Starting phenix.real_space_refine on Sun Aug 24 15:07:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p31_17382/08_2025/8p31_17382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p31_17382/08_2025/8p31_17382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p31_17382/08_2025/8p31_17382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p31_17382/08_2025/8p31_17382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p31_17382/08_2025/8p31_17382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p31_17382/08_2025/8p31_17382.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 114 5.16 5 C 13420 2.51 5 N 3356 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20752 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5980 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4221 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 20, 'TRANS': 551} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 6, 'PHE:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 4, 'NDG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, D, G, H Time building chain proxies: 6.81, per 1000 atoms: 0.33 Number of scatterers: 20752 At special positions: 0 Unit cell: (133.376, 105.953, 174.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 114 16.00 O 3860 8.00 N 3356 7.00 C 13420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 903 " - " ASN A 103 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 432 " " NAG A 906 " - " ASN A 546 " " NAG B 903 " - " ASN B 103 " " NAG B 904 " - " ASN B 322 " " NAG B 905 " - " ASN B 432 " " NAG B 906 " - " ASN B 546 " " NAG C 701 " - " ASN C 131 " " NAG C 702 " - " ASN C 357 " " NAG D 701 " - " ASN D 131 " " NAG D 702 " - " ASN D 357 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 90 " " NAG G 1 " - " ASN B 690 " " NAG H 1 " - " ASN B 90 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 677.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 378 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 374 " 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4964 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 10 sheets defined 72.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.870A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.737A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.520A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 250 removed outlier: 3.800A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.722A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.210A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.801A pdb=" N LYS A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.122A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.687A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.928A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 465 removed outlier: 3.790A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.574A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.777A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.636A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.524A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.563A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 707 through 716 removed outlier: 3.503A pdb=" N ILE A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 768 Processing helix chain 'B' and resid 21 through 53 removed outlier: 3.871A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.738A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.521A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 172 through 194 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 218 through 250 removed outlier: 3.800A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.724A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.211A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.802A pdb=" N LYS B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.123A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.687A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.927A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 431 through 465 removed outlier: 3.790A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 449 " --> pdb=" O THR B 445 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.575A pdb=" N GLU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.777A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.635A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 599 Proline residue: B 590 - end of helix removed outlier: 3.524A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 removed outlier: 3.563A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 707 through 716 removed outlier: 3.503A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 768 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.837A pdb=" N TYR C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Proline residue: C 46 - end of helix removed outlier: 3.785A pdb=" N VAL C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.570A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.936A pdb=" N SER C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 85 through 115 removed outlier: 3.592A pdb=" N VAL C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 167 through 188 removed outlier: 3.527A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.626A pdb=" N TYR C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 219 through 229 removed outlier: 3.906A pdb=" N GLY C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.748A pdb=" N TRP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.647A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 322 removed outlier: 3.542A pdb=" N HIS C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.742A pdb=" N TYR C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 372 through 384 Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.591A pdb=" N TRP C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Proline residue: C 417 - end of helix Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 429 through 445 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.795A pdb=" N MET C 450 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 3.813A pdb=" N TRP C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 485 through 498 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 552 through 582 removed outlier: 3.629A pdb=" N LEU C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Proline residue: C 571 - end of helix Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.837A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Proline residue: D 46 - end of helix removed outlier: 3.786A pdb=" N VAL D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 70 removed outlier: 3.571A pdb=" N LEU D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.937A pdb=" N SER D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 115 removed outlier: 3.591A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 167 through 188 removed outlier: 3.528A pdb=" N GLY D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.627A pdb=" N TYR D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 219 through 229 removed outlier: 3.906A pdb=" N GLY D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.748A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.648A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 322 removed outlier: 3.542A pdb=" N HIS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.742A pdb=" N TYR D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 Processing helix chain 'D' and resid 372 through 384 Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.592A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Proline residue: D 417 - end of helix Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 429 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.796A pdb=" N MET D 450 " --> pdb=" O VAL D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 3.811A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 482 Processing helix chain 'D' and resid 485 through 498 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 511 through 532 Processing helix chain 'D' and resid 552 through 582 removed outlier: 3.629A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Proline residue: D 571 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.195A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.196A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA8, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA9, first strand: chain 'C' and resid 535 through 540 Processing sheet with id=AB1, first strand: chain 'D' and resid 535 through 540 1283 hydrogen bonds defined for protein. 3753 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: 2.87 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4839 1.33 - 1.45: 4871 1.45 - 1.57: 11406 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 21304 Sorted by residual: bond pdb=" C YCP D 703 " pdb=" O YCP D 703 " ideal model delta sigma weight residual 1.231 1.307 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C YCP C 703 " pdb=" O YCP C 703 " ideal model delta sigma weight residual 1.231 1.307 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NDG A 902 " pdb=" O5 NDG A 902 " ideal model delta sigma weight residual 1.392 1.428 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NDG B 902 " pdb=" O5 NDG B 902 " ideal model delta sigma weight residual 1.392 1.428 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 28561 1.96 - 3.92: 434 3.92 - 5.87: 65 5.87 - 7.83: 7 7.83 - 9.79: 5 Bond angle restraints: 29072 Sorted by residual: angle pdb=" CA PRO C 353 " pdb=" N PRO C 353 " pdb=" CD PRO C 353 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CA PRO D 353 " pdb=" N PRO D 353 " pdb=" CD PRO D 353 " ideal model delta sigma weight residual 112.00 104.21 7.79 1.40e+00 5.10e-01 3.10e+01 angle pdb=" CA YCP D 703 " pdb=" C YCP D 703 " pdb=" O YCP D 703 " ideal model delta sigma weight residual 120.80 112.67 8.13 1.70e+00 3.46e-01 2.29e+01 angle pdb=" CA YCP C 703 " pdb=" C YCP C 703 " pdb=" O YCP C 703 " ideal model delta sigma weight residual 120.80 112.69 8.11 1.70e+00 3.46e-01 2.27e+01 angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 113.71 109.63 4.08 9.50e-01 1.11e+00 1.85e+01 ... (remaining 29067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 11988 22.39 - 44.77: 580 44.77 - 67.16: 82 67.16 - 89.54: 30 89.54 - 111.93: 22 Dihedral angle restraints: 12702 sinusoidal: 4970 harmonic: 7732 Sorted by residual: dihedral pdb=" CA ASN B 718 " pdb=" C ASN B 718 " pdb=" N ASP B 719 " pdb=" CA ASP B 719 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN A 718 " pdb=" C ASN A 718 " pdb=" N ASP A 719 " pdb=" CA ASP A 719 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C3 NDG B 902 " pdb=" C4 NDG B 902 " pdb=" C5 NDG B 902 " pdb=" O5 NDG B 902 " ideal model delta sinusoidal sigma weight residual 53.31 -58.62 111.93 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 12699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2673 0.053 - 0.106: 555 0.106 - 0.159: 52 0.159 - 0.213: 2 0.213 - 0.266: 8 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C4 NDG B 902 " pdb=" C3 NDG B 902 " pdb=" C5 NDG B 902 " pdb=" O4 NDG B 902 " both_signs ideal model delta sigma weight residual False -2.30 -2.56 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3287 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 352 " 0.092 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO D 353 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO D 353 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 353 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 352 " -0.092 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO C 353 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO C 353 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 353 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 396 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C PHE D 396 " -0.081 2.00e-02 2.50e+03 pdb=" O PHE D 396 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE D 397 " 0.028 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 163 2.60 - 3.18: 18769 3.18 - 3.75: 33349 3.75 - 4.33: 44466 4.33 - 4.90: 73803 Nonbonded interactions: 170550 Sorted by model distance: nonbonded pdb=" SG CYS C 126 " pdb=" SG CYS C 139 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 309 " pdb=" SG CYS C 358 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 126 " pdb=" SG CYS D 139 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 309 " pdb=" SG CYS D 358 " model vdw 2.029 3.760 nonbonded pdb=" OH TYR C 204 " pdb=" OG1 THR C 286 " model vdw 2.129 3.040 ... (remaining 170545 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.900 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.076 21338 Z= 0.182 Angle : 0.623 9.791 29150 Z= 0.329 Chirality : 0.043 0.266 3290 Planarity : 0.005 0.134 3668 Dihedral : 14.189 111.930 7720 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.68 % Allowed : 9.65 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2634 helix: 1.47 (0.13), residues: 1684 sheet: 0.12 (0.65), residues: 58 loop : -0.63 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 30 TYR 0.016 0.001 TYR D 348 PHE 0.011 0.001 PHE D 460 TRP 0.020 0.001 TRP D 178 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00378 (21304) covalent geometry : angle 0.61100 (29072) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.73158 ( 12) hydrogen bonds : bond 0.14013 ( 1283) hydrogen bonds : angle 6.10624 ( 3753) metal coordination : bond 0.00263 ( 4) Misc. bond : bond 0.00009 ( 2) link_BETA1-4 : bond 0.01122 ( 6) link_BETA1-4 : angle 3.31669 ( 18) link_NAG-ASN : bond 0.00305 ( 16) link_NAG-ASN : angle 2.24311 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 382 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8849 (tppt) cc_final: 0.8572 (mtpt) REVERT: A 401 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.8216 (t-90) REVERT: A 435 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7787 (mt-10) REVERT: A 579 MET cc_start: 0.8931 (ptp) cc_final: 0.8705 (ptt) REVERT: A 713 ASP cc_start: 0.8575 (m-30) cc_final: 0.8323 (m-30) REVERT: B 114 LYS cc_start: 0.8809 (tppt) cc_final: 0.8532 (mtpp) REVERT: B 360 MET cc_start: 0.8221 (ttm) cc_final: 0.7897 (ttm) REVERT: B 393 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8082 (mtt90) REVERT: B 401 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.8016 (t-90) REVERT: B 435 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7676 (mt-10) REVERT: B 455 MET cc_start: 0.9022 (tmm) cc_final: 0.8715 (tmm) REVERT: C 213 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.6994 (tpm170) REVERT: C 406 SER cc_start: 0.8569 (m) cc_final: 0.8095 (p) REVERT: C 478 ILE cc_start: 0.8507 (mm) cc_final: 0.8239 (pt) REVERT: C 504 TYR cc_start: 0.8152 (t80) cc_final: 0.7555 (t80) REVERT: C 505 TRP cc_start: 0.8068 (m100) cc_final: 0.6776 (m100) REVERT: C 540 ASP cc_start: 0.7755 (t0) cc_final: 0.7552 (t0) REVERT: D 173 CYS cc_start: 0.8202 (m) cc_final: 0.7776 (m) REVERT: D 213 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7042 (tpp-160) REVERT: D 385 MET cc_start: 0.6827 (mmt) cc_final: 0.6266 (mmt) REVERT: D 406 SER cc_start: 0.8767 (m) cc_final: 0.8239 (p) REVERT: D 504 TYR cc_start: 0.8085 (t80) cc_final: 0.7438 (t80) REVERT: D 505 TRP cc_start: 0.8163 (m100) cc_final: 0.6684 (m100) REVERT: D 540 ASP cc_start: 0.7536 (t0) cc_final: 0.7295 (t0) outliers start: 14 outliers final: 2 residues processed: 394 average time/residue: 0.1330 time to fit residues: 81.0328 Evaluate side-chains 214 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 731 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 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 96 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 718 ASN B 250 ASN B 718 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 243 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.147506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.084456 restraints weight = 38198.987| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.73 r_work: 0.2970 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21338 Z= 0.129 Angle : 0.573 9.688 29150 Z= 0.287 Chirality : 0.041 0.267 3290 Planarity : 0.004 0.077 3668 Dihedral : 8.316 76.314 3352 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.54 % Allowed : 12.79 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.17), residues: 2634 helix: 1.82 (0.13), residues: 1710 sheet: 0.69 (0.67), residues: 54 loop : -0.48 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 78 TYR 0.016 0.001 TYR B 516 PHE 0.025 0.001 PHE C 523 TRP 0.014 0.001 TRP B 742 HIS 0.005 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00267 (21304) covalent geometry : angle 0.56245 (29072) SS BOND : bond 0.00303 ( 6) SS BOND : angle 1.13626 ( 12) hydrogen bonds : bond 0.04495 ( 1283) hydrogen bonds : angle 4.25858 ( 3753) metal coordination : bond 0.00127 ( 4) Misc. bond : bond 0.00045 ( 2) link_BETA1-4 : bond 0.01126 ( 6) link_BETA1-4 : angle 3.01042 ( 18) link_NAG-ASN : bond 0.00271 ( 16) link_NAG-ASN : angle 2.02640 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8483 (mp10) cc_final: 0.8237 (mp10) REVERT: A 114 LYS cc_start: 0.8998 (tppt) cc_final: 0.8568 (mtpt) REVERT: A 123 MET cc_start: 0.8789 (mtm) cc_final: 0.8583 (mtm) REVERT: A 401 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8244 (t-90) REVERT: A 408 MET cc_start: 0.9437 (mmt) cc_final: 0.9112 (mmm) REVERT: A 480 MET cc_start: 0.8744 (mtp) cc_final: 0.8446 (mtp) REVERT: A 582 ARG cc_start: 0.8850 (tpp80) cc_final: 0.8609 (mmm-85) REVERT: A 675 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.8966 (tt) REVERT: A 679 ILE cc_start: 0.8640 (mt) cc_final: 0.8410 (mm) REVERT: B 114 LYS cc_start: 0.9012 (tppt) cc_final: 0.8631 (mtpt) REVERT: B 190 MET cc_start: 0.9021 (tmm) cc_final: 0.8808 (tmm) REVERT: B 360 MET cc_start: 0.8318 (ttm) cc_final: 0.8105 (ttm) REVERT: B 366 MET cc_start: 0.8510 (ttm) cc_final: 0.8045 (mtp) REVERT: B 393 ARG cc_start: 0.8628 (mtt180) cc_final: 0.7972 (mtt90) REVERT: B 408 MET cc_start: 0.9473 (mmt) cc_final: 0.9233 (mmm) REVERT: B 430 GLU cc_start: 0.9276 (pm20) cc_final: 0.8861 (mp0) REVERT: B 455 MET cc_start: 0.9383 (tmm) cc_final: 0.9075 (tmm) REVERT: B 582 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8662 (mmm-85) REVERT: B 675 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8796 (tt) REVERT: C 50 MET cc_start: 0.9164 (mmp) cc_final: 0.8814 (mpp) REVERT: C 68 ARG cc_start: 0.7712 (tmt-80) cc_final: 0.6446 (tpp-160) REVERT: C 69 MET cc_start: 0.8222 (mmp) cc_final: 0.7658 (tpp) REVERT: C 213 ARG cc_start: 0.7640 (tpp-160) cc_final: 0.6686 (tpm170) REVERT: C 227 MET cc_start: 0.6711 (ttt) cc_final: 0.6443 (ttt) REVERT: C 243 ASN cc_start: 0.8388 (m110) cc_final: 0.8183 (m-40) REVERT: C 406 SER cc_start: 0.8445 (m) cc_final: 0.8207 (p) REVERT: C 458 ASP cc_start: 0.9336 (m-30) cc_final: 0.8877 (m-30) REVERT: C 462 ASP cc_start: 0.8892 (t0) cc_final: 0.8606 (t0) REVERT: C 504 TYR cc_start: 0.8333 (t80) cc_final: 0.7689 (t80) REVERT: C 505 TRP cc_start: 0.8175 (m100) cc_final: 0.7404 (m100) REVERT: D 68 ARG cc_start: 0.7643 (tmt-80) cc_final: 0.6319 (tpp-160) REVERT: D 69 MET cc_start: 0.8142 (mmp) cc_final: 0.6905 (tpt) REVERT: D 173 CYS cc_start: 0.8236 (m) cc_final: 0.7782 (m) REVERT: D 213 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7139 (tpp-160) REVERT: D 243 ASN cc_start: 0.8843 (m110) cc_final: 0.8515 (m110) REVERT: D 406 SER cc_start: 0.8584 (m) cc_final: 0.8293 (p) REVERT: D 407 MET cc_start: 0.7713 (tpt) cc_final: 0.7438 (tpt) REVERT: D 458 ASP cc_start: 0.9313 (m-30) cc_final: 0.8861 (m-30) REVERT: D 462 ASP cc_start: 0.8969 (t0) cc_final: 0.8698 (t0) REVERT: D 504 TYR cc_start: 0.8433 (t80) cc_final: 0.7786 (t80) REVERT: D 505 TRP cc_start: 0.8344 (m100) cc_final: 0.7630 (m100) REVERT: D 535 LYS cc_start: 0.8363 (mtpp) cc_final: 0.7964 (mmmt) outliers start: 32 outliers final: 14 residues processed: 264 average time/residue: 0.1205 time to fit residues: 50.8441 Evaluate side-chains 209 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 380 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 96 GLN A 277 ASN A 535 HIS A 718 ASN B 24 GLN B 61 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 535 HIS B 718 ASN C 67 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 461 ASN D 106 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.145594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082672 restraints weight = 37708.730| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.64 r_work: 0.2912 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21338 Z= 0.166 Angle : 0.566 8.712 29150 Z= 0.281 Chirality : 0.042 0.259 3290 Planarity : 0.004 0.058 3668 Dihedral : 6.725 77.021 3350 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.22 % Allowed : 12.93 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.17), residues: 2634 helix: 1.84 (0.12), residues: 1736 sheet: 0.63 (0.66), residues: 54 loop : -0.45 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 559 TYR 0.021 0.001 TYR D 101 PHE 0.016 0.001 PHE D 96 TRP 0.025 0.001 TRP D 509 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00378 (21304) covalent geometry : angle 0.55569 (29072) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.96259 ( 12) hydrogen bonds : bond 0.04223 ( 1283) hydrogen bonds : angle 4.01357 ( 3753) metal coordination : bond 0.00269 ( 4) Misc. bond : bond 0.00094 ( 2) link_BETA1-4 : bond 0.00994 ( 6) link_BETA1-4 : angle 2.90947 ( 18) link_NAG-ASN : bond 0.00196 ( 16) link_NAG-ASN : angle 1.95323 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LYS cc_start: 0.9522 (ptmm) cc_final: 0.9278 (ptpt) REVERT: A 102 GLN cc_start: 0.8485 (mp10) cc_final: 0.8239 (mp10) REVERT: A 114 LYS cc_start: 0.9091 (tppt) cc_final: 0.8615 (mtpt) REVERT: A 190 MET cc_start: 0.9043 (tmm) cc_final: 0.8705 (tmm) REVERT: A 393 ARG cc_start: 0.8408 (mtt180) cc_final: 0.8114 (mtt90) REVERT: A 401 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: A 408 MET cc_start: 0.9389 (mmt) cc_final: 0.9008 (mmm) REVERT: A 430 GLU cc_start: 0.9286 (pm20) cc_final: 0.8814 (mp0) REVERT: A 480 MET cc_start: 0.8724 (mtp) cc_final: 0.8375 (mtp) REVERT: A 582 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8656 (mmm-85) REVERT: A 675 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9089 (tt) REVERT: A 699 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 40 PHE cc_start: 0.9272 (t80) cc_final: 0.8938 (t80) REVERT: B 114 LYS cc_start: 0.9040 (tppt) cc_final: 0.8645 (mtpt) REVERT: B 190 MET cc_start: 0.8997 (tmm) cc_final: 0.8726 (tmm) REVERT: B 360 MET cc_start: 0.8354 (ttm) cc_final: 0.8057 (ttm) REVERT: B 366 MET cc_start: 0.8614 (ttm) cc_final: 0.8304 (ttm) REVERT: B 393 ARG cc_start: 0.8404 (mtt180) cc_final: 0.8117 (mtt90) REVERT: B 408 MET cc_start: 0.9454 (mmt) cc_final: 0.9138 (mmm) REVERT: B 430 GLU cc_start: 0.9287 (pm20) cc_final: 0.8821 (mp0) REVERT: B 455 MET cc_start: 0.9376 (tmm) cc_final: 0.9039 (tmm) REVERT: B 582 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8651 (mmm-85) REVERT: B 675 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.8995 (tt) REVERT: C 68 ARG cc_start: 0.7720 (tmt-80) cc_final: 0.6364 (tpp-160) REVERT: C 69 MET cc_start: 0.8343 (mmp) cc_final: 0.7129 (tpp) REVERT: C 100 MET cc_start: 0.8752 (mtt) cc_final: 0.8494 (mtt) REVERT: C 213 ARG cc_start: 0.7604 (tpp-160) cc_final: 0.7390 (tpp-160) REVERT: C 227 MET cc_start: 0.6940 (ttt) cc_final: 0.6699 (ttt) REVERT: C 243 ASN cc_start: 0.8444 (m110) cc_final: 0.8242 (m110) REVERT: C 406 SER cc_start: 0.8496 (m) cc_final: 0.8254 (p) REVERT: C 458 ASP cc_start: 0.9384 (m-30) cc_final: 0.8857 (m-30) REVERT: C 462 ASP cc_start: 0.8906 (t0) cc_final: 0.8497 (t0) REVERT: C 504 TYR cc_start: 0.8303 (t80) cc_final: 0.8003 (t80) REVERT: D 68 ARG cc_start: 0.7704 (tmt-80) cc_final: 0.7220 (tpp-160) REVERT: D 100 MET cc_start: 0.8679 (mtt) cc_final: 0.8428 (mtt) REVERT: D 213 ARG cc_start: 0.7562 (tpp-160) cc_final: 0.7281 (tpp-160) REVERT: D 243 ASN cc_start: 0.8841 (m110) cc_final: 0.8529 (m110) REVERT: D 378 TYR cc_start: 0.8754 (m-80) cc_final: 0.8497 (m-80) REVERT: D 406 SER cc_start: 0.8675 (m) cc_final: 0.8373 (p) REVERT: D 407 MET cc_start: 0.7709 (tpt) cc_final: 0.7321 (tpt) REVERT: D 458 ASP cc_start: 0.9290 (m-30) cc_final: 0.8755 (m-30) REVERT: D 462 ASP cc_start: 0.9021 (t0) cc_final: 0.8641 (t0) REVERT: D 504 TYR cc_start: 0.8425 (t80) cc_final: 0.8163 (t80) REVERT: D 535 LYS cc_start: 0.8398 (mtpp) cc_final: 0.7995 (mmmt) outliers start: 46 outliers final: 18 residues processed: 245 average time/residue: 0.1282 time to fit residues: 49.3175 Evaluate side-chains 214 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 185 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 134 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079843 restraints weight = 37842.559| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.69 r_work: 0.2849 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21338 Z= 0.254 Angle : 0.619 8.045 29150 Z= 0.309 Chirality : 0.045 0.250 3290 Planarity : 0.004 0.048 3668 Dihedral : 6.453 76.704 3350 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.65 % Allowed : 12.74 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.16), residues: 2634 helix: 1.74 (0.12), residues: 1732 sheet: 0.37 (0.56), residues: 70 loop : -0.51 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 115 TYR 0.025 0.002 TYR A 183 PHE 0.022 0.002 PHE A 40 TRP 0.014 0.002 TRP A 477 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00597 (21304) covalent geometry : angle 0.61003 (29072) SS BOND : bond 0.00330 ( 6) SS BOND : angle 0.98723 ( 12) hydrogen bonds : bond 0.04366 ( 1283) hydrogen bonds : angle 4.01269 ( 3753) metal coordination : bond 0.00457 ( 4) Misc. bond : bond 0.00110 ( 2) link_BETA1-4 : bond 0.01017 ( 6) link_BETA1-4 : angle 2.75213 ( 18) link_NAG-ASN : bond 0.00252 ( 16) link_NAG-ASN : angle 2.04682 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.564 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 62 MET cc_start: 0.9038 (mtm) cc_final: 0.8824 (mtm) REVERT: A 102 GLN cc_start: 0.8515 (mp10) cc_final: 0.8226 (mp10) REVERT: A 114 LYS cc_start: 0.9040 (tppt) cc_final: 0.8574 (mtpt) REVERT: A 190 MET cc_start: 0.9052 (tmm) cc_final: 0.8710 (tmm) REVERT: A 393 ARG cc_start: 0.8425 (mtt180) cc_final: 0.8117 (mtt90) REVERT: A 401 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8237 (t-90) REVERT: A 408 MET cc_start: 0.9418 (mmt) cc_final: 0.9039 (mmm) REVERT: A 455 MET cc_start: 0.9369 (tmm) cc_final: 0.9032 (tmm) REVERT: A 480 MET cc_start: 0.8782 (mtp) cc_final: 0.8439 (mtp) REVERT: A 582 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8653 (mmm-85) REVERT: A 675 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9132 (tt) REVERT: A 699 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: B 40 PHE cc_start: 0.9266 (t80) cc_final: 0.8906 (t80) REVERT: B 114 LYS cc_start: 0.9075 (tppt) cc_final: 0.8662 (mtpt) REVERT: B 190 MET cc_start: 0.9000 (tmm) cc_final: 0.8716 (tmm) REVERT: B 360 MET cc_start: 0.8474 (ttm) cc_final: 0.8121 (ttm) REVERT: B 393 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8093 (mtt90) REVERT: B 408 MET cc_start: 0.9429 (mmt) cc_final: 0.9062 (mmm) REVERT: B 455 MET cc_start: 0.9383 (tmm) cc_final: 0.9024 (tmm) REVERT: B 582 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8651 (mmm-85) REVERT: B 675 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9147 (tt) REVERT: C 68 ARG cc_start: 0.7584 (tmt-80) cc_final: 0.6580 (tpp-160) REVERT: C 100 MET cc_start: 0.8806 (mtt) cc_final: 0.8501 (mtt) REVERT: C 213 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7295 (tpp-160) REVERT: C 225 MET cc_start: 0.8111 (ptt) cc_final: 0.7709 (ptp) REVERT: C 243 ASN cc_start: 0.8491 (m110) cc_final: 0.8200 (m-40) REVERT: C 344 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.5997 (p90) REVERT: C 351 MET cc_start: 0.8706 (ptp) cc_final: 0.8454 (ptt) REVERT: C 406 SER cc_start: 0.8529 (m) cc_final: 0.8295 (p) REVERT: C 407 MET cc_start: 0.7683 (tpt) cc_final: 0.7143 (tpt) REVERT: C 446 MET cc_start: 0.8812 (mmm) cc_final: 0.8418 (mmm) REVERT: C 451 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7396 (tm-30) REVERT: C 458 ASP cc_start: 0.9403 (m-30) cc_final: 0.8918 (m-30) REVERT: C 462 ASP cc_start: 0.8926 (t0) cc_final: 0.8503 (t0) REVERT: C 504 TYR cc_start: 0.8345 (t80) cc_final: 0.8053 (t80) REVERT: D 68 ARG cc_start: 0.7597 (tmt-80) cc_final: 0.6610 (tpp-160) REVERT: D 100 MET cc_start: 0.8719 (mtt) cc_final: 0.8425 (mtt) REVERT: D 213 ARG cc_start: 0.7542 (tpp-160) cc_final: 0.7330 (tpp-160) REVERT: D 227 MET cc_start: 0.6672 (ttt) cc_final: 0.6446 (ttt) REVERT: D 243 ASN cc_start: 0.8867 (m110) cc_final: 0.8544 (m110) REVERT: D 344 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6030 (p90) REVERT: D 451 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7789 (tt0) REVERT: D 458 ASP cc_start: 0.9334 (m-30) cc_final: 0.8861 (m-30) REVERT: D 462 ASP cc_start: 0.9029 (t0) cc_final: 0.8618 (t0) REVERT: D 504 TYR cc_start: 0.8458 (t80) cc_final: 0.8185 (t80) REVERT: D 535 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7994 (mmmt) outliers start: 55 outliers final: 26 residues processed: 251 average time/residue: 0.1266 time to fit residues: 49.8936 Evaluate side-chains 218 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN B 718 ASN C 106 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.144985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082377 restraints weight = 37549.398| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.67 r_work: 0.2914 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21338 Z= 0.116 Angle : 0.534 9.602 29150 Z= 0.261 Chirality : 0.041 0.248 3290 Planarity : 0.004 0.047 3668 Dihedral : 6.001 76.243 3350 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.83 % Allowed : 13.71 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.16), residues: 2634 helix: 1.83 (0.12), residues: 1744 sheet: 0.40 (0.61), residues: 58 loop : -0.41 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 559 TYR 0.017 0.001 TYR A 50 PHE 0.014 0.001 PHE B 746 TRP 0.015 0.001 TRP C 77 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00249 (21304) covalent geometry : angle 0.52506 (29072) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.73797 ( 12) hydrogen bonds : bond 0.03819 ( 1283) hydrogen bonds : angle 3.83926 ( 3753) metal coordination : bond 0.00262 ( 4) Misc. bond : bond 0.00065 ( 2) link_BETA1-4 : bond 0.01228 ( 6) link_BETA1-4 : angle 2.79342 ( 18) link_NAG-ASN : bond 0.00172 ( 16) link_NAG-ASN : angle 1.79269 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.625 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 62 MET cc_start: 0.9037 (mtm) cc_final: 0.8765 (mtm) REVERT: A 102 GLN cc_start: 0.8375 (mt0) cc_final: 0.8162 (mp10) REVERT: A 114 LYS cc_start: 0.8989 (tppt) cc_final: 0.8581 (mtpt) REVERT: A 190 MET cc_start: 0.9108 (tmm) cc_final: 0.8765 (tmm) REVERT: A 393 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8037 (mtt90) REVERT: A 401 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8194 (t-90) REVERT: A 408 MET cc_start: 0.9395 (mmt) cc_final: 0.8987 (mmm) REVERT: A 480 MET cc_start: 0.8755 (mtp) cc_final: 0.8479 (mtp) REVERT: A 582 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8676 (mmm-85) REVERT: A 625 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8444 (mmtt) REVERT: A 675 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9115 (tt) REVERT: A 679 ILE cc_start: 0.8666 (mt) cc_final: 0.8454 (mm) REVERT: A 699 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: B 40 PHE cc_start: 0.9289 (t80) cc_final: 0.8921 (t80) REVERT: B 114 LYS cc_start: 0.9023 (tppt) cc_final: 0.8620 (mtpt) REVERT: B 360 MET cc_start: 0.8365 (ttm) cc_final: 0.8021 (ttm) REVERT: B 376 MET cc_start: 0.9158 (ttt) cc_final: 0.8803 (ttt) REVERT: B 393 ARG cc_start: 0.8313 (mtt180) cc_final: 0.8012 (mtt90) REVERT: B 408 MET cc_start: 0.9401 (mmt) cc_final: 0.9018 (mmm) REVERT: B 430 GLU cc_start: 0.9201 (pm20) cc_final: 0.8694 (pt0) REVERT: B 455 MET cc_start: 0.9374 (tmm) cc_final: 0.9048 (tmm) REVERT: B 582 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8653 (mmm-85) REVERT: B 675 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9124 (tt) REVERT: B 750 MET cc_start: 0.4903 (tmm) cc_final: 0.4689 (tpt) REVERT: C 68 ARG cc_start: 0.7600 (tmt-80) cc_final: 0.6437 (tpp-160) REVERT: C 69 MET cc_start: 0.8316 (mmt) cc_final: 0.7491 (tpp) REVERT: C 100 MET cc_start: 0.8781 (mtt) cc_final: 0.8438 (mtt) REVERT: C 213 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.7240 (tpp-160) REVERT: C 225 MET cc_start: 0.8301 (ptt) cc_final: 0.7836 (mtm) REVERT: C 243 ASN cc_start: 0.8396 (m110) cc_final: 0.8076 (m-40) REVERT: C 256 PHE cc_start: 0.7858 (m-80) cc_final: 0.7565 (m-80) REVERT: C 378 TYR cc_start: 0.8672 (m-80) cc_final: 0.8463 (m-80) REVERT: C 406 SER cc_start: 0.8553 (m) cc_final: 0.8318 (p) REVERT: C 407 MET cc_start: 0.7742 (tpt) cc_final: 0.7243 (tpt) REVERT: C 446 MET cc_start: 0.8695 (mmm) cc_final: 0.8390 (mmm) REVERT: C 451 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7437 (tm-30) REVERT: C 458 ASP cc_start: 0.9388 (m-30) cc_final: 0.8906 (m-30) REVERT: C 462 ASP cc_start: 0.8868 (t0) cc_final: 0.8405 (t0) REVERT: C 509 TRP cc_start: 0.8401 (m-10) cc_final: 0.7771 (m-90) REVERT: D 50 MET cc_start: 0.9203 (mmp) cc_final: 0.8774 (mpp) REVERT: D 68 ARG cc_start: 0.7638 (tmt-80) cc_final: 0.6520 (tpp-160) REVERT: D 69 MET cc_start: 0.8320 (mmt) cc_final: 0.7213 (tpp) REVERT: D 100 MET cc_start: 0.8635 (mtt) cc_final: 0.8327 (mtt) REVERT: D 172 LEU cc_start: 0.8898 (tp) cc_final: 0.8670 (tp) REVERT: D 215 LEU cc_start: 0.8858 (mt) cc_final: 0.8641 (mt) REVERT: D 227 MET cc_start: 0.6530 (ttt) cc_final: 0.6316 (ttt) REVERT: D 243 ASN cc_start: 0.8830 (m110) cc_final: 0.8494 (m110) REVERT: D 458 ASP cc_start: 0.9332 (m-30) cc_final: 0.8830 (m-30) REVERT: D 462 ASP cc_start: 0.8972 (t0) cc_final: 0.8561 (t0) REVERT: D 504 TYR cc_start: 0.8456 (t80) cc_final: 0.8200 (t80) outliers start: 38 outliers final: 22 residues processed: 230 average time/residue: 0.1280 time to fit residues: 46.3020 Evaluate side-chains 213 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 256 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 172 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079604 restraints weight = 37303.112| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.57 r_work: 0.2866 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21338 Z= 0.207 Angle : 0.575 10.113 29150 Z= 0.285 Chirality : 0.043 0.240 3290 Planarity : 0.004 0.044 3668 Dihedral : 6.054 76.516 3350 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.56 % Allowed : 13.56 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.16), residues: 2634 helix: 1.80 (0.12), residues: 1742 sheet: 0.38 (0.54), residues: 74 loop : -0.48 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 559 TYR 0.022 0.002 TYR B 50 PHE 0.014 0.001 PHE A 274 TRP 0.013 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00483 (21304) covalent geometry : angle 0.56673 (29072) SS BOND : bond 0.00312 ( 6) SS BOND : angle 0.85036 ( 12) hydrogen bonds : bond 0.04029 ( 1283) hydrogen bonds : angle 3.88550 ( 3753) metal coordination : bond 0.00381 ( 4) Misc. bond : bond 0.00079 ( 2) link_BETA1-4 : bond 0.01059 ( 6) link_BETA1-4 : angle 2.73636 ( 18) link_NAG-ASN : bond 0.00250 ( 16) link_NAG-ASN : angle 1.85680 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8407 (mt0) cc_final: 0.8120 (mp10) REVERT: A 114 LYS cc_start: 0.9051 (tppt) cc_final: 0.8600 (mtpt) REVERT: A 190 MET cc_start: 0.9101 (tmm) cc_final: 0.8694 (tmm) REVERT: A 393 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8059 (mtt90) REVERT: A 401 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8262 (t-90) REVERT: A 408 MET cc_start: 0.9435 (mmt) cc_final: 0.9040 (mmm) REVERT: A 430 GLU cc_start: 0.9213 (pm20) cc_final: 0.8744 (pt0) REVERT: A 455 MET cc_start: 0.9373 (tmm) cc_final: 0.9024 (tmm) REVERT: A 480 MET cc_start: 0.8817 (mtp) cc_final: 0.8484 (mtp) REVERT: A 582 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8734 (mmm-85) REVERT: A 675 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9186 (tt) REVERT: A 679 ILE cc_start: 0.8758 (mt) cc_final: 0.8532 (mm) REVERT: A 699 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 40 PHE cc_start: 0.9282 (t80) cc_final: 0.8925 (t80) REVERT: B 114 LYS cc_start: 0.9090 (tppt) cc_final: 0.8686 (mtpt) REVERT: B 323 MET cc_start: 0.9305 (mmm) cc_final: 0.9084 (mmm) REVERT: B 360 MET cc_start: 0.8495 (ttm) cc_final: 0.8087 (ttm) REVERT: B 393 ARG cc_start: 0.8373 (mtt180) cc_final: 0.8115 (mtt90) REVERT: B 408 MET cc_start: 0.9426 (mmt) cc_final: 0.9047 (mmm) REVERT: B 430 GLU cc_start: 0.9188 (pm20) cc_final: 0.8778 (mp0) REVERT: B 455 MET cc_start: 0.9392 (tmm) cc_final: 0.9026 (tmm) REVERT: B 582 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8714 (mmm-85) REVERT: B 675 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9097 (tt) REVERT: B 750 MET cc_start: 0.4941 (tmm) cc_final: 0.4731 (tpt) REVERT: C 68 ARG cc_start: 0.7483 (tmt-80) cc_final: 0.6203 (tpp-160) REVERT: C 69 MET cc_start: 0.8387 (mmt) cc_final: 0.7607 (tpp) REVERT: C 100 MET cc_start: 0.8877 (mtt) cc_final: 0.8567 (mtt) REVERT: C 225 MET cc_start: 0.8328 (ptt) cc_final: 0.7820 (mtm) REVERT: C 243 ASN cc_start: 0.8454 (m110) cc_final: 0.8139 (m-40) REVERT: C 256 PHE cc_start: 0.7912 (m-80) cc_final: 0.7647 (m-80) REVERT: C 344 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6126 (p90) REVERT: C 406 SER cc_start: 0.8532 (m) cc_final: 0.8326 (p) REVERT: C 446 MET cc_start: 0.8705 (mmm) cc_final: 0.8464 (mmm) REVERT: C 451 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7472 (tm-30) REVERT: C 458 ASP cc_start: 0.9397 (m-30) cc_final: 0.8956 (m-30) REVERT: C 462 ASP cc_start: 0.8863 (t0) cc_final: 0.8404 (t0) REVERT: D 50 MET cc_start: 0.9347 (mmp) cc_final: 0.8837 (mpp) REVERT: D 68 ARG cc_start: 0.7669 (tmt-80) cc_final: 0.7024 (tpp-160) REVERT: D 69 MET cc_start: 0.8347 (mmt) cc_final: 0.7480 (tpp) REVERT: D 100 MET cc_start: 0.8655 (mtt) cc_final: 0.8350 (mtt) REVERT: D 172 LEU cc_start: 0.8951 (tp) cc_final: 0.8734 (tp) REVERT: D 215 LEU cc_start: 0.8819 (mt) cc_final: 0.8577 (mt) REVERT: D 227 MET cc_start: 0.6931 (ttt) cc_final: 0.6730 (ttt) REVERT: D 243 ASN cc_start: 0.8861 (m110) cc_final: 0.8530 (m110) REVERT: D 344 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.6276 (p90) REVERT: D 451 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7765 (tt0) REVERT: D 458 ASP cc_start: 0.9372 (m-30) cc_final: 0.8889 (m-30) REVERT: D 462 ASP cc_start: 0.8977 (t0) cc_final: 0.8540 (t0) REVERT: D 504 TYR cc_start: 0.8472 (t80) cc_final: 0.8189 (t80) outliers start: 53 outliers final: 36 residues processed: 239 average time/residue: 0.1364 time to fit residues: 51.5376 Evaluate side-chains 237 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 254 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 236 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 239 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.144802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082228 restraints weight = 37663.017| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.63 r_work: 0.2917 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21338 Z= 0.113 Angle : 0.528 12.347 29150 Z= 0.258 Chirality : 0.040 0.245 3290 Planarity : 0.003 0.046 3668 Dihedral : 5.832 76.229 3350 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 14.19 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.16), residues: 2634 helix: 1.85 (0.12), residues: 1748 sheet: 0.49 (0.61), residues: 58 loop : -0.41 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 78 TYR 0.024 0.001 TYR A 50 PHE 0.028 0.001 PHE A 40 TRP 0.021 0.001 TRP C 77 HIS 0.005 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00243 (21304) covalent geometry : angle 0.51935 (29072) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.64795 ( 12) hydrogen bonds : bond 0.03663 ( 1283) hydrogen bonds : angle 3.80927 ( 3753) metal coordination : bond 0.00184 ( 4) Misc. bond : bond 0.00043 ( 2) link_BETA1-4 : bond 0.01094 ( 6) link_BETA1-4 : angle 2.72917 ( 18) link_NAG-ASN : bond 0.00160 ( 16) link_NAG-ASN : angle 1.67522 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8385 (mt0) cc_final: 0.8104 (mp10) REVERT: A 114 LYS cc_start: 0.8998 (tppt) cc_final: 0.8585 (mtpt) REVERT: A 190 MET cc_start: 0.9089 (tmm) cc_final: 0.8753 (tmm) REVERT: A 393 ARG cc_start: 0.8336 (mtt180) cc_final: 0.8064 (mtt90) REVERT: A 401 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.8182 (t-90) REVERT: A 408 MET cc_start: 0.9389 (mmt) cc_final: 0.8987 (mmm) REVERT: A 430 GLU cc_start: 0.9059 (pm20) cc_final: 0.8638 (pt0) REVERT: A 480 MET cc_start: 0.8788 (mtp) cc_final: 0.8519 (mtp) REVERT: A 582 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8701 (mmm-85) REVERT: A 625 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8512 (mmtp) REVERT: A 675 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9054 (tt) REVERT: A 679 ILE cc_start: 0.8652 (mt) cc_final: 0.8428 (mm) REVERT: B 40 PHE cc_start: 0.9315 (t80) cc_final: 0.8939 (t80) REVERT: B 91 LEU cc_start: 0.9210 (mt) cc_final: 0.9001 (pt) REVERT: B 114 LYS cc_start: 0.9035 (tppt) cc_final: 0.8626 (mtpt) REVERT: B 357 ARG cc_start: 0.8998 (mtt180) cc_final: 0.8237 (mtt-85) REVERT: B 360 MET cc_start: 0.8388 (ttm) cc_final: 0.8023 (ttm) REVERT: B 393 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8131 (mtt90) REVERT: B 408 MET cc_start: 0.9409 (mmt) cc_final: 0.9016 (mmm) REVERT: B 430 GLU cc_start: 0.9179 (pm20) cc_final: 0.8672 (pt0) REVERT: B 463 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8954 (p) REVERT: B 582 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8700 (mmm-85) REVERT: B 675 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9052 (tt) REVERT: B 750 MET cc_start: 0.4930 (tmm) cc_final: 0.4714 (tpt) REVERT: C 68 ARG cc_start: 0.7561 (tmt-80) cc_final: 0.6351 (tpp-160) REVERT: C 69 MET cc_start: 0.8325 (mmt) cc_final: 0.7519 (tpp) REVERT: C 100 MET cc_start: 0.8767 (mtt) cc_final: 0.8417 (mtt) REVERT: C 225 MET cc_start: 0.8355 (ptt) cc_final: 0.8124 (ptt) REVERT: C 243 ASN cc_start: 0.8443 (m110) cc_final: 0.8122 (m-40) REVERT: C 344 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.6158 (p90) REVERT: C 407 MET cc_start: 0.7762 (tpt) cc_final: 0.7418 (tpt) REVERT: C 446 MET cc_start: 0.8683 (mmm) cc_final: 0.8444 (mmm) REVERT: C 451 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7349 (tm-30) REVERT: C 458 ASP cc_start: 0.9388 (m-30) cc_final: 0.8925 (m-30) REVERT: C 462 ASP cc_start: 0.8857 (t0) cc_final: 0.8391 (t0) REVERT: D 68 ARG cc_start: 0.7658 (tmt-80) cc_final: 0.6999 (tpp-160) REVERT: D 69 MET cc_start: 0.8407 (mmt) cc_final: 0.7500 (tpp) REVERT: D 100 MET cc_start: 0.8647 (mtt) cc_final: 0.8348 (mtt) REVERT: D 172 LEU cc_start: 0.8935 (tp) cc_final: 0.8727 (tp) REVERT: D 215 LEU cc_start: 0.8721 (mt) cc_final: 0.8245 (mt) REVERT: D 225 MET cc_start: 0.8184 (ptt) cc_final: 0.7655 (mtm) REVERT: D 344 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.6247 (p90) REVERT: D 451 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7701 (tm-30) REVERT: D 458 ASP cc_start: 0.9337 (m-30) cc_final: 0.8793 (m-30) REVERT: D 462 ASP cc_start: 0.8982 (t0) cc_final: 0.8572 (t0) REVERT: D 504 TYR cc_start: 0.8354 (t80) cc_final: 0.8152 (t80) outliers start: 42 outliers final: 20 residues processed: 232 average time/residue: 0.1325 time to fit residues: 48.7540 Evaluate side-chains 209 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 165 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.144324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081792 restraints weight = 37258.256| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.62 r_work: 0.2904 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21338 Z= 0.148 Angle : 0.556 12.382 29150 Z= 0.271 Chirality : 0.042 0.322 3290 Planarity : 0.004 0.044 3668 Dihedral : 5.757 76.420 3346 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.36 % Allowed : 14.53 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.17), residues: 2634 helix: 1.86 (0.12), residues: 1748 sheet: 0.50 (0.55), residues: 74 loop : -0.41 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 559 TYR 0.026 0.001 TYR B 50 PHE 0.012 0.001 PHE B 327 TRP 0.016 0.001 TRP C 505 HIS 0.005 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00342 (21304) covalent geometry : angle 0.54758 (29072) SS BOND : bond 0.00289 ( 6) SS BOND : angle 1.51577 ( 12) hydrogen bonds : bond 0.03755 ( 1283) hydrogen bonds : angle 3.82005 ( 3753) metal coordination : bond 0.00362 ( 4) Misc. bond : bond 0.00056 ( 2) link_BETA1-4 : bond 0.01074 ( 6) link_BETA1-4 : angle 2.70012 ( 18) link_NAG-ASN : bond 0.00170 ( 16) link_NAG-ASN : angle 1.69464 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8991 (tppt) cc_final: 0.8572 (mtpt) REVERT: A 190 MET cc_start: 0.9088 (tmm) cc_final: 0.8691 (tmm) REVERT: A 393 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8063 (mtt90) REVERT: A 401 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8170 (t-90) REVERT: A 408 MET cc_start: 0.9402 (mmt) cc_final: 0.8994 (mmm) REVERT: A 430 GLU cc_start: 0.9065 (pm20) cc_final: 0.8674 (mp0) REVERT: A 455 MET cc_start: 0.9356 (tmm) cc_final: 0.8985 (tmm) REVERT: A 463 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9045 (p) REVERT: A 480 MET cc_start: 0.8802 (mtp) cc_final: 0.8520 (mtp) REVERT: A 582 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8633 (mmm-85) REVERT: A 625 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8525 (mmtp) REVERT: A 675 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9138 (tt) REVERT: A 679 ILE cc_start: 0.8713 (mt) cc_final: 0.8484 (mm) REVERT: A 699 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 40 PHE cc_start: 0.9293 (t80) cc_final: 0.8930 (t80) REVERT: B 91 LEU cc_start: 0.9208 (mt) cc_final: 0.9006 (pt) REVERT: B 114 LYS cc_start: 0.9053 (tppt) cc_final: 0.8634 (mtpt) REVERT: B 393 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8141 (mtt90) REVERT: B 408 MET cc_start: 0.9411 (mmt) cc_final: 0.9008 (mmm) REVERT: B 455 MET cc_start: 0.9388 (tmm) cc_final: 0.9027 (tmm) REVERT: B 582 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8619 (mmm-85) REVERT: B 675 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9148 (tt) REVERT: B 750 MET cc_start: 0.4941 (tmm) cc_final: 0.4722 (tpt) REVERT: C 68 ARG cc_start: 0.7547 (tmt-80) cc_final: 0.6338 (tpp-160) REVERT: C 69 MET cc_start: 0.8234 (mmt) cc_final: 0.7454 (tpp) REVERT: C 100 MET cc_start: 0.8795 (mtt) cc_final: 0.8458 (mtt) REVERT: C 225 MET cc_start: 0.8310 (ptt) cc_final: 0.8071 (ptt) REVERT: C 243 ASN cc_start: 0.8417 (m110) cc_final: 0.8122 (m-40) REVERT: C 344 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.6150 (p90) REVERT: C 407 MET cc_start: 0.7706 (tpt) cc_final: 0.7415 (tpt) REVERT: C 446 MET cc_start: 0.8645 (mmm) cc_final: 0.8431 (mmm) REVERT: C 451 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7457 (tm-30) REVERT: C 458 ASP cc_start: 0.9379 (m-30) cc_final: 0.8968 (m-30) REVERT: C 462 ASP cc_start: 0.8851 (t0) cc_final: 0.8385 (t0) REVERT: D 68 ARG cc_start: 0.7571 (tmt-80) cc_final: 0.6966 (tpp-160) REVERT: D 69 MET cc_start: 0.8366 (mmt) cc_final: 0.7507 (tpp) REVERT: D 100 MET cc_start: 0.8640 (mtt) cc_final: 0.8336 (mtt) REVERT: D 215 LEU cc_start: 0.8735 (mt) cc_final: 0.8271 (mt) REVERT: D 225 MET cc_start: 0.8241 (ptt) cc_final: 0.7729 (mtm) REVERT: D 243 ASN cc_start: 0.8846 (m110) cc_final: 0.8599 (m-40) REVERT: D 344 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.6226 (p90) REVERT: D 451 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7910 (tt0) REVERT: D 458 ASP cc_start: 0.9370 (m-30) cc_final: 0.8842 (m-30) REVERT: D 462 ASP cc_start: 0.8980 (t0) cc_final: 0.8565 (t0) REVERT: D 504 TYR cc_start: 0.8377 (t80) cc_final: 0.8164 (t80) REVERT: D 540 ASP cc_start: 0.7899 (t0) cc_final: 0.6665 (p0) outliers start: 49 outliers final: 27 residues processed: 228 average time/residue: 0.1552 time to fit residues: 56.1286 Evaluate side-chains 218 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 39 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.144512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081994 restraints weight = 37524.449| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.61 r_work: 0.2913 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21338 Z= 0.127 Angle : 0.552 13.042 29150 Z= 0.267 Chirality : 0.041 0.337 3290 Planarity : 0.004 0.044 3668 Dihedral : 5.696 76.411 3346 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.17 % Allowed : 14.77 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.17), residues: 2634 helix: 1.86 (0.12), residues: 1750 sheet: 0.56 (0.54), residues: 74 loop : -0.35 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 559 TYR 0.028 0.001 TYR B 50 PHE 0.018 0.001 PHE A 327 TRP 0.021 0.001 TRP C 505 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (21304) covalent geometry : angle 0.54394 (29072) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.82990 ( 12) hydrogen bonds : bond 0.03618 ( 1283) hydrogen bonds : angle 3.80749 ( 3753) metal coordination : bond 0.00216 ( 4) Misc. bond : bond 0.00045 ( 2) link_BETA1-4 : bond 0.01090 ( 6) link_BETA1-4 : angle 2.67367 ( 18) link_NAG-ASN : bond 0.00170 ( 16) link_NAG-ASN : angle 1.63173 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8417 (t60) cc_final: 0.8134 (t60) REVERT: A 114 LYS cc_start: 0.8984 (tppt) cc_final: 0.8554 (mtpt) REVERT: A 190 MET cc_start: 0.9109 (tmm) cc_final: 0.8777 (tmm) REVERT: A 393 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8108 (mtt90) REVERT: A 401 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: A 408 MET cc_start: 0.9401 (mmt) cc_final: 0.8994 (mmm) REVERT: A 430 GLU cc_start: 0.9050 (pm20) cc_final: 0.8659 (mp0) REVERT: A 463 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9023 (p) REVERT: A 480 MET cc_start: 0.8800 (mtp) cc_final: 0.8535 (mtp) REVERT: A 582 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8649 (mmm-85) REVERT: A 625 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8564 (mmtp) REVERT: A 675 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9134 (tt) REVERT: A 679 ILE cc_start: 0.8649 (mt) cc_final: 0.8421 (mm) REVERT: A 699 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: B 40 PHE cc_start: 0.9326 (t80) cc_final: 0.8963 (t80) REVERT: B 91 LEU cc_start: 0.9204 (mt) cc_final: 0.9003 (pt) REVERT: B 114 LYS cc_start: 0.9044 (tppt) cc_final: 0.8633 (mtpt) REVERT: B 302 TRP cc_start: 0.8615 (m100) cc_final: 0.8251 (m100) REVERT: B 357 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8184 (mtt-85) REVERT: B 393 ARG cc_start: 0.8371 (mtt180) cc_final: 0.8139 (mtt90) REVERT: B 408 MET cc_start: 0.9408 (mmt) cc_final: 0.8997 (mmm) REVERT: B 430 GLU cc_start: 0.9058 (pm20) cc_final: 0.8622 (pt0) REVERT: B 463 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 582 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8629 (mmm-85) REVERT: B 675 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9123 (tt) REVERT: B 750 MET cc_start: 0.4970 (tmm) cc_final: 0.4746 (tpt) REVERT: C 68 ARG cc_start: 0.7559 (tmt-80) cc_final: 0.6337 (tpp-160) REVERT: C 69 MET cc_start: 0.8189 (mmt) cc_final: 0.7433 (tpp) REVERT: C 96 PHE cc_start: 0.8961 (m-80) cc_final: 0.8710 (m-80) REVERT: C 100 MET cc_start: 0.8793 (mtt) cc_final: 0.8405 (mtt) REVERT: C 225 MET cc_start: 0.8287 (ptt) cc_final: 0.8041 (ptt) REVERT: C 243 ASN cc_start: 0.8467 (m110) cc_final: 0.8143 (m-40) REVERT: C 344 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6123 (p90) REVERT: C 407 MET cc_start: 0.7712 (tpt) cc_final: 0.7439 (tpt) REVERT: C 446 MET cc_start: 0.8610 (mmm) cc_final: 0.8399 (mmm) REVERT: C 451 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7506 (tm-30) REVERT: C 458 ASP cc_start: 0.9360 (m-30) cc_final: 0.8881 (m-30) REVERT: C 462 ASP cc_start: 0.8846 (t0) cc_final: 0.8372 (t0) REVERT: D 68 ARG cc_start: 0.7585 (tmt-80) cc_final: 0.6931 (tpp-160) REVERT: D 69 MET cc_start: 0.8403 (mmt) cc_final: 0.7568 (tpp) REVERT: D 100 MET cc_start: 0.8645 (mtt) cc_final: 0.8330 (mtt) REVERT: D 215 LEU cc_start: 0.8718 (mt) cc_final: 0.8284 (mt) REVERT: D 225 MET cc_start: 0.8248 (ptt) cc_final: 0.7677 (mmt) REVERT: D 344 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6182 (p90) REVERT: D 451 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7933 (tt0) REVERT: D 458 ASP cc_start: 0.9363 (m-30) cc_final: 0.8841 (m-30) REVERT: D 462 ASP cc_start: 0.9001 (t0) cc_final: 0.8624 (t0) REVERT: D 504 TYR cc_start: 0.8376 (t80) cc_final: 0.8166 (t80) REVERT: D 540 ASP cc_start: 0.7941 (t0) cc_final: 0.6708 (p0) outliers start: 45 outliers final: 28 residues processed: 228 average time/residue: 0.1590 time to fit residues: 56.5667 Evaluate side-chains 223 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 148 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.144608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081965 restraints weight = 37508.641| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.63 r_work: 0.2911 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21338 Z= 0.129 Angle : 0.553 12.903 29150 Z= 0.267 Chirality : 0.041 0.352 3290 Planarity : 0.003 0.044 3668 Dihedral : 5.657 76.402 3346 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 15.06 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.17), residues: 2634 helix: 1.87 (0.12), residues: 1752 sheet: 0.37 (0.62), residues: 58 loop : -0.31 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 559 TYR 0.033 0.001 TYR A 50 PHE 0.022 0.001 PHE A 28 TRP 0.029 0.001 TRP C 505 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00293 (21304) covalent geometry : angle 0.54463 (29072) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.51328 ( 12) hydrogen bonds : bond 0.03612 ( 1283) hydrogen bonds : angle 3.81551 ( 3753) metal coordination : bond 0.00173 ( 4) Misc. bond : bond 0.00045 ( 2) link_BETA1-4 : bond 0.01067 ( 6) link_BETA1-4 : angle 2.64665 ( 18) link_NAG-ASN : bond 0.00163 ( 16) link_NAG-ASN : angle 1.59830 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.9288 (t80) cc_final: 0.8995 (t80) REVERT: A 114 LYS cc_start: 0.8983 (tppt) cc_final: 0.8550 (mtpt) REVERT: A 190 MET cc_start: 0.9120 (tmm) cc_final: 0.8788 (tmm) REVERT: A 401 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.8093 (t-90) REVERT: A 408 MET cc_start: 0.9404 (mmt) cc_final: 0.8994 (mmm) REVERT: A 430 GLU cc_start: 0.9045 (pm20) cc_final: 0.8650 (mp0) REVERT: A 463 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9039 (p) REVERT: A 480 MET cc_start: 0.8806 (mtp) cc_final: 0.8543 (mtp) REVERT: A 582 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8602 (mmm-85) REVERT: A 625 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8486 (mmtt) REVERT: A 675 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9100 (tt) REVERT: A 679 ILE cc_start: 0.8653 (mt) cc_final: 0.8390 (mm) REVERT: A 699 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: B 40 PHE cc_start: 0.9296 (t80) cc_final: 0.8937 (t80) REVERT: B 114 LYS cc_start: 0.9050 (tppt) cc_final: 0.8578 (mtpp) REVERT: B 302 TRP cc_start: 0.8608 (m100) cc_final: 0.8272 (m100) REVERT: B 357 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8154 (mtt-85) REVERT: B 393 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8142 (mtt90) REVERT: B 408 MET cc_start: 0.9407 (mmt) cc_final: 0.8989 (mmm) REVERT: B 430 GLU cc_start: 0.9059 (pm20) cc_final: 0.8623 (pt0) REVERT: B 455 MET cc_start: 0.9389 (tmm) cc_final: 0.9029 (tmm) REVERT: B 463 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9019 (p) REVERT: B 582 ARG cc_start: 0.8872 (tpp80) cc_final: 0.8635 (mmm-85) REVERT: B 675 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9102 (tt) REVERT: C 68 ARG cc_start: 0.7550 (tmt-80) cc_final: 0.6863 (tpp-160) REVERT: C 69 MET cc_start: 0.8372 (mmt) cc_final: 0.7711 (tpp) REVERT: C 96 PHE cc_start: 0.8956 (m-80) cc_final: 0.8704 (m-80) REVERT: C 100 MET cc_start: 0.8793 (mtt) cc_final: 0.8412 (mtt) REVERT: C 225 MET cc_start: 0.8266 (ptt) cc_final: 0.7801 (mtm) REVERT: C 243 ASN cc_start: 0.8462 (m110) cc_final: 0.8168 (m-40) REVERT: C 344 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6178 (p90) REVERT: C 407 MET cc_start: 0.7725 (tpt) cc_final: 0.7422 (tpt) REVERT: C 446 MET cc_start: 0.8587 (mmm) cc_final: 0.8382 (mmm) REVERT: C 451 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7525 (tm-30) REVERT: C 458 ASP cc_start: 0.9357 (m-30) cc_final: 0.8882 (m-30) REVERT: C 462 ASP cc_start: 0.8857 (t0) cc_final: 0.8415 (t0) REVERT: D 68 ARG cc_start: 0.7551 (tmt-80) cc_final: 0.6942 (tpp-160) REVERT: D 69 MET cc_start: 0.8371 (mmt) cc_final: 0.7539 (tpp) REVERT: D 100 MET cc_start: 0.8579 (mtt) cc_final: 0.8272 (mtt) REVERT: D 215 LEU cc_start: 0.8769 (mt) cc_final: 0.8356 (mt) REVERT: D 225 MET cc_start: 0.8245 (ptt) cc_final: 0.7701 (mtm) REVERT: D 344 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.6191 (p90) REVERT: D 451 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7927 (tt0) REVERT: D 458 ASP cc_start: 0.9357 (m-30) cc_final: 0.8842 (m-30) REVERT: D 462 ASP cc_start: 0.8996 (t0) cc_final: 0.8622 (t0) REVERT: D 504 TYR cc_start: 0.8363 (t80) cc_final: 0.8149 (t80) REVERT: D 540 ASP cc_start: 0.7956 (t0) cc_final: 0.6778 (p0) outliers start: 42 outliers final: 30 residues processed: 224 average time/residue: 0.1495 time to fit residues: 52.6182 Evaluate side-chains 226 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 561 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 114 optimal weight: 0.0370 chunk 254 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 113 optimal weight: 0.0770 chunk 201 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 overall best weight: 0.8818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.145133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082793 restraints weight = 37606.112| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.62 r_work: 0.2926 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21338 Z= 0.117 Angle : 0.548 13.082 29150 Z= 0.265 Chirality : 0.041 0.336 3290 Planarity : 0.003 0.044 3668 Dihedral : 5.615 76.425 3346 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 15.35 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.17), residues: 2634 helix: 1.90 (0.12), residues: 1754 sheet: -0.09 (0.56), residues: 70 loop : -0.31 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 393 TYR 0.030 0.001 TYR A 50 PHE 0.018 0.001 PHE A 327 TRP 0.029 0.001 TRP A 69 HIS 0.003 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00261 (21304) covalent geometry : angle 0.54055 (29072) SS BOND : bond 0.00235 ( 6) SS BOND : angle 1.43308 ( 12) hydrogen bonds : bond 0.03510 ( 1283) hydrogen bonds : angle 3.79259 ( 3753) metal coordination : bond 0.00156 ( 4) Misc. bond : bond 0.00035 ( 2) link_BETA1-4 : bond 0.01112 ( 6) link_BETA1-4 : angle 2.64709 ( 18) link_NAG-ASN : bond 0.00159 ( 16) link_NAG-ASN : angle 1.54824 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7306.76 seconds wall clock time: 125 minutes 3.65 seconds (7503.65 seconds total)