Starting phenix.real_space_refine on Wed Jun 18 05:56:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p31_17382/06_2025/8p31_17382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p31_17382/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p31_17382/06_2025/8p31_17382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p31_17382/06_2025/8p31_17382.map" model { file = "/net/cci-nas-00/data/ceres_data/8p31_17382/06_2025/8p31_17382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p31_17382/06_2025/8p31_17382.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, '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: {'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} 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: D, B, H, G Time building chain proxies: 19.89, per 1000 atoms: 0.96 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: 5.74 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 1.88 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: 6.32 Time building geometry restraints manager: 6.66 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: 0.11 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 1.050 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: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 57.750 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.190 ------------------------------------------------------------------------------- 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 : 6.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.020 0.001 TRP D 178 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.001 PHE D 460 TYR 0.016 0.001 TYR D 348 ARG 0.003 0.001 ARG C 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 16) link_NAG-ASN : angle 2.24311 ( 48) link_BETA1-4 : bond 0.01122 ( 6) link_BETA1-4 : angle 3.31669 ( 18) hydrogen bonds : bond 0.14013 ( 1283) hydrogen bonds : angle 6.10624 ( 3753) metal coordination : bond 0.00263 ( 4) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.73158 ( 12) covalent geometry : bond 0.00378 (21304) covalent geometry : angle 0.61100 (29072) Misc. bond : bond 0.00009 ( 2) *********************** 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 : 2.188 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 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: 0.8017 (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: 0.8714 (tmm) REVERT: C 213 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.7244 (tpp-160) REVERT: C 406 SER cc_start: 0.8569 (m) cc_final: 0.8097 (p) REVERT: C 478 ILE cc_start: 0.8507 (mm) cc_final: 0.8240 (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: 0.6777 (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: 0.7775 (m) REVERT: D 213 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7043 (tpp-160) REVERT: D 385 MET cc_start: 0.6827 (mmt) cc_final: 0.6267 (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: 0.6685 (m100) REVERT: D 540 ASP cc_start: 0.7536 (t0) cc_final: 0.7294 (t0) outliers start: 14 outliers final: 2 residues processed: 394 average time/residue: 0.3368 time to fit residues: 205.6337 Evaluate side-chains 213 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 209 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 221 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 277 ASN A 535 HIS A 718 ASN B 24 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 277 ASN B 535 HIS B 718 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.145306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081698 restraints weight = 38159.545| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.76 r_work: 0.2892 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21338 Z= 0.195 Angle : 0.609 9.897 29150 Z= 0.306 Chirality : 0.043 0.268 3290 Planarity : 0.004 0.077 3668 Dihedral : 8.279 77.238 3352 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.83 % Allowed : 13.08 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2634 helix: 1.77 (0.13), residues: 1722 sheet: 0.83 (0.67), residues: 54 loop : -0.64 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.004 0.001 HIS B 241 PHE 0.024 0.002 PHE C 523 TYR 0.019 0.002 TYR A 183 ARG 0.005 0.001 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 16) link_NAG-ASN : angle 2.11810 ( 48) link_BETA1-4 : bond 0.01114 ( 6) link_BETA1-4 : angle 3.01568 ( 18) hydrogen bonds : bond 0.04674 ( 1283) hydrogen bonds : angle 4.28110 ( 3753) metal coordination : bond 0.00311 ( 4) SS BOND : bond 0.00365 ( 6) SS BOND : angle 1.43862 ( 12) covalent geometry : bond 0.00443 (21304) covalent geometry : angle 0.59803 (29072) Misc. bond : bond 0.00089 ( 2) *********************** 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 260 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 2.315 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: 0.8466 (mp10) cc_final: 0.8215 (mp10) REVERT: A 114 LYS cc_start: 0.9019 (tppt) cc_final: 0.8567 (mtpt) REVERT: A 401 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8217 (t-90) REVERT: A 408 MET cc_start: 0.9426 (mmt) cc_final: 0.9105 (mmm) REVERT: A 480 MET cc_start: 0.8799 (mtp) cc_final: 0.8481 (mtp) REVERT: A 582 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8620 (mmm-85) REVERT: A 675 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9046 (tt) REVERT: A 750 MET cc_start: 0.4899 (tmm) cc_final: 0.4563 (tpt) REVERT: B 114 LYS cc_start: 0.9031 (tppt) cc_final: 0.8615 (mtpt) REVERT: B 190 MET cc_start: 0.8983 (tmm) cc_final: 0.8731 (tmm) REVERT: B 360 MET cc_start: 0.8401 (ttm) cc_final: 0.8161 (ttm) REVERT: B 366 MET cc_start: 0.8488 (ttm) cc_final: 0.8007 (mtp) REVERT: B 393 ARG cc_start: 0.8651 (mtt180) cc_final: 0.7958 (mtt90) REVERT: B 401 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.8165 (t-90) REVERT: B 408 MET cc_start: 0.9431 (mmt) cc_final: 0.9164 (mmm) REVERT: B 430 GLU cc_start: 0.9307 (pm20) cc_final: 0.8874 (mp0) REVERT: B 455 MET cc_start: 0.9388 (tmm) cc_final: 0.9085 (tmm) REVERT: B 582 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8668 (mmm-85) REVERT: B 675 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9026 (tt) REVERT: C 50 MET cc_start: 0.9138 (mmp) cc_final: 0.8739 (mpp) REVERT: C 68 ARG cc_start: 0.7717 (tmt-80) cc_final: 0.6448 (tpp-160) REVERT: C 69 MET cc_start: 0.8293 (mmp) cc_final: 0.7689 (tpp) REVERT: C 213 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7218 (tpp-160) REVERT: C 227 MET cc_start: 0.6816 (ttt) cc_final: 0.6586 (ttt) REVERT: C 406 SER cc_start: 0.8459 (m) cc_final: 0.8212 (p) REVERT: C 458 ASP cc_start: 0.9380 (m-30) cc_final: 0.8938 (m-30) REVERT: C 462 ASP cc_start: 0.8909 (t0) cc_final: 0.8642 (t0) REVERT: C 504 TYR cc_start: 0.8374 (t80) cc_final: 0.7702 (t80) REVERT: C 505 TRP cc_start: 0.8226 (m100) cc_final: 0.7345 (m100) REVERT: D 68 ARG cc_start: 0.7655 (tmt-80) cc_final: 0.6380 (tpp-160) REVERT: D 69 MET cc_start: 0.8097 (mmp) cc_final: 0.7174 (tpp) REVERT: D 173 CYS cc_start: 0.8262 (m) cc_final: 0.7816 (m) REVERT: D 213 ARG cc_start: 0.7473 (tpp-160) cc_final: 0.7138 (tpp-160) REVERT: D 243 ASN cc_start: 0.8872 (m110) cc_final: 0.8557 (m110) REVERT: D 406 SER cc_start: 0.8583 (m) cc_final: 0.8279 (p) REVERT: D 407 MET cc_start: 0.7730 (tpt) cc_final: 0.7491 (tpt) REVERT: D 458 ASP cc_start: 0.9318 (m-30) cc_final: 0.8873 (m-30) REVERT: D 462 ASP cc_start: 0.8979 (t0) cc_final: 0.8697 (t0) REVERT: D 504 TYR cc_start: 0.8436 (t80) cc_final: 0.8191 (t80) REVERT: D 509 TRP cc_start: 0.8188 (m-10) cc_final: 0.7757 (m-90) REVERT: D 535 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7965 (mmmt) REVERT: D 540 ASP cc_start: 0.7574 (t0) cc_final: 0.7373 (t0) outliers start: 38 outliers final: 13 residues processed: 257 average time/residue: 0.3125 time to fit residues: 127.0703 Evaluate side-chains 212 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 401 HIS 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 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 29 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 718 ASN B 718 ASN C 67 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN D 67 GLN D 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.145965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082963 restraints weight = 37190.154| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.64 r_work: 0.2921 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2259 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= 0.135 Angle : 0.550 8.794 29150 Z= 0.271 Chirality : 0.041 0.260 3290 Planarity : 0.004 0.059 3668 Dihedral : 6.668 76.911 3352 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.22 % Allowed : 13.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2634 helix: 1.81 (0.12), residues: 1744 sheet: 0.77 (0.66), residues: 54 loop : -0.48 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 302 HIS 0.003 0.001 HIS D 275 PHE 0.018 0.001 PHE A 28 TYR 0.020 0.001 TYR D 101 ARG 0.004 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 16) link_NAG-ASN : angle 1.90704 ( 48) link_BETA1-4 : bond 0.01095 ( 6) link_BETA1-4 : angle 2.82209 ( 18) hydrogen bonds : bond 0.04137 ( 1283) hydrogen bonds : angle 3.97936 ( 3753) metal coordination : bond 0.00194 ( 4) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.91811 ( 12) covalent geometry : bond 0.00300 (21304) covalent geometry : angle 0.54047 (29072) Misc. bond : bond 0.00068 ( 2) *********************** 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 254 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 2.327 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 102 GLN cc_start: 0.8491 (mp10) cc_final: 0.8255 (mp10) REVERT: A 114 LYS cc_start: 0.9019 (tppt) cc_final: 0.8575 (mtpt) REVERT: A 190 MET cc_start: 0.9032 (tmm) cc_final: 0.8744 (tmm) REVERT: A 393 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8108 (mtt90) REVERT: A 401 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8206 (t-90) REVERT: A 408 MET cc_start: 0.9387 (mmt) cc_final: 0.9001 (mmm) REVERT: A 430 GLU cc_start: 0.9244 (pm20) cc_final: 0.8837 (mp0) REVERT: A 480 MET cc_start: 0.8713 (mtp) cc_final: 0.8418 (mtp) REVERT: A 582 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8624 (mmm-85) REVERT: A 675 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9099 (tt) REVERT: A 679 ILE cc_start: 0.8676 (mt) cc_final: 0.8434 (mm) REVERT: A 699 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: B 40 PHE cc_start: 0.9270 (t80) cc_final: 0.8946 (t80) REVERT: B 114 LYS cc_start: 0.9027 (tppt) cc_final: 0.8623 (mtpt) REVERT: B 123 MET cc_start: 0.8915 (mtm) cc_final: 0.8650 (mtm) REVERT: B 190 MET cc_start: 0.8994 (tmm) cc_final: 0.8746 (tmm) REVERT: B 360 MET cc_start: 0.8326 (ttm) cc_final: 0.8033 (ttm) REVERT: B 366 MET cc_start: 0.8589 (ttm) cc_final: 0.8274 (ttm) REVERT: B 393 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8113 (mtt90) REVERT: B 408 MET cc_start: 0.9410 (mmt) cc_final: 0.9059 (mmm) REVERT: B 430 GLU cc_start: 0.9237 (pm20) cc_final: 0.8836 (mp0) REVERT: B 455 MET cc_start: 0.9392 (tmm) cc_final: 0.9071 (tmm) REVERT: B 520 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8648 (mp) REVERT: B 675 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9074 (tt) REVERT: C 68 ARG cc_start: 0.7814 (tmt-80) cc_final: 0.6611 (tpp-160) REVERT: C 69 MET cc_start: 0.8345 (mmp) cc_final: 0.7125 (tpp) REVERT: C 100 MET cc_start: 0.8743 (mtt) cc_final: 0.8487 (mtt) REVERT: C 213 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7295 (tpp-160) REVERT: C 227 MET cc_start: 0.7015 (ttt) cc_final: 0.6805 (ttt) REVERT: C 406 SER cc_start: 0.8516 (m) cc_final: 0.8279 (p) REVERT: C 458 ASP cc_start: 0.9382 (m-30) cc_final: 0.8866 (m-30) REVERT: C 462 ASP cc_start: 0.8917 (t0) cc_final: 0.8543 (t0) REVERT: C 504 TYR cc_start: 0.8281 (t80) cc_final: 0.7976 (t80) REVERT: D 68 ARG cc_start: 0.7767 (tmt-80) cc_final: 0.6857 (tpp-160) REVERT: D 100 MET cc_start: 0.8716 (mtt) cc_final: 0.8479 (mtt) REVERT: D 101 TYR cc_start: 0.7796 (p90) cc_final: 0.7501 (p90) REVERT: D 213 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.7221 (tpp-160) REVERT: D 243 ASN cc_start: 0.8852 (m110) cc_final: 0.8536 (m110) REVERT: D 378 TYR cc_start: 0.8733 (m-80) cc_final: 0.8485 (m-80) REVERT: D 406 SER cc_start: 0.8692 (m) cc_final: 0.8380 (p) REVERT: D 407 MET cc_start: 0.7655 (tpt) cc_final: 0.7146 (tpt) REVERT: D 458 ASP cc_start: 0.9322 (m-30) cc_final: 0.8754 (m-30) REVERT: D 462 ASP cc_start: 0.9018 (t0) cc_final: 0.8614 (t0) REVERT: D 504 TYR cc_start: 0.8453 (t80) cc_final: 0.8191 (t80) REVERT: D 535 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8000 (mmmt) REVERT: D 540 ASP cc_start: 0.7681 (t0) cc_final: 0.7463 (t0) outliers start: 46 outliers final: 19 residues processed: 247 average time/residue: 0.3206 time to fit residues: 123.8969 Evaluate side-chains 215 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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 249 MET Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 520 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 47 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 718 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4056 r_free = 0.4056 target = 0.144747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081115 restraints weight = 37706.645| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.65 r_work: 0.2883 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21338 Z= 0.182 Angle : 0.564 8.564 29150 Z= 0.279 Chirality : 0.043 0.251 3290 Planarity : 0.004 0.050 3668 Dihedral : 6.207 76.651 3350 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.80 % Allowed : 12.93 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2634 helix: 1.80 (0.12), residues: 1744 sheet: 0.41 (0.62), residues: 58 loop : -0.47 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 509 HIS 0.004 0.001 HIS B 378 PHE 0.024 0.001 PHE A 40 TYR 0.019 0.001 TYR A 183 ARG 0.004 0.001 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 16) link_NAG-ASN : angle 1.91027 ( 48) link_BETA1-4 : bond 0.01027 ( 6) link_BETA1-4 : angle 2.79216 ( 18) hydrogen bonds : bond 0.04081 ( 1283) hydrogen bonds : angle 3.91298 ( 3753) metal coordination : bond 0.00351 ( 4) SS BOND : bond 0.00290 ( 6) SS BOND : angle 0.86470 ( 12) covalent geometry : bond 0.00422 (21304) covalent geometry : angle 0.55471 (29072) Misc. bond : bond 0.00089 ( 2) *********************** 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 263 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.8486 (mt0) cc_final: 0.8130 (mp10) REVERT: A 114 LYS cc_start: 0.9013 (tppt) cc_final: 0.8570 (mtpt) REVERT: A 190 MET cc_start: 0.9048 (tmm) cc_final: 0.8708 (tmm) REVERT: A 393 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8122 (mtt90) REVERT: A 401 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (t-90) REVERT: A 408 MET cc_start: 0.9402 (mmt) cc_final: 0.8997 (mmm) REVERT: A 455 MET cc_start: 0.9367 (tmm) cc_final: 0.9025 (tmm) REVERT: A 480 MET cc_start: 0.8788 (mtp) cc_final: 0.8474 (mtp) REVERT: A 582 ARG cc_start: 0.8855 (tpp80) cc_final: 0.8633 (mmm-85) REVERT: A 640 MET cc_start: 0.9309 (tpt) cc_final: 0.9102 (tpp) REVERT: A 675 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9106 (tt) REVERT: A 679 ILE cc_start: 0.8731 (mt) cc_final: 0.8496 (mm) REVERT: A 699 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: B 40 PHE cc_start: 0.9288 (t80) cc_final: 0.8939 (t80) REVERT: B 62 MET cc_start: 0.8858 (mtm) cc_final: 0.8542 (mtm) REVERT: B 114 LYS cc_start: 0.9058 (tppt) cc_final: 0.8644 (mtpt) REVERT: B 123 MET cc_start: 0.8847 (mtm) cc_final: 0.8542 (mtm) REVERT: B 360 MET cc_start: 0.8403 (ttm) cc_final: 0.8081 (ttm) REVERT: B 366 MET cc_start: 0.8552 (ttm) cc_final: 0.8281 (ttm) REVERT: B 393 ARG cc_start: 0.8369 (mtt180) cc_final: 0.8091 (mtt90) REVERT: B 408 MET cc_start: 0.9443 (mmt) cc_final: 0.9073 (mmm) REVERT: B 455 MET cc_start: 0.9402 (tmm) cc_final: 0.9056 (tmm) REVERT: B 520 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 675 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9138 (tt) REVERT: C 68 ARG cc_start: 0.7684 (tmt-80) cc_final: 0.6431 (tpp-160) REVERT: C 69 MET cc_start: 0.8299 (mmt) cc_final: 0.7382 (tpp) REVERT: C 100 MET cc_start: 0.8795 (mtt) cc_final: 0.8469 (mtt) REVERT: C 213 ARG cc_start: 0.7467 (tpp-160) cc_final: 0.7234 (tpp-160) REVERT: C 225 MET cc_start: 0.8119 (ptt) cc_final: 0.7740 (ptp) REVERT: C 243 ASN cc_start: 0.8829 (m110) cc_final: 0.8619 (m110) REVERT: C 351 MET cc_start: 0.8624 (ptp) cc_final: 0.8390 (ptt) REVERT: C 378 TYR cc_start: 0.8682 (m-80) cc_final: 0.8475 (m-80) REVERT: C 406 SER cc_start: 0.8562 (m) cc_final: 0.8321 (p) REVERT: C 458 ASP cc_start: 0.9396 (m-30) cc_final: 0.8888 (m-30) REVERT: C 462 ASP cc_start: 0.8922 (t0) cc_final: 0.8501 (t0) REVERT: C 509 TRP cc_start: 0.8405 (m-10) cc_final: 0.7755 (m-90) REVERT: D 50 MET cc_start: 0.9238 (mmp) cc_final: 0.8800 (mpp) REVERT: D 68 ARG cc_start: 0.7701 (tmt-80) cc_final: 0.6735 (tpp-160) REVERT: D 100 MET cc_start: 0.8715 (mtt) cc_final: 0.8405 (mtt) REVERT: D 213 ARG cc_start: 0.7538 (tpp-160) cc_final: 0.7279 (tpp-160) REVERT: D 243 ASN cc_start: 0.8922 (m110) cc_final: 0.8603 (m110) REVERT: D 407 MET cc_start: 0.7696 (tpt) cc_final: 0.7305 (tpt) REVERT: D 458 ASP cc_start: 0.9341 (m-30) cc_final: 0.8861 (m-30) REVERT: D 462 ASP cc_start: 0.9008 (t0) cc_final: 0.8581 (t0) REVERT: D 504 TYR cc_start: 0.8460 (t80) cc_final: 0.8199 (t80) REVERT: D 535 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8000 (mmmt) outliers start: 58 outliers final: 30 residues processed: 253 average time/residue: 0.3156 time to fit residues: 126.6687 Evaluate side-chains 226 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 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 197 GLU 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 463 VAL Chi-restraints excluded: chain B residue 520 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 365 ASP Chi-restraints excluded: chain C residue 398 MET 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 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 237 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 32 optimal weight: 0.0020 chunk 62 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 45 optimal weight: 0.0000 chunk 162 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.146005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083440 restraints weight = 37393.702| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.63 r_work: 0.2940 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21338 Z= 0.105 Angle : 0.518 7.971 29150 Z= 0.253 Chirality : 0.040 0.249 3290 Planarity : 0.003 0.049 3668 Dihedral : 5.884 76.347 3350 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.79 % Allowed : 13.80 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.16), residues: 2634 helix: 1.85 (0.12), residues: 1752 sheet: 0.37 (0.61), residues: 58 loop : -0.43 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 509 HIS 0.004 0.001 HIS B 374 PHE 0.024 0.001 PHE B 746 TYR 0.017 0.001 TYR A 50 ARG 0.005 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 16) link_NAG-ASN : angle 1.72287 ( 48) link_BETA1-4 : bond 0.01156 ( 6) link_BETA1-4 : angle 2.73981 ( 18) hydrogen bonds : bond 0.03654 ( 1283) hydrogen bonds : angle 3.77722 ( 3753) metal coordination : bond 0.00116 ( 4) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.71858 ( 12) covalent geometry : bond 0.00219 (21304) covalent geometry : angle 0.50916 (29072) Misc. bond : bond 0.00037 ( 2) *********************** 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 236 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 2.451 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 102 GLN cc_start: 0.8364 (mt0) cc_final: 0.8147 (mp10) REVERT: A 114 LYS cc_start: 0.9024 (tppt) cc_final: 0.8596 (mtpt) REVERT: A 190 MET cc_start: 0.9090 (tmm) cc_final: 0.8778 (tmm) REVERT: A 393 ARG cc_start: 0.8295 (mtt180) cc_final: 0.8053 (mtt90) REVERT: A 401 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: A 408 MET cc_start: 0.9361 (mmt) cc_final: 0.8944 (mmm) REVERT: A 480 MET cc_start: 0.8730 (mtp) cc_final: 0.8481 (mtp) REVERT: A 582 ARG cc_start: 0.8882 (tpp80) cc_final: 0.8659 (mmm-85) REVERT: A 675 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9079 (tt) REVERT: A 679 ILE cc_start: 0.8635 (mt) cc_final: 0.8394 (mm) REVERT: A 699 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: B 40 PHE cc_start: 0.9302 (t80) cc_final: 0.8905 (t80) REVERT: B 62 MET cc_start: 0.8957 (mtm) cc_final: 0.8739 (mtm) REVERT: B 114 LYS cc_start: 0.9003 (tppt) cc_final: 0.8608 (mtpt) REVERT: B 360 MET cc_start: 0.8358 (ttm) cc_final: 0.8061 (ttm) REVERT: B 366 MET cc_start: 0.8526 (ttm) cc_final: 0.8244 (ttm) REVERT: B 393 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8067 (mtt90) REVERT: B 408 MET cc_start: 0.9388 (mmt) cc_final: 0.8987 (mmm) REVERT: B 430 GLU cc_start: 0.9205 (pm20) cc_final: 0.8701 (pt0) REVERT: B 455 MET cc_start: 0.9382 (tmm) cc_final: 0.9055 (tmm) REVERT: B 463 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 520 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8557 (mp) REVERT: B 675 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9051 (tt) REVERT: C 50 MET cc_start: 0.9422 (mmm) cc_final: 0.9027 (mpp) REVERT: C 68 ARG cc_start: 0.7597 (tmt-80) cc_final: 0.6439 (tpp-160) REVERT: C 69 MET cc_start: 0.8308 (mmt) cc_final: 0.7499 (tpp) REVERT: C 100 MET cc_start: 0.8783 (mtt) cc_final: 0.8443 (mtt) REVERT: C 215 LEU cc_start: 0.8823 (mt) cc_final: 0.8622 (mt) REVERT: C 225 MET cc_start: 0.8269 (ptt) cc_final: 0.7784 (mtm) REVERT: C 243 ASN cc_start: 0.8830 (m110) cc_final: 0.8616 (m110) REVERT: C 344 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.6074 (p90) REVERT: C 406 SER cc_start: 0.8561 (m) cc_final: 0.8335 (p) REVERT: C 407 MET cc_start: 0.7685 (tpt) cc_final: 0.7205 (tpt) REVERT: C 458 ASP cc_start: 0.9383 (m-30) cc_final: 0.8892 (m-30) REVERT: C 462 ASP cc_start: 0.8858 (t0) cc_final: 0.8382 (t0) REVERT: C 509 TRP cc_start: 0.8396 (m-10) cc_final: 0.7773 (m-90) REVERT: D 50 MET cc_start: 0.9220 (mmp) cc_final: 0.8739 (mpp) REVERT: D 68 ARG cc_start: 0.7639 (tmt-80) cc_final: 0.6510 (tpp-160) REVERT: D 69 MET cc_start: 0.8360 (mmt) cc_final: 0.7261 (tpp) REVERT: D 100 MET cc_start: 0.8684 (mtt) cc_final: 0.8366 (mtt) REVERT: D 215 LEU cc_start: 0.8824 (mt) cc_final: 0.8612 (mt) REVERT: D 243 ASN cc_start: 0.8869 (m110) cc_final: 0.8532 (m110) REVERT: D 344 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6109 (p90) REVERT: D 407 MET cc_start: 0.7680 (tpt) cc_final: 0.7427 (tpt) REVERT: D 458 ASP cc_start: 0.9331 (m-30) cc_final: 0.8826 (m-30) REVERT: D 462 ASP cc_start: 0.8957 (t0) cc_final: 0.8538 (t0) REVERT: D 504 TYR cc_start: 0.8438 (t80) cc_final: 0.8195 (t80) outliers start: 37 outliers final: 19 residues processed: 231 average time/residue: 0.3214 time to fit residues: 116.5983 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 : 2.215 ------------------------------------------------------------------------------- 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 291 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL 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 463 VAL Chi-restraints excluded: chain B residue 520 LEU 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 398 MET 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 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 128 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 61 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN C 146 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.142108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077417 restraints weight = 37660.949| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.63 r_work: 0.2817 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 21338 Z= 0.345 Angle : 0.670 10.658 29150 Z= 0.338 Chirality : 0.047 0.237 3290 Planarity : 0.004 0.042 3668 Dihedral : 6.329 76.789 3350 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.56 % Allowed : 13.51 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2634 helix: 1.65 (0.12), residues: 1732 sheet: 0.21 (0.55), residues: 72 loop : -0.58 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 477 HIS 0.005 0.001 HIS A 378 PHE 0.024 0.002 PHE A 40 TYR 0.030 0.002 TYR B 183 ARG 0.006 0.001 ARG B 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 16) link_NAG-ASN : angle 2.02364 ( 48) link_BETA1-4 : bond 0.00911 ( 6) link_BETA1-4 : angle 2.75751 ( 18) hydrogen bonds : bond 0.04541 ( 1283) hydrogen bonds : angle 4.04778 ( 3753) metal coordination : bond 0.00704 ( 4) SS BOND : bond 0.00411 ( 6) SS BOND : angle 1.03255 ( 12) covalent geometry : bond 0.00811 (21304) covalent geometry : angle 0.66227 (29072) Misc. bond : bond 0.00124 ( 2) *********************** 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 245 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 2.213 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: 0.8511 (mt0) cc_final: 0.8262 (mp10) REVERT: A 114 LYS cc_start: 0.9099 (tppt) cc_final: 0.8630 (mtpt) REVERT: A 323 MET cc_start: 0.9341 (mmm) cc_final: 0.8973 (mmm) REVERT: A 393 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8092 (mtt90) REVERT: A 401 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8305 (t-90) REVERT: A 408 MET cc_start: 0.9453 (mmt) cc_final: 0.9080 (mmm) REVERT: A 430 GLU cc_start: 0.9236 (pm20) cc_final: 0.8766 (pt0) REVERT: A 455 MET cc_start: 0.9393 (tmm) cc_final: 0.9037 (tmm) REVERT: A 480 MET cc_start: 0.8849 (mtp) cc_final: 0.8482 (mtp) REVERT: A 582 ARG cc_start: 0.8958 (tpp80) cc_final: 0.8756 (mmm-85) REVERT: A 675 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9212 (tt) REVERT: A 699 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: B 40 PHE cc_start: 0.9297 (t80) cc_final: 0.8949 (t80) REVERT: B 114 LYS cc_start: 0.9143 (tppt) cc_final: 0.8717 (mtpt) REVERT: B 123 MET cc_start: 0.8874 (mtm) cc_final: 0.8585 (mtm) REVERT: B 190 MET cc_start: 0.9104 (tmm) cc_final: 0.8736 (tmm) REVERT: B 360 MET cc_start: 0.8578 (ttm) cc_final: 0.8132 (ttm) REVERT: B 393 ARG cc_start: 0.8540 (mtt180) cc_final: 0.8303 (mtt90) REVERT: B 408 MET cc_start: 0.9455 (mmt) cc_final: 0.9087 (mmm) REVERT: B 455 MET cc_start: 0.9425 (tmm) cc_final: 0.9061 (tmm) REVERT: C 50 MET cc_start: 0.9488 (mmm) cc_final: 0.9114 (mpp) REVERT: C 68 ARG cc_start: 0.7514 (tmt-80) cc_final: 0.6403 (tpp-160) REVERT: C 69 MET cc_start: 0.8262 (mmt) cc_final: 0.7389 (tpp) REVERT: C 100 MET cc_start: 0.8902 (mtt) cc_final: 0.8606 (mtt) REVERT: C 243 ASN cc_start: 0.8875 (m110) cc_final: 0.8621 (m110) REVERT: C 256 PHE cc_start: 0.7743 (m-80) cc_final: 0.7516 (m-80) REVERT: C 344 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6046 (p90) REVERT: C 351 MET cc_start: 0.8555 (ptp) cc_final: 0.8334 (ptt) REVERT: C 407 MET cc_start: 0.7757 (tpt) cc_final: 0.7290 (tpt) REVERT: C 451 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7704 (tm-30) REVERT: C 462 ASP cc_start: 0.8862 (t0) cc_final: 0.8414 (t0) REVERT: D 68 ARG cc_start: 0.7544 (tmt-80) cc_final: 0.6844 (tpp-160) REVERT: D 69 MET cc_start: 0.8370 (mmt) cc_final: 0.7503 (tpp) REVERT: D 100 MET cc_start: 0.8812 (mtt) cc_final: 0.8484 (mtt) REVERT: D 225 MET cc_start: 0.8247 (ptt) cc_final: 0.7720 (mtm) REVERT: D 243 ASN cc_start: 0.8941 (m110) cc_final: 0.8628 (m110) REVERT: D 298 TYR cc_start: 0.7689 (t80) cc_final: 0.7327 (t80) REVERT: D 344 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.6210 (p90) REVERT: D 407 MET cc_start: 0.7791 (tpt) cc_final: 0.7301 (tpt) REVERT: D 458 ASP cc_start: 0.9351 (m-30) cc_final: 0.8845 (m-30) REVERT: D 462 ASP cc_start: 0.9005 (t0) cc_final: 0.8571 (t0) REVERT: D 504 TYR cc_start: 0.8501 (t80) cc_final: 0.8201 (t80) outliers start: 53 outliers final: 34 residues processed: 236 average time/residue: 0.3035 time to fit residues: 113.3013 Evaluate side-chains 223 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 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 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 379 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER 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 504 TYR 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 398 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 169 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN B 61 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.143410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080309 restraints weight = 37244.764| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.64 r_work: 0.2881 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3093 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= 0.143 Angle : 0.558 10.683 29150 Z= 0.272 Chirality : 0.041 0.238 3290 Planarity : 0.004 0.045 3668 Dihedral : 5.981 76.463 3348 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.12 % Allowed : 15.06 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.16), residues: 2634 helix: 1.76 (0.12), residues: 1744 sheet: 0.46 (0.53), residues: 74 loop : -0.53 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 77 HIS 0.004 0.001 HIS B 345 PHE 0.012 0.001 PHE A 683 TYR 0.014 0.001 TYR A 50 ARG 0.004 0.001 ARG B 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 16) link_NAG-ASN : angle 1.77853 ( 48) link_BETA1-4 : bond 0.01210 ( 6) link_BETA1-4 : angle 2.75607 ( 18) hydrogen bonds : bond 0.03940 ( 1283) hydrogen bonds : angle 3.86721 ( 3753) metal coordination : bond 0.00238 ( 4) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.01259 ( 12) covalent geometry : bond 0.00322 (21304) covalent geometry : angle 0.54949 (29072) Misc. bond : bond 0.00078 ( 2) *********************** 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 241 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 2.336 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: 0.8457 (mt0) cc_final: 0.8232 (mp10) REVERT: A 114 LYS cc_start: 0.9034 (tppt) cc_final: 0.8605 (mtpt) REVERT: A 190 MET cc_start: 0.9143 (tmm) cc_final: 0.8794 (tmm) REVERT: A 323 MET cc_start: 0.9294 (mmm) cc_final: 0.8973 (mmm) REVERT: A 393 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8082 (mtt90) REVERT: A 401 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8207 (t-90) REVERT: A 408 MET cc_start: 0.9397 (mmt) cc_final: 0.9013 (mmm) REVERT: A 430 GLU cc_start: 0.9076 (pm20) cc_final: 0.8663 (pt0) REVERT: A 455 MET cc_start: 0.9365 (tmm) cc_final: 0.9032 (tmm) REVERT: A 480 MET cc_start: 0.8833 (mtp) cc_final: 0.8553 (mtp) REVERT: A 582 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8686 (mmm-85) REVERT: A 625 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8573 (mmtp) REVERT: A 675 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9169 (tt) REVERT: A 679 ILE cc_start: 0.8721 (mt) cc_final: 0.8517 (mm) REVERT: A 699 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 40 PHE cc_start: 0.9301 (t80) cc_final: 0.8929 (t80) REVERT: B 62 MET cc_start: 0.8964 (mtm) cc_final: 0.8737 (mtm) REVERT: B 114 LYS cc_start: 0.9072 (tppt) cc_final: 0.8591 (mtpp) REVERT: B 123 MET cc_start: 0.8794 (mtm) cc_final: 0.8450 (mtm) REVERT: B 302 TRP cc_start: 0.8646 (m100) cc_final: 0.8335 (m100) REVERT: B 360 MET cc_start: 0.8510 (ttm) cc_final: 0.8111 (ttm) REVERT: B 393 ARG cc_start: 0.8398 (mtt180) cc_final: 0.8169 (mtt90) REVERT: B 408 MET cc_start: 0.9420 (mmt) cc_final: 0.9038 (mmm) REVERT: B 430 GLU cc_start: 0.9181 (pm20) cc_final: 0.8744 (mp0) REVERT: B 455 MET cc_start: 0.9394 (tmm) cc_final: 0.9057 (tmm) REVERT: B 463 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9027 (p) REVERT: C 50 MET cc_start: 0.9482 (mmm) cc_final: 0.9081 (mpp) REVERT: C 68 ARG cc_start: 0.7480 (tmt-80) cc_final: 0.6229 (tpp-160) REVERT: C 69 MET cc_start: 0.8238 (mmt) cc_final: 0.7455 (tpp) REVERT: C 100 MET cc_start: 0.8881 (mtt) cc_final: 0.8571 (mtt) REVERT: C 215 LEU cc_start: 0.8869 (mt) cc_final: 0.8660 (mt) REVERT: C 225 MET cc_start: 0.8371 (ptt) cc_final: 0.7749 (mmt) REVERT: C 243 ASN cc_start: 0.8861 (m110) cc_final: 0.8595 (m110) REVERT: C 256 PHE cc_start: 0.7812 (m-80) cc_final: 0.7602 (m-80) REVERT: C 344 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6116 (p90) REVERT: C 451 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7558 (tm-30) REVERT: C 458 ASP cc_start: 0.9393 (m-30) cc_final: 0.8939 (m-30) REVERT: C 462 ASP cc_start: 0.8863 (t0) cc_final: 0.8394 (t0) REVERT: D 68 ARG cc_start: 0.7460 (tmt-80) cc_final: 0.6844 (tpp-160) REVERT: D 69 MET cc_start: 0.8403 (mmt) cc_final: 0.7558 (tpp) REVERT: D 100 MET cc_start: 0.8750 (mtt) cc_final: 0.8436 (mtt) REVERT: D 215 LEU cc_start: 0.8772 (mt) cc_final: 0.8560 (mt) REVERT: D 243 ASN cc_start: 0.8911 (m110) cc_final: 0.8574 (m110) REVERT: D 344 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6145 (p90) REVERT: D 407 MET cc_start: 0.7802 (tpt) cc_final: 0.7522 (tpt) REVERT: D 458 ASP cc_start: 0.9346 (m-30) cc_final: 0.8825 (m-30) REVERT: D 462 ASP cc_start: 0.9013 (t0) cc_final: 0.8559 (t0) REVERT: D 504 TYR cc_start: 0.8357 (t80) cc_final: 0.8139 (t80) REVERT: D 540 ASP cc_start: 0.7818 (t0) cc_final: 0.6482 (p0) outliers start: 44 outliers final: 29 residues processed: 234 average time/residue: 0.3002 time to fit residues: 112.7630 Evaluate side-chains 233 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 2.283 ------------------------------------------------------------------------------- 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 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 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 291 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 136 ASP 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 398 MET 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 561 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 101 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 82 optimal weight: 0.0370 chunk 184 optimal weight: 0.8980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 61 ASN A 718 ASN B 718 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.145062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082432 restraints weight = 37532.620| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.65 r_work: 0.2920 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3192 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= 0.108 Angle : 0.540 10.706 29150 Z= 0.260 Chirality : 0.040 0.234 3290 Planarity : 0.004 0.046 3668 Dihedral : 5.714 76.393 3346 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.88 % Allowed : 15.64 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2634 helix: 1.88 (0.12), residues: 1746 sheet: 0.39 (0.62), residues: 58 loop : -0.41 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 505 HIS 0.006 0.001 HIS A 345 PHE 0.029 0.001 PHE A 40 TYR 0.026 0.001 TYR B 50 ARG 0.005 0.000 ARG B 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 16) link_NAG-ASN : angle 1.64367 ( 48) link_BETA1-4 : bond 0.01118 ( 6) link_BETA1-4 : angle 2.72723 ( 18) hydrogen bonds : bond 0.03559 ( 1283) hydrogen bonds : angle 3.79308 ( 3753) metal coordination : bond 0.00092 ( 4) SS BOND : bond 0.00360 ( 6) SS BOND : angle 1.26680 ( 12) covalent geometry : bond 0.00233 (21304) covalent geometry : angle 0.53121 (29072) Misc. bond : bond 0.00033 ( 2) *********************** 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 231 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8974 (tppt) cc_final: 0.8544 (mtpt) REVERT: A 190 MET cc_start: 0.9147 (tmm) cc_final: 0.8829 (tmm) REVERT: A 297 MET cc_start: 0.9052 (mtm) cc_final: 0.8696 (mtm) REVERT: A 393 ARG cc_start: 0.8307 (mtt180) cc_final: 0.8066 (mtt90) REVERT: A 401 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: A 408 MET cc_start: 0.9373 (mmt) cc_final: 0.8953 (mmm) REVERT: A 430 GLU cc_start: 0.9066 (pm20) cc_final: 0.8656 (pt0) REVERT: A 463 VAL cc_start: 0.9283 (OUTLIER) cc_final: 0.9004 (p) REVERT: A 480 MET cc_start: 0.8786 (mtp) cc_final: 0.8536 (mtp) REVERT: A 582 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8658 (mmm-85) REVERT: A 625 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (mmtp) REVERT: A 675 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9121 (tt) REVERT: A 679 ILE cc_start: 0.8652 (mt) cc_final: 0.8413 (mm) REVERT: A 699 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: B 40 PHE cc_start: 0.9302 (t80) cc_final: 0.8935 (t80) REVERT: B 114 LYS cc_start: 0.9028 (tppt) cc_final: 0.8561 (mtpp) REVERT: B 302 TRP cc_start: 0.8623 (m100) cc_final: 0.8290 (m100) REVERT: B 357 ARG cc_start: 0.8944 (mtt180) cc_final: 0.8165 (mtt-85) REVERT: B 393 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8104 (mtt90) REVERT: B 408 MET cc_start: 0.9398 (mmt) cc_final: 0.8990 (mmm) REVERT: B 430 GLU cc_start: 0.9102 (pm20) cc_final: 0.8635 (pt0) REVERT: B 463 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9010 (p) REVERT: C 50 MET cc_start: 0.9490 (mmm) cc_final: 0.9065 (mpp) REVERT: C 68 ARG cc_start: 0.7549 (tmt-80) cc_final: 0.6344 (tpp-160) REVERT: C 69 MET cc_start: 0.8181 (mmt) cc_final: 0.7412 (tpp) REVERT: C 100 MET cc_start: 0.8795 (mtt) cc_final: 0.8457 (mtt) REVERT: C 215 LEU cc_start: 0.8788 (mt) cc_final: 0.8351 (mt) REVERT: C 225 MET cc_start: 0.8465 (ptt) cc_final: 0.7906 (mmt) REVERT: C 243 ASN cc_start: 0.8799 (m110) cc_final: 0.8534 (m110) REVERT: C 344 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6118 (p90) REVERT: C 451 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7554 (tm-30) REVERT: C 458 ASP cc_start: 0.9387 (m-30) cc_final: 0.8948 (m-30) REVERT: C 462 ASP cc_start: 0.8890 (t0) cc_final: 0.8432 (t0) REVERT: C 540 ASP cc_start: 0.8098 (t0) cc_final: 0.6921 (p0) REVERT: D 68 ARG cc_start: 0.7577 (tmt-80) cc_final: 0.6963 (tpp-160) REVERT: D 69 MET cc_start: 0.8404 (mmt) cc_final: 0.7571 (tpp) REVERT: D 100 MET cc_start: 0.8726 (mtt) cc_final: 0.8401 (mtt) REVERT: D 215 LEU cc_start: 0.8715 (mt) cc_final: 0.8256 (mt) REVERT: D 225 MET cc_start: 0.8180 (ptt) cc_final: 0.7781 (ptp) REVERT: D 344 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.6240 (p90) REVERT: D 451 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7732 (tm-30) REVERT: D 458 ASP cc_start: 0.9371 (m-30) cc_final: 0.8848 (m-30) REVERT: D 462 ASP cc_start: 0.8967 (t0) cc_final: 0.8548 (t0) REVERT: D 504 TYR cc_start: 0.8368 (t80) cc_final: 0.8162 (t80) REVERT: D 540 ASP cc_start: 0.7855 (t0) cc_final: 0.6556 (p0) outliers start: 39 outliers final: 20 residues processed: 222 average time/residue: 0.3154 time to fit residues: 110.8450 Evaluate side-chains 213 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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 401 HIS 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 731 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 379 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 398 MET 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 561 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 19 optimal weight: 0.2980 chunk 173 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 255 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** D 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.144795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082220 restraints weight = 37503.807| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.62 r_work: 0.2925 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3268 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= 0.119 Angle : 0.544 11.332 29150 Z= 0.263 Chirality : 0.041 0.230 3290 Planarity : 0.003 0.045 3668 Dihedral : 5.679 76.428 3346 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.93 % Allowed : 15.44 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2634 helix: 1.88 (0.12), residues: 1750 sheet: 0.34 (0.61), residues: 58 loop : -0.40 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 505 HIS 0.004 0.001 HIS B 378 PHE 0.025 0.001 PHE A 40 TYR 0.027 0.001 TYR A 50 ARG 0.005 0.000 ARG B 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 16) link_NAG-ASN : angle 1.63264 ( 48) link_BETA1-4 : bond 0.01012 ( 6) link_BETA1-4 : angle 2.66827 ( 18) hydrogen bonds : bond 0.03568 ( 1283) hydrogen bonds : angle 3.78205 ( 3753) metal coordination : bond 0.00188 ( 4) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.69297 ( 12) covalent geometry : bond 0.00266 (21304) covalent geometry : angle 0.53596 (29072) Misc. bond : bond 0.00040 ( 2) *********************** 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 233 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 2.321 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: 0.9253 (t80) cc_final: 0.9006 (t80) REVERT: A 69 TRP cc_start: 0.8419 (t60) cc_final: 0.8125 (t60) REVERT: A 114 LYS cc_start: 0.8979 (tppt) cc_final: 0.8545 (mtpt) REVERT: A 190 MET cc_start: 0.9159 (tmm) cc_final: 0.8796 (tmm) REVERT: A 401 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: A 408 MET cc_start: 0.9367 (mmt) cc_final: 0.8941 (mmm) REVERT: A 430 GLU cc_start: 0.9068 (pm20) cc_final: 0.8673 (mp0) REVERT: A 463 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.8999 (p) REVERT: A 480 MET cc_start: 0.8773 (mtp) cc_final: 0.8534 (mtp) REVERT: A 582 ARG cc_start: 0.8859 (tpp80) cc_final: 0.8624 (mmm-85) REVERT: A 625 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8444 (mmtt) REVERT: A 675 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9105 (tt) REVERT: A 679 ILE cc_start: 0.8651 (mt) cc_final: 0.8385 (mm) REVERT: A 699 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: B 40 PHE cc_start: 0.9302 (t80) cc_final: 0.8934 (t80) REVERT: B 114 LYS cc_start: 0.9035 (tppt) cc_final: 0.8561 (mtpp) REVERT: B 302 TRP cc_start: 0.8625 (m100) cc_final: 0.8260 (m100) REVERT: B 357 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8123 (mtt-85) REVERT: B 393 ARG cc_start: 0.8376 (mtt180) cc_final: 0.8126 (mtt90) REVERT: B 408 MET cc_start: 0.9400 (mmt) cc_final: 0.8986 (mmm) REVERT: B 430 GLU cc_start: 0.9091 (pm20) cc_final: 0.8647 (pt0) REVERT: B 463 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9004 (p) REVERT: C 50 MET cc_start: 0.9448 (mmm) cc_final: 0.9031 (mpp) REVERT: C 68 ARG cc_start: 0.7545 (tmt-80) cc_final: 0.6333 (tpp-160) REVERT: C 69 MET cc_start: 0.8168 (mmt) cc_final: 0.7401 (tpp) REVERT: C 96 PHE cc_start: 0.8950 (m-80) cc_final: 0.8701 (m-80) REVERT: C 100 MET cc_start: 0.8803 (mtt) cc_final: 0.8422 (mtt) REVERT: C 215 LEU cc_start: 0.8730 (mt) cc_final: 0.8308 (mt) REVERT: C 225 MET cc_start: 0.8461 (ptt) cc_final: 0.7895 (mmt) REVERT: C 243 ASN cc_start: 0.8790 (m110) cc_final: 0.8524 (m110) REVERT: C 344 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.6121 (p90) REVERT: C 451 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7581 (tm-30) REVERT: C 458 ASP cc_start: 0.9358 (m-30) cc_final: 0.8879 (m-30) REVERT: C 462 ASP cc_start: 0.8899 (t0) cc_final: 0.8441 (t0) REVERT: C 540 ASP cc_start: 0.7934 (t0) cc_final: 0.6750 (p0) REVERT: D 68 ARG cc_start: 0.7578 (tmt-80) cc_final: 0.6920 (tpp-160) REVERT: D 69 MET cc_start: 0.8393 (mmt) cc_final: 0.7554 (tpp) REVERT: D 100 MET cc_start: 0.8719 (mtt) cc_final: 0.8404 (mtt) REVERT: D 215 LEU cc_start: 0.8735 (mt) cc_final: 0.8268 (mt) REVERT: D 225 MET cc_start: 0.8175 (ptt) cc_final: 0.7652 (mmt) REVERT: D 344 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.6213 (p90) REVERT: D 451 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7741 (tm-30) REVERT: D 458 ASP cc_start: 0.9359 (m-30) cc_final: 0.8843 (m-30) REVERT: D 462 ASP cc_start: 0.8965 (t0) cc_final: 0.8552 (t0) REVERT: D 504 TYR cc_start: 0.8346 (t80) cc_final: 0.8135 (t80) REVERT: D 540 ASP cc_start: 0.7872 (t0) cc_final: 0.6571 (p0) outliers start: 40 outliers final: 25 residues processed: 224 average time/residue: 0.3340 time to fit residues: 117.1925 Evaluate side-chains 218 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 2.512 ------------------------------------------------------------------------------- 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 307 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 731 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 249 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 398 MET 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 561 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 172 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.145200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082649 restraints weight = 37415.796| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.64 r_work: 0.2925 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21338 Z= 0.112 Angle : 0.544 11.810 29150 Z= 0.262 Chirality : 0.040 0.225 3290 Planarity : 0.003 0.044 3668 Dihedral : 5.617 76.457 3346 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.88 % Allowed : 15.73 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2634 helix: 1.91 (0.12), residues: 1754 sheet: 0.32 (0.61), residues: 58 loop : -0.37 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 77 HIS 0.004 0.001 HIS B 374 PHE 0.025 0.001 PHE A 40 TYR 0.027 0.001 TYR A 50 ARG 0.004 0.000 ARG B 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 16) link_NAG-ASN : angle 1.56495 ( 48) link_BETA1-4 : bond 0.01111 ( 6) link_BETA1-4 : angle 2.67729 ( 18) hydrogen bonds : bond 0.03479 ( 1283) hydrogen bonds : angle 3.75778 ( 3753) metal coordination : bond 0.00148 ( 4) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.51090 ( 12) covalent geometry : bond 0.00248 (21304) covalent geometry : angle 0.53561 (29072) Misc. bond : bond 0.00034 ( 2) ********************** 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 230 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 2.535 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: 0.8977 (tppt) cc_final: 0.8545 (mtpt) REVERT: A 190 MET cc_start: 0.9165 (tmm) cc_final: 0.8864 (tmm) REVERT: A 302 TRP cc_start: 0.8555 (m100) cc_final: 0.8243 (m100) REVERT: A 401 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8101 (t-90) REVERT: A 408 MET cc_start: 0.9375 (mmt) cc_final: 0.8945 (mmm) REVERT: A 430 GLU cc_start: 0.9051 (pm20) cc_final: 0.8663 (mp0) REVERT: A 463 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9003 (p) REVERT: A 480 MET cc_start: 0.8788 (mtp) cc_final: 0.8536 (mtp) REVERT: A 582 ARG cc_start: 0.8873 (tpp80) cc_final: 0.8627 (mmm-85) REVERT: A 625 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8436 (mmtt) REVERT: A 675 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9077 (tt) REVERT: A 679 ILE cc_start: 0.8622 (mt) cc_final: 0.8363 (mm) REVERT: A 699 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: B 40 PHE cc_start: 0.9301 (t80) cc_final: 0.8938 (t80) REVERT: B 114 LYS cc_start: 0.9037 (tppt) cc_final: 0.8571 (mtpp) REVERT: B 302 TRP cc_start: 0.8590 (m100) cc_final: 0.8262 (m100) REVERT: B 357 ARG cc_start: 0.8907 (mtt180) cc_final: 0.8089 (mtt-85) REVERT: B 393 ARG cc_start: 0.8360 (mtt180) cc_final: 0.8120 (mtt90) REVERT: B 408 MET cc_start: 0.9399 (mmt) cc_final: 0.8979 (mmm) REVERT: B 430 GLU cc_start: 0.9092 (pm20) cc_final: 0.8634 (pt0) REVERT: B 463 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9003 (p) REVERT: C 50 MET cc_start: 0.9449 (mmm) cc_final: 0.9133 (mpp) REVERT: C 68 ARG cc_start: 0.7538 (tmt-80) cc_final: 0.6333 (tpp-160) REVERT: C 69 MET cc_start: 0.8361 (mmt) cc_final: 0.7612 (tpp) REVERT: C 96 PHE cc_start: 0.9027 (m-80) cc_final: 0.8763 (m-80) REVERT: C 100 MET cc_start: 0.8770 (mtt) cc_final: 0.8384 (mtt) REVERT: C 215 LEU cc_start: 0.8719 (mt) cc_final: 0.8359 (mt) REVERT: C 225 MET cc_start: 0.8534 (ptt) cc_final: 0.7887 (mmt) REVERT: C 243 ASN cc_start: 0.8788 (m110) cc_final: 0.8518 (m110) REVERT: C 344 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6012 (p90) REVERT: C 451 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7580 (tm-30) REVERT: C 458 ASP cc_start: 0.9354 (m-30) cc_final: 0.8884 (m-30) REVERT: C 462 ASP cc_start: 0.8897 (t0) cc_final: 0.8431 (t0) REVERT: C 540 ASP cc_start: 0.7904 (t0) cc_final: 0.6709 (p0) REVERT: D 68 ARG cc_start: 0.7545 (tmt-80) cc_final: 0.6931 (tpp-160) REVERT: D 69 MET cc_start: 0.8367 (mmt) cc_final: 0.7531 (tpp) REVERT: D 100 MET cc_start: 0.8689 (mtt) cc_final: 0.8394 (mtt) REVERT: D 215 LEU cc_start: 0.8703 (mt) cc_final: 0.8314 (mt) REVERT: D 225 MET cc_start: 0.8236 (ptt) cc_final: 0.7726 (mmt) REVERT: D 344 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.6127 (p90) REVERT: D 451 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7925 (tt0) REVERT: D 458 ASP cc_start: 0.9354 (m-30) cc_final: 0.8842 (m-30) REVERT: D 462 ASP cc_start: 0.8984 (t0) cc_final: 0.8606 (t0) REVERT: D 504 TYR cc_start: 0.8348 (t80) cc_final: 0.8140 (t80) REVERT: D 540 ASP cc_start: 0.7952 (t0) cc_final: 0.6697 (p0) outliers start: 39 outliers final: 27 residues processed: 219 average time/residue: 0.3178 time to fit residues: 109.7635 Evaluate side-chains 220 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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 307 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 731 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 249 MET Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 344 TYR Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 398 MET 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 561 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 153 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 141 optimal weight: 0.0980 chunk 11 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.143740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080786 restraints weight = 37472.858| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.60 r_work: 0.2895 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21338 Z= 0.161 Angle : 0.562 11.475 29150 Z= 0.274 Chirality : 0.042 0.222 3290 Planarity : 0.004 0.043 3668 Dihedral : 5.710 76.538 3346 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.93 % Allowed : 15.54 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2634 helix: 1.92 (0.12), residues: 1746 sheet: 0.36 (0.61), residues: 58 loop : -0.43 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 69 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.001 PHE A 40 TYR 0.023 0.001 TYR B 50 ARG 0.004 0.001 ARG B 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 16) link_NAG-ASN : angle 1.60510 ( 48) link_BETA1-4 : bond 0.01030 ( 6) link_BETA1-4 : angle 2.63730 ( 18) hydrogen bonds : bond 0.03707 ( 1283) hydrogen bonds : angle 3.80689 ( 3753) metal coordination : bond 0.00295 ( 4) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.49340 ( 12) covalent geometry : bond 0.00372 (21304) covalent geometry : angle 0.55402 (29072) Misc. bond : bond 0.00065 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14532.96 seconds wall clock time: 247 minutes 54.38 seconds (14874.38 seconds total)