 527 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 437 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 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 506 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 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 434 ILE Chi-restraints excluded: chain B residue 448 ARG 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 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 732 SER Chi-restraints excluded: chain B residue 798 HIS Chi-restraints excluded: chain D residue 34 LEU 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 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 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 800 HIS 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 248 optimal weight: 0.0570 chunk 29 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 216 optimal weight: 10.0000 chunk 143 optimal weight: 0.0570 chunk 256 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 682 ASN B 683 HIS F 160 GLN E 55 GLN C 798 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22452 Z= 0.187 Angle : 0.620 12.109 30578 Z= 0.310 Chirality : 0.048 0.716 3524 Planarity : 0.004 0.065 3793 Dihedral : 5.982 86.292 3336 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 3.98 % Allowed : 24.41 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2672 helix: 1.38 (0.30), residues: 313 sheet: 0.27 (0.19), residues: 755 loop : -0.60 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 583 HIS 0.006 0.001 HIS A 710 PHE 0.014 0.001 PHE A 336 TYR 0.013 0.001 TYR B 807 ARG 0.010 0.000 ARG C 647 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 440 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7661 (mmtm) REVERT: A 270 GLN cc_start: 0.7660 (pm20) cc_final: 0.7170 (pm20) REVERT: A 395 ASN cc_start: 0.7230 (p0) cc_final: 0.6924 (p0) REVERT: A 422 TYR cc_start: 0.8718 (p90) cc_final: 0.8119 (p90) REVERT: A 424 GLU cc_start: 0.8066 (pt0) cc_final: 0.7848 (pt0) REVERT: A 449 TRP cc_start: 0.7664 (p-90) cc_final: 0.7374 (p-90) REVERT: A 463 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: A 469 SER cc_start: 0.7840 (m) cc_final: 0.7441 (t) REVERT: A 521 SER cc_start: 0.7698 (p) cc_final: 0.7362 (m) REVERT: A 574 TYR cc_start: 0.7942 (p90) cc_final: 0.7689 (p90) REVERT: A 584 LYS cc_start: 0.8780 (pptt) cc_final: 0.8439 (pttp) REVERT: A 669 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8699 (mmmm) REVERT: A 693 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 707 GLU cc_start: 0.7538 (pp20) cc_final: 0.7094 (pp20) REVERT: A 731 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: A 771 ILE cc_start: 0.8722 (mm) cc_final: 0.8328 (mm) REVERT: A 773 GLU cc_start: 0.7324 (pm20) cc_final: 0.6979 (pm20) REVERT: A 787 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8101 (ttp80) REVERT: A 823 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7341 (tttm) REVERT: B 375 LYS cc_start: 0.7497 (tptm) cc_final: 0.7176 (tptm) REVERT: B 407 TYR cc_start: 0.8137 (p90) cc_final: 0.7813 (p90) REVERT: B 439 ASP cc_start: 0.8063 (t0) cc_final: 0.7647 (t70) REVERT: B 486 LYS cc_start: 0.8245 (tppt) cc_final: 0.7613 (tptp) REVERT: B 544 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7355 (mtmm) REVERT: B 550 ASN cc_start: 0.7871 (t0) cc_final: 0.7447 (t0) REVERT: B 682 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6855 (t0) REVERT: B 700 LYS cc_start: 0.8436 (pttt) cc_final: 0.8217 (pttt) REVERT: B 787 ARG cc_start: 0.7419 (tpp80) cc_final: 0.7181 (tpp80) REVERT: B 788 ILE cc_start: 0.8023 (tp) cc_final: 0.7760 (tp) REVERT: D 89 MET cc_start: 0.7486 (tpp) cc_final: 0.7133 (tpp) REVERT: D 149 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7368 (ptp-170) REVERT: F 26 LYS cc_start: 0.7449 (tptp) cc_final: 0.7149 (tptp) REVERT: F 43 ASN cc_start: 0.8326 (m-40) cc_final: 0.7952 (m-40) REVERT: F 156 ASP cc_start: 0.7427 (m-30) cc_final: 0.7190 (m-30) REVERT: E 89 MET cc_start: 0.8412 (mpp) cc_final: 0.8155 (mtm) REVERT: E 96 GLN cc_start: 0.8378 (tp-100) cc_final: 0.8116 (tp40) REVERT: E 159 TRP cc_start: 0.7915 (t60) cc_final: 0.7409 (t60) REVERT: E 160 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7831 (mm-40) REVERT: C 243 LEU cc_start: 0.2153 (OUTLIER) cc_final: 0.0413 (tt) REVERT: C 307 GLN cc_start: 0.7808 (mp-120) cc_final: 0.7594 (mp10) REVERT: C 387 HIS cc_start: 0.8893 (m-70) cc_final: 0.8683 (m-70) REVERT: C 428 ILE cc_start: 0.3845 (OUTLIER) cc_final: 0.3590 (mp) REVERT: C 457 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.1368 (mm) REVERT: C 484 GLU cc_start: 0.8068 (mp0) cc_final: 0.7840 (mp0) REVERT: C 506 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.7842 (tp) REVERT: C 544 LYS cc_start: 0.8188 (tptt) cc_final: 0.7783 (tptt) REVERT: C 587 GLU cc_start: 0.7617 (mp0) cc_final: 0.7395 (mp0) REVERT: C 662 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6820 (mm) REVERT: C 675 SER cc_start: 0.7728 (t) cc_final: 0.7499 (p) outliers start: 100 outliers final: 78 residues processed: 505 average time/residue: 0.3233 time to fit residues: 252.1882 Evaluate side-chains 517 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 430 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 505 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 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 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 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 669 LYS Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 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 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 3.9990 chunk 102 optimal weight: 0.0570 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 201 optimal weight: 10.0000 overall best weight: 0.4900 ------------------------------------------------------------------------------- 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 ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22452 Z= 0.206 Angle : 0.632 12.188 30578 Z= 0.314 Chirality : 0.048 0.756 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.804 84.542 3336 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 4.29 % Allowed : 24.53 % Favored : 71.17 % 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: -0.16 (0.17), residues: 2672 helix: 1.41 (0.30), residues: 313 sheet: 0.30 (0.19), residues: 757 loop : -0.60 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 583 HIS 0.006 0.001 HIS B 683 PHE 0.025 0.001 PHE C 703 TYR 0.013 0.001 TYR B 807 ARG 0.011 0.001 ARG C 647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 447 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7652 (mmtm) REVERT: A 270 GLN cc_start: 0.7614 (pm20) cc_final: 0.7164 (pm20) REVERT: A 335 TYR cc_start: 0.7717 (m-10) cc_final: 0.7212 (m-80) REVERT: A 395 ASN cc_start: 0.7358 (p0) cc_final: 0.6844 (p0) REVERT: A 422 TYR cc_start: 0.8721 (p90) cc_final: 0.8100 (p90) REVERT: A 424 GLU cc_start: 0.8077 (pt0) cc_final: 0.7873 (pt0) REVERT: A 449 TRP cc_start: 0.7658 (p-90) cc_final: 0.7373 (p-90) REVERT: A 463 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6607 (tm-30) REVERT: A 469 SER cc_start: 0.7825 (m) cc_final: 0.7428 (t) REVERT: A 521 SER cc_start: 0.7717 (p) cc_final: 0.7371 (m) REVERT: A 574 TYR cc_start: 0.7995 (p90) cc_final: 0.7740 (p90) REVERT: A 584 LYS cc_start: 0.8789 (pptt) cc_final: 0.8484 (pttp) REVERT: A 624 ASN cc_start: 0.5944 (p0) cc_final: 0.5701 (p0) REVERT: A 669 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8708 (mmmm) REVERT: A 693 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 707 GLU cc_start: 0.7523 (pp20) cc_final: 0.7079 (pp20) REVERT: A 731 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: A 771 ILE cc_start: 0.8720 (mm) cc_final: 0.8351 (mm) REVERT: A 773 GLU cc_start: 0.7456 (pm20) cc_final: 0.7123 (pm20) REVERT: A 823 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7484 (tttm) REVERT: B 375 LYS cc_start: 0.7507 (tptm) cc_final: 0.7196 (tptm) REVERT: B 407 TYR cc_start: 0.8119 (p90) cc_final: 0.7788 (p90) REVERT: B 439 ASP cc_start: 0.8059 (t0) cc_final: 0.7640 (t70) REVERT: B 486 LYS cc_start: 0.8293 (tppt) cc_final: 0.7630 (tptp) REVERT: B 544 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7382 (mtmm) REVERT: B 550 ASN cc_start: 0.7864 (t0) cc_final: 0.7444 (t0) REVERT: B 669 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8369 (mtmm) REVERT: B 682 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.6779 (t0) REVERT: B 700 LYS cc_start: 0.8425 (pttt) cc_final: 0.8221 (pttt) REVERT: D 89 MET cc_start: 0.7489 (tpp) cc_final: 0.7129 (tpp) REVERT: D 149 ARG cc_start: 0.8002 (ptp-170) cc_final: 0.7362 (ptp-170) REVERT: F 26 LYS cc_start: 0.7460 (tptp) cc_final: 0.7219 (tptp) REVERT: F 43 ASN cc_start: 0.8316 (m-40) cc_final: 0.7931 (m-40) REVERT: F 156 ASP cc_start: 0.7430 (m-30) cc_final: 0.7184 (m-30) REVERT: E 89 MET cc_start: 0.8403 (mpp) cc_final: 0.8149 (mtm) REVERT: E 96 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8108 (tp40) REVERT: C 243 LEU cc_start: 0.2155 (OUTLIER) cc_final: 0.0420 (tt) REVERT: C 307 GLN cc_start: 0.7757 (mp-120) cc_final: 0.7542 (mp10) REVERT: C 394 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: C 428 ILE cc_start: 0.3849 (OUTLIER) cc_final: 0.3590 (mp) REVERT: C 457 LEU cc_start: 0.2384 (OUTLIER) cc_final: 0.1335 (mm) REVERT: C 506 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7831 (tp) REVERT: C 544 LYS cc_start: 0.8193 (tptt) cc_final: 0.7786 (tptt) REVERT: C 662 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6795 (mm) REVERT: C 675 SER cc_start: 0.7607 (t) cc_final: 0.7306 (p) REVERT: C 703 PHE cc_start: 0.4991 (t80) cc_final: 0.4774 (t80) outliers start: 108 outliers final: 83 residues processed: 522 average time/residue: 0.3300 time to fit residues: 264.0469 Evaluate side-chains 536 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 442 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 463 GLN 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 604 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 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 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 369 TRP Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 104 optimal weight: 0.0040 chunk 187 optimal weight: 0.9980 chunk 73 optimal weight: 0.0050 chunk 215 optimal weight: 20.0000 chunk 225 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS B 682 ASN B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22452 Z= 0.198 Angle : 0.647 13.262 30578 Z= 0.322 Chirality : 0.047 0.605 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.650 82.534 3334 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 4.14 % Allowed : 25.05 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2672 helix: 1.36 (0.30), residues: 313 sheet: 0.31 (0.19), residues: 757 loop : -0.59 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 368 HIS 0.006 0.001 HIS E 47 PHE 0.024 0.001 PHE C 703 TYR 0.014 0.001 TYR B 807 ARG 0.011 0.000 ARG C 647 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 454 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7623 (mmtm) REVERT: A 270 GLN cc_start: 0.7584 (pm20) cc_final: 0.7142 (pm20) REVERT: A 395 ASN cc_start: 0.7439 (p0) cc_final: 0.7238 (p0) REVERT: A 422 TYR cc_start: 0.8714 (p90) cc_final: 0.8145 (p90) REVERT: A 449 TRP cc_start: 0.7625 (p-90) cc_final: 0.7362 (p-90) REVERT: A 463 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: A 469 SER cc_start: 0.7805 (m) cc_final: 0.7410 (t) REVERT: A 521 SER cc_start: 0.7714 (p) cc_final: 0.7371 (m) REVERT: A 574 TYR cc_start: 0.7979 (p90) cc_final: 0.7706 (p90) REVERT: A 584 LYS cc_start: 0.8775 (pptt) cc_final: 0.8416 (pttp) REVERT: A 669 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8665 (mmmm) REVERT: A 693 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 707 GLU cc_start: 0.7522 (pp20) cc_final: 0.7093 (pp20) REVERT: A 731 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: A 771 ILE cc_start: 0.8700 (mm) cc_final: 0.8320 (mm) REVERT: A 773 GLU cc_start: 0.7441 (pm20) cc_final: 0.7169 (pm20) REVERT: A 787 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8114 (ttp80) REVERT: A 823 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7386 (tttm) REVERT: B 375 LYS cc_start: 0.7505 (tptm) cc_final: 0.7193 (tptm) REVERT: B 407 TYR cc_start: 0.8127 (p90) cc_final: 0.7799 (p90) REVERT: B 439 ASP cc_start: 0.8047 (t0) cc_final: 0.7632 (t70) REVERT: B 486 LYS cc_start: 0.8280 (tppt) cc_final: 0.7619 (tptp) REVERT: B 544 LYS cc_start: 0.7697 (mtmm) cc_final: 0.7371 (mtmm) REVERT: B 550 ASN cc_start: 0.7861 (t0) cc_final: 0.7453 (t0) REVERT: B 558 TRP cc_start: 0.8503 (p90) cc_final: 0.7965 (p90) REVERT: B 669 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: B 682 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6767 (t0) REVERT: B 700 LYS cc_start: 0.8420 (pttt) cc_final: 0.8212 (pttt) REVERT: D 89 MET cc_start: 0.7486 (tpp) cc_final: 0.7120 (tpp) REVERT: D 149 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.7392 (ptp-170) REVERT: F 26 LYS cc_start: 0.7425 (tptp) cc_final: 0.7179 (tptp) REVERT: F 43 ASN cc_start: 0.8285 (m-40) cc_final: 0.7910 (m-40) REVERT: F 156 ASP cc_start: 0.7404 (m-30) cc_final: 0.7169 (m-30) REVERT: E 30 ASP cc_start: 0.7292 (m-30) cc_final: 0.7054 (m-30) REVERT: E 89 MET cc_start: 0.8428 (mpp) cc_final: 0.8172 (mtm) REVERT: E 96 GLN cc_start: 0.8384 (tp-100) cc_final: 0.8096 (tp40) REVERT: C 243 LEU cc_start: 0.2126 (OUTLIER) cc_final: 0.0393 (tt) REVERT: C 307 GLN cc_start: 0.7756 (mp-120) cc_final: 0.7545 (mp10) REVERT: C 394 PHE cc_start: 0.5813 (OUTLIER) cc_final: 0.5111 (m-80) REVERT: C 428 ILE cc_start: 0.3828 (OUTLIER) cc_final: 0.3572 (mp) REVERT: C 457 LEU cc_start: 0.2391 (OUTLIER) cc_final: 0.1347 (mm) REVERT: C 506 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.7790 (tp) REVERT: C 544 LYS cc_start: 0.8212 (tptt) cc_final: 0.7948 (tptt) REVERT: C 587 GLU cc_start: 0.7645 (mp0) cc_final: 0.7384 (mp0) REVERT: C 662 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6750 (mm) REVERT: C 675 SER cc_start: 0.7567 (t) cc_final: 0.7254 (p) outliers start: 104 outliers final: 86 residues processed: 524 average time/residue: 0.3232 time to fit residues: 260.6785 Evaluate side-chains 538 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 441 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 463 GLN 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 604 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 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 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 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 572 ILE Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 798 HIS Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS B 682 ASN B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22452 Z= 0.235 Angle : 0.680 13.192 30578 Z= 0.338 Chirality : 0.049 0.875 3524 Planarity : 0.004 0.065 3793 Dihedral : 5.659 80.788 3334 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 4.02 % Allowed : 25.25 % Favored : 70.74 % 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: -0.22 (0.17), residues: 2672 helix: 1.26 (0.30), residues: 313 sheet: 0.26 (0.19), residues: 754 loop : -0.62 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 625 HIS 0.020 0.001 HIS C 798 PHE 0.025 0.001 PHE C 828 TYR 0.015 0.001 TYR B 807 ARG 0.013 0.001 ARG C 647 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 446 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLN cc_start: 0.7640 (pm20) cc_final: 0.7248 (pm20) REVERT: A 449 TRP cc_start: 0.7587 (p-90) cc_final: 0.7365 (p-90) REVERT: A 463 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6642 (tm-30) REVERT: A 469 SER cc_start: 0.7753 (m) cc_final: 0.7372 (t) REVERT: A 521 SER cc_start: 0.7810 (p) cc_final: 0.7459 (m) REVERT: A 584 LYS cc_start: 0.8776 (pptt) cc_final: 0.8422 (pttp) REVERT: A 636 ILE cc_start: 0.7560 (mm) cc_final: 0.7328 (tt) REVERT: A 669 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8707 (mmmm) REVERT: A 693 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 707 GLU cc_start: 0.7528 (pp20) cc_final: 0.7075 (pp20) REVERT: A 731 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: A 771 ILE cc_start: 0.8708 (mm) cc_final: 0.8409 (mm) REVERT: A 787 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8121 (ttp80) REVERT: A 823 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7465 (tttm) REVERT: B 375 LYS cc_start: 0.7530 (tptm) cc_final: 0.7227 (tptm) REVERT: B 407 TYR cc_start: 0.8120 (p90) cc_final: 0.7746 (p90) REVERT: B 439 ASP cc_start: 0.8060 (t0) cc_final: 0.7632 (t70) REVERT: B 486 LYS cc_start: 0.8289 (tppt) cc_final: 0.7969 (tptp) REVERT: B 544 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7387 (mtmm) REVERT: B 550 ASN cc_start: 0.7885 (t0) cc_final: 0.7456 (t0) REVERT: B 669 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8344 (mtmm) REVERT: B 682 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6875 (t0) REVERT: B 700 LYS cc_start: 0.8426 (pttt) cc_final: 0.8217 (pttt) REVERT: B 795 TYR cc_start: 0.7609 (t80) cc_final: 0.7372 (t80) REVERT: D 149 ARG cc_start: 0.8036 (ptp-170) cc_final: 0.7415 (ptp-170) REVERT: F 26 LYS cc_start: 0.7457 (tptp) cc_final: 0.7178 (tptp) REVERT: F 43 ASN cc_start: 0.8304 (m-40) cc_final: 0.7927 (m-40) REVERT: F 156 ASP cc_start: 0.7417 (m-30) cc_final: 0.7192 (m-30) REVERT: E 89 MET cc_start: 0.8444 (mpp) cc_final: 0.8175 (mtm) REVERT: E 96 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8089 (tp40) REVERT: C 243 LEU cc_start: 0.2213 (OUTLIER) cc_final: 0.0460 (tt) REVERT: C 307 GLN cc_start: 0.7748 (mp-120) cc_final: 0.7541 (mp10) REVERT: C 394 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5039 (m-80) REVERT: C 428 ILE cc_start: 0.3859 (OUTLIER) cc_final: 0.3597 (mp) REVERT: C 457 LEU cc_start: 0.2475 (OUTLIER) cc_final: 0.1430 (mm) REVERT: C 506 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.7812 (tp) REVERT: C 523 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7278 (t70) REVERT: C 544 LYS cc_start: 0.8203 (tptt) cc_final: 0.7610 (tptt) REVERT: C 546 GLU cc_start: 0.7472 (pm20) cc_final: 0.6116 (pm20) REVERT: C 662 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6726 (mm) REVERT: C 675 SER cc_start: 0.7525 (t) cc_final: 0.7201 (p) outliers start: 101 outliers final: 86 residues processed: 512 average time/residue: 0.3341 time to fit residues: 262.7638 Evaluate side-chains 533 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 435 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 463 GLN 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 604 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain A residue 684 HIS Chi-restraints excluded: chain A residue 698 HIS Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 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 556 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 411 TYR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 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 810 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 211 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS B 682 ASN B 683 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.211190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163996 restraints weight = 48912.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168293 restraints weight = 23893.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.171011 restraints weight = 14816.914| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22452 Z= 0.246 Angle : 0.688 13.050 30578 Z= 0.341 Chirality : 0.048 0.763 3524 Planarity : 0.004 0.064 3793 Dihedral : 5.624 78.900 3334 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.83 % Favored : 95.06 % Rotamer: Outliers : 4.02 % Allowed : 25.45 % Favored : 70.54 % 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: -0.25 (0.17), residues: 2672 helix: 1.21 (0.30), residues: 313 sheet: 0.25 (0.19), residues: 754 loop : -0.63 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 368 HIS 0.006 0.001 HIS B 467 PHE 0.026 0.001 PHE C 703 TYR 0.020 0.001 TYR B 422 ARG 0.013 0.001 ARG C 647 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.50 seconds wall clock time: 116 minutes 7.66 seconds (6967.66 seconds total)