Starting phenix.real_space_refine on Thu Sep 18 08:43:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cv7_45957/09_2025/9cv7_45957.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cv7_45957/09_2025/9cv7_45957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cv7_45957/09_2025/9cv7_45957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cv7_45957/09_2025/9cv7_45957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cv7_45957/09_2025/9cv7_45957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cv7_45957/09_2025/9cv7_45957.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 9610 2.51 5 N 2590 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15291 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4411 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 24, 'TRANS': 532} Chain breaks: 4 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4311 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 24, 'TRANS': 521} Chain breaks: 5 Chain: "D" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4233 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 24, 'TRANS': 509} Chain breaks: 5 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "G" 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: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.17, per 1000 atoms: 0.27 Number of scatterers: 15291 At special positions: 0 Unit cell: (109.567, 119.619, 131.681, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 2976 8.00 N 2590 7.00 C 9610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.02 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.00 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=1.85 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " 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-ASN " NAG A 1 " - " ASN B 262 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 197 " " NAG B 703 " - " ASN B 230 " " NAG B 704 " - " ASN B 234 " " NAG B 705 " - " ASN B 229 " " NAG B 706 " - " ASN B 289 " " NAG B 707 " - " ASN B 301 " " NAG B 708 " - " ASN B 332 " " NAG B 709 " - " ASN B 386 " " NAG B 710 " - " ASN B 448 " " NAG B 711 " - " ASN B 611 " " NAG C 701 " - " ASN C 230 " " NAG C 702 " - " ASN C 234 " " NAG C 703 " - " ASN C 241 " " NAG C 704 " - " ASN C 289 " " NAG C 705 " - " ASN C 332 " " NAG C 706 " - " ASN C 386 " " NAG C 707 " - " ASN C 88 " " NAG C 708 " - " ASN C 276 " " NAG C 709 " - " ASN C 293 " " NAG C 710 " - " ASN C 355 " " NAG C 711 " - " ASN C 413 " " NAG D 701 " - " ASN D 160 " " NAG D 702 " - " ASN D 197 " " NAG D 703 " - " ASN D 230 " " NAG D 704 " - " ASN D 234 " " NAG D 705 " - " ASN D 241 " " NAG D 706 " - " ASN D 289 " " NAG D 707 " - " ASN D 332 " " NAG D 708 " - " ASN D 386 " " NAG E 1 " - " ASN C 197 " " NAG F 1 " - " ASN C 262 " " NAG G 1 " - " ASN D 262 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 696.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 33 sheets defined 25.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.756A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.265A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 126 removed outlier: 4.038A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 126' Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 334 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.695A pdb=" N PHE B 391 " --> pdb=" O THR B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.171A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.739A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.877A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.934A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.275A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.577A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.645A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 483 " --> pdb=" O TRP C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 544 removed outlier: 3.731A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 597 Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.618A pdb=" N TRP C 614 " --> pdb=" O ASN C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 626 removed outlier: 4.243A pdb=" N ASP C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.614A pdb=" N CYS C 662 " --> pdb=" O LYS C 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.471A pdb=" N ASP D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.512A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 126' Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.523A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.870A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 545 removed outlier: 3.610A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 627 through 659 removed outlier: 4.806A pdb=" N ASN D 637 " --> pdb=" O ARG D 633 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N HIS D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP D 640 " --> pdb=" O GLY D 636 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 648 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 494 through 498 removed outlier: 5.330A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.616A pdb=" N ARG B 46 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 490 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.478A pdb=" N ILE B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 424 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 177 removed outlier: 4.200A pdb=" N ARG B 170 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET B 161 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET B 154 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 134 " --> pdb=" O MET B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.641A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N LYS B 446 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N ILE B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 288 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 271 through 274 removed outlier: 3.676A pdb=" N LEU B 288 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N GLU B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ASN B 448 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N ILE B 292 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N LYS B 446 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N ILE B 294 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N THR B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 312 removed outlier: 6.727A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.987A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP H 72 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AB4, first strand: chain 'H' and resid 88 through 90 Processing sheet with id=AB5, first strand: chain 'L' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AB7, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AB8, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.620A pdb=" N ARG C 46 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 490 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.591A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.363A pdb=" N TYR C 134 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLU C 153 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N SER C 132 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N LYS C 155 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N ASP C 130 " --> pdb=" O LYS C 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 200 through 201 removed outlier: 6.544A pdb=" N THR C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR C 435 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.650A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.650A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.866A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.516A pdb=" N ASN C 301 " --> pdb=" O VAL C 323A" (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.880A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 495 through 496 removed outlier: 4.586A pdb=" N VAL D 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AD2, first strand: chain 'D' and resid 169 through 177 removed outlier: 7.257A pdb=" N MET D 154 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 134 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 129 " --> pdb=" O TYR D 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.784A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.363A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N ILE D 292 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N LYS D 446 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 11.630A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 301 through 312 removed outlier: 6.471A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 309 " --> pdb=" O GLN D 315 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.844A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS D 331 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 416 " --> pdb=" O CYS D 331 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4808 1.35 - 1.48: 3954 1.48 - 1.61: 6679 1.61 - 1.74: 0 1.74 - 1.87: 161 Bond restraints: 15602 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" C2 NAG A 2 " ideal model delta sigma weight residual 1.532 1.571 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" CB LYS C 574 " pdb=" CG LYS C 574 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" CB GLN D 650 " pdb=" CG GLN D 650 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.65e+00 bond pdb=" CB CYS C 239 " pdb=" SG CYS C 239 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.36e+00 bond pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " ideal model delta sigma weight residual 1.808 1.867 -0.059 3.30e-02 9.18e+02 3.22e+00 ... (remaining 15597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 20150 2.25 - 4.50: 819 4.50 - 6.74: 176 6.74 - 8.99: 30 8.99 - 11.24: 8 Bond angle restraints: 21183 Sorted by residual: angle pdb=" CA TRP H 95 " pdb=" CB TRP H 95 " pdb=" CG TRP H 95 " ideal model delta sigma weight residual 113.60 123.07 -9.47 1.90e+00 2.77e-01 2.48e+01 angle pdb=" CA CYS C 228 " pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " ideal model delta sigma weight residual 114.40 103.20 11.20 2.30e+00 1.89e-01 2.37e+01 angle pdb=" CA PHE H 33 " pdb=" CB PHE H 33 " pdb=" CG PHE H 33 " ideal model delta sigma weight residual 113.80 118.46 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.74 104.13 6.61 1.66e+00 3.63e-01 1.58e+01 angle pdb=" N ASN C 607 " pdb=" CA ASN C 607 " pdb=" C ASN C 607 " ideal model delta sigma weight residual 110.80 118.85 -8.05 2.13e+00 2.20e-01 1.43e+01 ... (remaining 21178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 9279 26.53 - 53.06: 582 53.06 - 79.58: 106 79.58 - 106.11: 15 106.11 - 132.64: 1 Dihedral angle restraints: 9983 sinusoidal: 4584 harmonic: 5399 Sorted by residual: dihedral pdb=" CB CYS B 501 " pdb=" SG CYS B 501 " pdb=" SG CYS C 662 " pdb=" CB CYS C 662 " ideal model delta sinusoidal sigma weight residual 93.00 151.35 -58.35 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CB CYS C 598 " pdb=" SG CYS C 598 " pdb=" SG CYS C 604 " pdb=" CB CYS C 604 " ideal model delta sinusoidal sigma weight residual 93.00 145.66 -52.66 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -135.53 49.53 1 1.00e+01 1.00e-02 3.37e+01 ... (remaining 9980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2065 0.068 - 0.136: 374 0.136 - 0.204: 73 0.204 - 0.273: 6 0.273 - 0.341: 4 Chirality restraints: 2522 Sorted by residual: chirality pdb=" C1 NAG B 705 " pdb=" ND2 ASN B 229 " pdb=" C2 NAG B 705 " pdb=" O5 NAG B 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C4 NAG B 707 " pdb=" C3 NAG B 707 " pdb=" C5 NAG B 707 " pdb=" O4 NAG B 707 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" N2 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.20 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2519 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 486 " -0.020 2.00e-02 2.50e+03 1.94e-02 7.49e+00 pdb=" CG TYR D 486 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 486 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR D 486 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 486 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 486 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 486 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 486 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 292 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C ILE B 292 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE B 292 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 293 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 341 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C THR B 341 " -0.045 2.00e-02 2.50e+03 pdb=" O THR B 341 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 342 " 0.015 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 487 2.69 - 3.24: 15326 3.24 - 3.80: 24156 3.80 - 4.35: 31430 4.35 - 4.90: 51235 Nonbonded interactions: 122634 Sorted by model distance: nonbonded pdb=" OG SER B 364 " pdb=" O PRO B 470 " model vdw 2.141 3.040 nonbonded pdb=" NE1 TRP D 45 " pdb=" OE2 GLU D 91 " model vdw 2.157 3.120 nonbonded pdb=" O SER D 256 " pdb=" ND2 ASN D 478 " model vdw 2.165 3.120 nonbonded pdb=" O THR B 50 " pdb=" NE2 GLN B 103 " model vdw 2.168 3.120 nonbonded pdb=" ND2 ASN H 35 " pdb=" CD2 TYR H 50 " model vdw 2.183 3.420 ... (remaining 122629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 33 through 56 or resid 70 through 500 or resid 525 through \ 545 or resid 571 through 659 or resid 704 through 711)) selection = (chain 'C' and (resid 33 through 56 or resid 70 through 500 or resid 525 through \ 545 or resid 571 through 659 or resid 704 through 711)) selection = (chain 'D' and (resid 33 through 56 or resid 70 through 500 or resid 525 through \ 708)) } ncs_group { reference = chain 'F' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.280 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.006 0.178 15678 Z= 0.252 Angle : 1.177 45.020 21377 Z= 0.565 Chirality : 0.057 0.341 2522 Planarity : 0.005 0.053 2631 Dihedral : 16.808 132.640 6385 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.42 % Allowed : 19.82 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.19), residues: 1825 helix: 0.51 (0.26), residues: 385 sheet: -1.17 (0.26), residues: 402 loop : -1.34 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 26 TYR 0.049 0.003 TYR D 486 PHE 0.029 0.003 PHE D 233 TRP 0.026 0.002 TRP B 628 HIS 0.024 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00569 (15602) covalent geometry : angle 1.07636 (21183) SS BOND : bond 0.03117 ( 34) SS BOND : angle 6.12217 ( 68) hydrogen bonds : bond 0.13179 ( 505) hydrogen bonds : angle 6.89135 ( 1401) link_ALPHA1-3 : bond 0.00334 ( 1) link_ALPHA1-3 : angle 4.09488 ( 3) link_ALPHA1-6 : bond 0.03676 ( 1) link_ALPHA1-6 : angle 6.89980 ( 3) link_BETA1-4 : bond 0.02056 ( 6) link_BETA1-4 : angle 6.92973 ( 18) link_NAG-ASN : bond 0.00640 ( 34) link_NAG-ASN : angle 3.77338 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 341 time to evaluate : 0.684 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: B 109 ILE cc_start: 0.8417 (mt) cc_final: 0.7931 (tt) REVERT: B 156 ILE cc_start: 0.7784 (tp) cc_final: 0.7557 (pt) REVERT: B 232 THR cc_start: 0.8668 (p) cc_final: 0.8422 (t) REVERT: H 69 ILE cc_start: 0.3301 (mm) cc_final: 0.2730 (mm) REVERT: H 81 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7226 (mmtt) REVERT: H 98 TYR cc_start: 0.7728 (m-80) cc_final: 0.7506 (m-10) REVERT: L 77 ASN cc_start: 0.7926 (t0) cc_final: 0.7717 (t0) REVERT: C 369 LEU cc_start: 0.8411 (tp) cc_final: 0.8125 (pt) REVERT: C 423 ILE cc_start: 0.7934 (mt) cc_final: 0.7713 (mt) REVERT: C 477 ASN cc_start: 0.8298 (m-40) cc_final: 0.7928 (m110) REVERT: C 644 ARG cc_start: 0.8515 (mmp80) cc_final: 0.8173 (mmp80) REVERT: D 115 SER cc_start: 0.9225 (m) cc_final: 0.8932 (p) REVERT: D 430 VAL cc_start: 0.8599 (m) cc_final: 0.8256 (p) REVERT: D 486 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: D 630 GLN cc_start: 0.8870 (tt0) cc_final: 0.8385 (tm-30) outliers start: 7 outliers final: 3 residues processed: 347 average time/residue: 0.1371 time to fit residues: 69.3943 Evaluate side-chains 259 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 255 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 486 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN B 478 ASN H 96 ASN C 72 HIS C 428 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 650 GLN D 98 ASN D 287 GLN D 330 HIS ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.103150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.089153 restraints weight = 57162.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.091400 restraints weight = 32514.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.092955 restraints weight = 21621.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.094031 restraints weight = 15863.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094803 restraints weight = 12609.823| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15678 Z= 0.160 Angle : 0.797 10.962 21377 Z= 0.375 Chirality : 0.051 0.385 2522 Planarity : 0.004 0.038 2631 Dihedral : 10.732 112.060 2866 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.13 % Allowed : 20.60 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.19), residues: 1825 helix: 1.35 (0.26), residues: 396 sheet: -1.03 (0.25), residues: 429 loop : -1.15 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 585 TYR 0.028 0.002 TYR L 94 PHE 0.028 0.002 PHE C 383 TRP 0.042 0.002 TRP H 95 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00348 (15602) covalent geometry : angle 0.74859 (21183) SS BOND : bond 0.00444 ( 34) SS BOND : angle 1.09664 ( 68) hydrogen bonds : bond 0.04683 ( 505) hydrogen bonds : angle 6.18348 ( 1401) link_ALPHA1-3 : bond 0.01520 ( 1) link_ALPHA1-3 : angle 2.03190 ( 3) link_ALPHA1-6 : bond 0.02879 ( 1) link_ALPHA1-6 : angle 4.33387 ( 3) link_BETA1-4 : bond 0.01288 ( 6) link_BETA1-4 : angle 3.33509 ( 18) link_NAG-ASN : bond 0.00506 ( 34) link_NAG-ASN : angle 3.66062 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 0.591 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: B 52 LEU cc_start: 0.7619 (mm) cc_final: 0.6795 (mm) REVERT: B 109 ILE cc_start: 0.8335 (mt) cc_final: 0.7950 (tt) REVERT: B 156 ILE cc_start: 0.7879 (tp) cc_final: 0.7675 (pt) REVERT: B 232 THR cc_start: 0.8547 (p) cc_final: 0.8331 (t) REVERT: H 81 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7111 (mmtt) REVERT: H 91 TYR cc_start: 0.6876 (m-80) cc_final: 0.6151 (m-10) REVERT: L 4 MET cc_start: 0.6704 (tpp) cc_final: 0.6261 (mmt) REVERT: C 161 MET cc_start: 0.5802 (mtp) cc_final: 0.5508 (mtp) REVERT: C 369 LEU cc_start: 0.8433 (tp) cc_final: 0.8143 (pt) REVERT: C 423 ILE cc_start: 0.8181 (mt) cc_final: 0.7949 (mt) REVERT: C 477 ASN cc_start: 0.8201 (m-40) cc_final: 0.7820 (m110) REVERT: C 643 TYR cc_start: 0.8918 (m-10) cc_final: 0.8641 (m-80) REVERT: C 644 ARG cc_start: 0.8647 (mmp80) cc_final: 0.8428 (mmp80) REVERT: D 115 SER cc_start: 0.9268 (m) cc_final: 0.9017 (p) REVERT: D 198 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7777 (p) REVERT: D 475 MET cc_start: 0.8127 (tpp) cc_final: 0.7789 (tpp) REVERT: D 477 ASN cc_start: 0.9470 (m-40) cc_final: 0.8930 (m110) REVERT: D 486 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: D 535 MET cc_start: 0.7615 (tpt) cc_final: 0.7329 (mmm) REVERT: D 588 LYS cc_start: 0.9181 (mttt) cc_final: 0.8971 (mttt) REVERT: D 630 GLN cc_start: 0.8911 (tt0) cc_final: 0.8429 (tm-30) outliers start: 52 outliers final: 30 residues processed: 301 average time/residue: 0.1288 time to fit residues: 57.7950 Evaluate side-chains 268 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 632 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN B 287 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.101587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087610 restraints weight = 58475.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.089811 restraints weight = 33429.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.091356 restraints weight = 22338.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.092427 restraints weight = 16495.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.093186 restraints weight = 13143.482| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15678 Z= 0.167 Angle : 0.767 11.131 21377 Z= 0.363 Chirality : 0.049 0.339 2522 Planarity : 0.004 0.067 2631 Dihedral : 10.635 113.002 2864 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.34 % Allowed : 20.66 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 1825 helix: 1.39 (0.26), residues: 392 sheet: -0.91 (0.25), residues: 431 loop : -1.05 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 344 TYR 0.024 0.002 TYR L 94 PHE 0.028 0.002 PHE C 383 TRP 0.045 0.002 TRP H 95 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00373 (15602) covalent geometry : angle 0.72024 (21183) SS BOND : bond 0.00532 ( 34) SS BOND : angle 1.19862 ( 68) hydrogen bonds : bond 0.04400 ( 505) hydrogen bonds : angle 6.00819 ( 1401) link_ALPHA1-3 : bond 0.00983 ( 1) link_ALPHA1-3 : angle 1.69821 ( 3) link_ALPHA1-6 : bond 0.03742 ( 1) link_ALPHA1-6 : angle 4.59711 ( 3) link_BETA1-4 : bond 0.00921 ( 6) link_BETA1-4 : angle 3.26880 ( 18) link_NAG-ASN : bond 0.00483 ( 34) link_NAG-ASN : angle 3.47582 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 0.636 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: B 232 THR cc_start: 0.8607 (p) cc_final: 0.8381 (t) REVERT: B 315 GLN cc_start: 0.7583 (mm110) cc_final: 0.7371 (mm-40) REVERT: B 442 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6640 (p0) REVERT: B 454 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7769 (mm) REVERT: H 81 LYS cc_start: 0.7567 (ttpp) cc_final: 0.7190 (mmmt) REVERT: L 69 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.7041 (tpp-160) REVERT: C 320 MET cc_start: 0.4630 (mpp) cc_final: 0.3796 (ptp) REVERT: C 369 LEU cc_start: 0.8348 (tp) cc_final: 0.8036 (pt) REVERT: C 423 ILE cc_start: 0.8277 (mt) cc_final: 0.8059 (mt) REVERT: C 477 ASN cc_start: 0.8088 (m-40) cc_final: 0.7558 (m110) REVERT: C 577 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8936 (tp40) REVERT: C 644 ARG cc_start: 0.8694 (mmp80) cc_final: 0.8416 (mmp80) REVERT: D 47 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6875 (p0) REVERT: D 95 MET cc_start: 0.8722 (ttp) cc_final: 0.8246 (mtp) REVERT: D 104 MET cc_start: 0.8656 (ttt) cc_final: 0.8322 (tmm) REVERT: D 161 MET cc_start: 0.8050 (tpp) cc_final: 0.7671 (tpp) REVERT: D 198 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7971 (p) REVERT: D 249 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.7044 (p-80) REVERT: D 477 ASN cc_start: 0.9452 (m-40) cc_final: 0.9066 (m110) REVERT: D 486 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: D 530 MET cc_start: 0.6698 (ptm) cc_final: 0.6095 (ptt) REVERT: D 535 MET cc_start: 0.7540 (tpt) cc_final: 0.7307 (mmm) REVERT: D 588 LYS cc_start: 0.9155 (mttt) cc_final: 0.8878 (mmtt) REVERT: D 630 GLN cc_start: 0.8864 (tt0) cc_final: 0.8398 (tm-30) outliers start: 72 outliers final: 44 residues processed: 304 average time/residue: 0.1227 time to fit residues: 56.3360 Evaluate side-chains 290 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** H 100EASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 300 ASN D 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.094119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.079607 restraints weight = 59361.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081781 restraints weight = 33008.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.083289 restraints weight = 21704.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.084326 restraints weight = 16040.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085089 restraints weight = 12814.994| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 15678 Z= 0.328 Angle : 0.909 14.514 21377 Z= 0.437 Chirality : 0.053 0.352 2522 Planarity : 0.006 0.057 2631 Dihedral : 10.997 112.455 2862 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.69 % Allowed : 21.27 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.19), residues: 1825 helix: 0.90 (0.26), residues: 402 sheet: -1.20 (0.25), residues: 406 loop : -1.30 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 298 TYR 0.022 0.003 TYR C 40 PHE 0.032 0.003 PHE C 383 TRP 0.057 0.003 TRP B 596 HIS 0.012 0.002 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00719 (15602) covalent geometry : angle 0.86544 (21183) SS BOND : bond 0.00602 ( 34) SS BOND : angle 1.47128 ( 68) hydrogen bonds : bond 0.05243 ( 505) hydrogen bonds : angle 6.43591 ( 1401) link_ALPHA1-3 : bond 0.00384 ( 1) link_ALPHA1-3 : angle 1.81987 ( 3) link_ALPHA1-6 : bond 0.03677 ( 1) link_ALPHA1-6 : angle 5.11565 ( 3) link_BETA1-4 : bond 0.00693 ( 6) link_BETA1-4 : angle 3.47807 ( 18) link_NAG-ASN : bond 0.00751 ( 34) link_NAG-ASN : angle 3.65358 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 237 time to evaluate : 0.720 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: B 95 MET cc_start: 0.7815 (ppp) cc_final: 0.7586 (ppp) REVERT: B 201 ILE cc_start: 0.8411 (mm) cc_final: 0.8124 (mm) REVERT: B 315 GLN cc_start: 0.8079 (mm110) cc_final: 0.7863 (mm-40) REVERT: B 544 LEU cc_start: 0.7445 (mt) cc_final: 0.7062 (mt) REVERT: B 593 LEU cc_start: 0.9340 (mt) cc_final: 0.8972 (mm) REVERT: B 596 TRP cc_start: 0.7859 (m-90) cc_final: 0.6979 (m-90) REVERT: H 89 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7581 (pt) REVERT: H 95 TRP cc_start: 0.8182 (t-100) cc_final: 0.7945 (t-100) REVERT: L 46 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8063 (mt) REVERT: L 69 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6496 (tpp-160) REVERT: C 39 TYR cc_start: 0.8652 (m-80) cc_final: 0.8235 (m-80) REVERT: C 163 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.6919 (p) REVERT: C 231 LYS cc_start: 0.8182 (mptt) cc_final: 0.7835 (mmtt) REVERT: C 369 LEU cc_start: 0.8484 (tp) cc_final: 0.8147 (pt) REVERT: C 427 TRP cc_start: 0.7366 (m100) cc_final: 0.6978 (m100) REVERT: C 477 ASN cc_start: 0.8273 (m-40) cc_final: 0.7659 (m110) REVERT: C 530 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.2339 (mtp) REVERT: C 629 MET cc_start: 0.6229 (mmp) cc_final: 0.4402 (mmt) REVERT: C 633 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8449 (mtt180) REVERT: C 644 ARG cc_start: 0.8687 (mmp80) cc_final: 0.8425 (mmp80) REVERT: D 47 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7114 (p0) REVERT: D 95 MET cc_start: 0.8927 (mtp) cc_final: 0.8466 (mtp) REVERT: D 129 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7458 (mt) REVERT: D 192 ARG cc_start: 0.7390 (ptm-80) cc_final: 0.6929 (ptm-80) REVERT: D 193 LEU cc_start: 0.8896 (mm) cc_final: 0.8433 (tp) REVERT: D 434 MET cc_start: 0.3916 (tmm) cc_final: 0.3361 (tmm) REVERT: D 475 MET cc_start: 0.7615 (tpp) cc_final: 0.7318 (mmm) REVERT: D 486 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: D 535 MET cc_start: 0.7782 (tpt) cc_final: 0.7439 (mmm) REVERT: D 542 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7408 (ttp-110) REVERT: D 588 LYS cc_start: 0.9304 (mttt) cc_final: 0.9007 (mmtt) REVERT: D 638 HIS cc_start: 0.4076 (OUTLIER) cc_final: 0.2899 (m90) outliers start: 111 outliers final: 68 residues processed: 306 average time/residue: 0.1194 time to fit residues: 55.9210 Evaluate side-chains 296 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 218 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100EASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN D 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.082535 restraints weight = 59296.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.084684 restraints weight = 33903.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.086177 restraints weight = 22678.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.087219 restraints weight = 16835.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.087968 restraints weight = 13464.225| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15678 Z= 0.181 Angle : 0.800 13.410 21377 Z= 0.378 Chirality : 0.049 0.318 2522 Planarity : 0.004 0.055 2631 Dihedral : 10.709 112.696 2862 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.24 % Allowed : 22.77 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1825 helix: 1.26 (0.26), residues: 390 sheet: -1.14 (0.25), residues: 411 loop : -1.29 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 54 TYR 0.016 0.002 TYR C 643 PHE 0.028 0.002 PHE C 383 TRP 0.036 0.002 TRP H 95 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00405 (15602) covalent geometry : angle 0.75280 (21183) SS BOND : bond 0.00452 ( 34) SS BOND : angle 1.62693 ( 68) hydrogen bonds : bond 0.04453 ( 505) hydrogen bonds : angle 6.10051 ( 1401) link_ALPHA1-3 : bond 0.01027 ( 1) link_ALPHA1-3 : angle 1.84978 ( 3) link_ALPHA1-6 : bond 0.03291 ( 1) link_ALPHA1-6 : angle 4.91504 ( 3) link_BETA1-4 : bond 0.00771 ( 6) link_BETA1-4 : angle 3.31400 ( 18) link_NAG-ASN : bond 0.00506 ( 34) link_NAG-ASN : angle 3.46555 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 0.623 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: B 152 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7927 (pttt) REVERT: B 201 ILE cc_start: 0.8328 (mm) cc_final: 0.8082 (mm) REVERT: B 315 GLN cc_start: 0.7782 (mm110) cc_final: 0.7568 (mm-40) REVERT: B 596 TRP cc_start: 0.7552 (m-10) cc_final: 0.7096 (m-90) REVERT: H 81 LYS cc_start: 0.7551 (ttpp) cc_final: 0.7048 (mmtt) REVERT: H 89 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7632 (pt) REVERT: L 69 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6223 (tpp-160) REVERT: L 89 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.5745 (tt0) REVERT: C 39 TYR cc_start: 0.8471 (m-80) cc_final: 0.8097 (m-80) REVERT: C 91 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6999 (mm-30) REVERT: C 163 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.6916 (p) REVERT: C 231 LYS cc_start: 0.8045 (mptt) cc_final: 0.7753 (mmtt) REVERT: C 477 ASN cc_start: 0.8112 (m-40) cc_final: 0.7557 (m110) REVERT: C 596 TRP cc_start: 0.8021 (m-10) cc_final: 0.7352 (m-90) REVERT: C 644 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8409 (mmp80) REVERT: C 648 ASP cc_start: 0.9098 (p0) cc_final: 0.8864 (p0) REVERT: D 47 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7126 (p0) REVERT: D 95 MET cc_start: 0.8788 (mtp) cc_final: 0.8369 (mtp) REVERT: D 104 MET cc_start: 0.8490 (ttt) cc_final: 0.8240 (tmm) REVERT: D 129 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7429 (mt) REVERT: D 161 MET cc_start: 0.8142 (tpp) cc_final: 0.7823 (tpp) REVERT: D 192 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7171 (ptm-80) REVERT: D 193 LEU cc_start: 0.8890 (mm) cc_final: 0.8426 (tp) REVERT: D 198 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8217 (p) REVERT: D 486 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: D 535 MET cc_start: 0.7554 (tpt) cc_final: 0.7304 (mmm) REVERT: D 588 LYS cc_start: 0.9147 (mttt) cc_final: 0.8830 (mmtt) REVERT: D 638 HIS cc_start: 0.4022 (OUTLIER) cc_final: 0.2866 (m90) outliers start: 87 outliers final: 61 residues processed: 295 average time/residue: 0.1240 time to fit residues: 55.6579 Evaluate side-chains 289 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 218 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 318 TYR Chi-restraints excluded: chain D residue 384 TYR Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 30 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN D 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.096606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.082644 restraints weight = 59414.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084779 restraints weight = 34141.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.086266 restraints weight = 22993.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087329 restraints weight = 17114.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.088056 restraints weight = 13689.363| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15678 Z= 0.186 Angle : 0.791 12.541 21377 Z= 0.372 Chirality : 0.049 0.311 2522 Planarity : 0.004 0.053 2631 Dihedral : 10.530 111.873 2862 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.27 % Allowed : 23.07 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.19), residues: 1825 helix: 1.27 (0.26), residues: 391 sheet: -1.21 (0.25), residues: 414 loop : -1.31 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 298 TYR 0.016 0.002 TYR D 302 PHE 0.026 0.002 PHE C 383 TRP 0.048 0.002 TRP H 95 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00415 (15602) covalent geometry : angle 0.74632 (21183) SS BOND : bond 0.00427 ( 34) SS BOND : angle 1.39640 ( 68) hydrogen bonds : bond 0.04336 ( 505) hydrogen bonds : angle 5.99700 ( 1401) link_ALPHA1-3 : bond 0.00843 ( 1) link_ALPHA1-3 : angle 1.92643 ( 3) link_ALPHA1-6 : bond 0.03066 ( 1) link_ALPHA1-6 : angle 4.84266 ( 3) link_BETA1-4 : bond 0.00735 ( 6) link_BETA1-4 : angle 3.19137 ( 18) link_NAG-ASN : bond 0.00508 ( 34) link_NAG-ASN : angle 3.40077 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 237 time to evaluate : 0.681 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: B 152 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8007 (pttt) REVERT: B 201 ILE cc_start: 0.8164 (mm) cc_final: 0.7894 (mm) REVERT: B 284 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7135 (mp) REVERT: B 315 GLN cc_start: 0.7749 (mm110) cc_final: 0.7538 (mm-40) REVERT: B 427 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.7405 (m100) REVERT: B 479 TRP cc_start: 0.8883 (OUTLIER) cc_final: 0.7085 (m100) REVERT: B 544 LEU cc_start: 0.7353 (mt) cc_final: 0.6907 (mt) REVERT: B 596 TRP cc_start: 0.7624 (m-10) cc_final: 0.7178 (m-90) REVERT: H 63 LEU cc_start: 0.9115 (mt) cc_final: 0.8765 (mp) REVERT: H 81 LYS cc_start: 0.7535 (ttpp) cc_final: 0.6869 (mmtt) REVERT: H 89 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7590 (pt) REVERT: L 89 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.5680 (tt0) REVERT: C 39 TYR cc_start: 0.8522 (m-80) cc_final: 0.8071 (m-80) REVERT: C 91 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6986 (mm-30) REVERT: C 231 LYS cc_start: 0.8140 (mptt) cc_final: 0.7817 (mmtt) REVERT: C 320 MET cc_start: 0.4756 (ptp) cc_final: 0.4043 (ptp) REVERT: C 477 ASN cc_start: 0.8150 (m-40) cc_final: 0.7603 (m110) REVERT: C 530 MET cc_start: 0.3889 (mmp) cc_final: 0.3612 (mmp) REVERT: C 596 TRP cc_start: 0.8116 (m-10) cc_final: 0.7568 (m-90) REVERT: C 644 ARG cc_start: 0.8614 (mmp80) cc_final: 0.8395 (mmp80) REVERT: C 648 ASP cc_start: 0.9076 (p0) cc_final: 0.8853 (p0) REVERT: D 47 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7175 (p0) REVERT: D 69 TRP cc_start: 0.6363 (OUTLIER) cc_final: 0.5335 (m100) REVERT: D 104 MET cc_start: 0.8522 (ttt) cc_final: 0.8231 (tmm) REVERT: D 129 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7417 (mt) REVERT: D 161 MET cc_start: 0.8152 (tpp) cc_final: 0.7765 (tpp) REVERT: D 166 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8202 (mtt90) REVERT: D 192 ARG cc_start: 0.7511 (ptm-80) cc_final: 0.7294 (ptm-80) REVERT: D 193 LEU cc_start: 0.8991 (mm) cc_final: 0.8769 (mm) REVERT: D 198 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8246 (p) REVERT: D 388 SER cc_start: 0.2055 (OUTLIER) cc_final: 0.1507 (p) REVERT: D 486 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: D 535 MET cc_start: 0.7621 (tpt) cc_final: 0.7357 (mmm) REVERT: D 588 LYS cc_start: 0.9128 (mttt) cc_final: 0.8838 (mmtt) REVERT: D 638 HIS cc_start: 0.4072 (OUTLIER) cc_final: 0.2855 (m90) outliers start: 104 outliers final: 72 residues processed: 306 average time/residue: 0.1178 time to fit residues: 55.6058 Evaluate side-chains 307 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 222 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 479 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 318 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 166 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100EASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 300 ASN D 301 ASN D 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.097102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.083050 restraints weight = 58292.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.085208 restraints weight = 33590.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.086734 restraints weight = 22513.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.087791 restraints weight = 16738.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.088517 restraints weight = 13380.515| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15678 Z= 0.157 Angle : 0.771 14.873 21377 Z= 0.361 Chirality : 0.049 0.308 2522 Planarity : 0.004 0.076 2631 Dihedral : 10.359 111.562 2862 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.36 % Allowed : 24.58 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.19), residues: 1825 helix: 1.42 (0.26), residues: 391 sheet: -1.16 (0.25), residues: 403 loop : -1.24 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 54 TYR 0.015 0.002 TYR C 435 PHE 0.028 0.002 PHE C 383 TRP 0.046 0.002 TRP H 95 HIS 0.006 0.001 HIS L 27 Details of bonding type rmsd covalent geometry : bond 0.00355 (15602) covalent geometry : angle 0.72674 (21183) SS BOND : bond 0.00389 ( 34) SS BOND : angle 1.38004 ( 68) hydrogen bonds : bond 0.04123 ( 505) hydrogen bonds : angle 5.81093 ( 1401) link_ALPHA1-3 : bond 0.00838 ( 1) link_ALPHA1-3 : angle 2.01643 ( 3) link_ALPHA1-6 : bond 0.03232 ( 1) link_ALPHA1-6 : angle 4.69955 ( 3) link_BETA1-4 : bond 0.00793 ( 6) link_BETA1-4 : angle 3.17341 ( 18) link_NAG-ASN : bond 0.00483 ( 34) link_NAG-ASN : angle 3.34530 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 235 time to evaluate : 0.675 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: B 152 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7985 (pttt) REVERT: B 284 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7145 (mp) REVERT: B 427 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.7414 (m100) REVERT: B 479 TRP cc_start: 0.8840 (OUTLIER) cc_final: 0.7033 (m100) REVERT: B 596 TRP cc_start: 0.7614 (m-10) cc_final: 0.7194 (m-90) REVERT: H 63 LEU cc_start: 0.9072 (mt) cc_final: 0.8725 (mp) REVERT: H 81 LYS cc_start: 0.7507 (ttpp) cc_final: 0.6889 (mmtt) REVERT: H 89 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7634 (pt) REVERT: L 89 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.5579 (tt0) REVERT: C 39 TYR cc_start: 0.8508 (m-80) cc_final: 0.8020 (m-80) REVERT: C 223 TYR cc_start: 0.6794 (m-80) cc_final: 0.6501 (m-80) REVERT: C 320 MET cc_start: 0.4906 (ptp) cc_final: 0.4678 (ptp) REVERT: C 477 ASN cc_start: 0.8084 (m-40) cc_final: 0.7521 (m110) REVERT: C 596 TRP cc_start: 0.8183 (m-10) cc_final: 0.7566 (m-90) REVERT: C 644 ARG cc_start: 0.8630 (mmp80) cc_final: 0.8421 (mmp80) REVERT: D 47 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7199 (p0) REVERT: D 69 TRP cc_start: 0.6219 (OUTLIER) cc_final: 0.5181 (m100) REVERT: D 104 MET cc_start: 0.8579 (ttt) cc_final: 0.8268 (tmm) REVERT: D 129 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7391 (mt) REVERT: D 166 ARG cc_start: 0.8489 (mmt90) cc_final: 0.8247 (mtt90) REVERT: D 193 LEU cc_start: 0.8968 (mm) cc_final: 0.8738 (mm) REVERT: D 198 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8221 (p) REVERT: D 388 SER cc_start: 0.2252 (OUTLIER) cc_final: 0.1591 (p) REVERT: D 475 MET cc_start: 0.8492 (mmm) cc_final: 0.7883 (mmm) REVERT: D 486 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: D 535 MET cc_start: 0.7580 (tpt) cc_final: 0.7322 (mmm) REVERT: D 588 LYS cc_start: 0.9113 (mttt) cc_final: 0.8827 (mmtt) REVERT: D 638 HIS cc_start: 0.4006 (OUTLIER) cc_final: 0.2844 (m90) outliers start: 89 outliers final: 66 residues processed: 296 average time/residue: 0.1067 time to fit residues: 49.1832 Evaluate side-chains 300 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 221 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 479 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN D 249 HIS D 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.081105 restraints weight = 59892.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.083229 restraints weight = 34340.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.084696 restraints weight = 23037.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085722 restraints weight = 17157.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086473 restraints weight = 13761.766| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15678 Z= 0.238 Angle : 0.830 13.707 21377 Z= 0.393 Chirality : 0.050 0.316 2522 Planarity : 0.004 0.051 2631 Dihedral : 10.524 112.278 2862 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.08 % Allowed : 24.10 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.19), residues: 1825 helix: 1.27 (0.26), residues: 391 sheet: -1.40 (0.24), residues: 428 loop : -1.33 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 54 TYR 0.015 0.002 TYR L 36 PHE 0.034 0.002 PHE C 383 TRP 0.046 0.002 TRP H 95 HIS 0.005 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00527 (15602) covalent geometry : angle 0.78550 (21183) SS BOND : bond 0.00502 ( 34) SS BOND : angle 1.53435 ( 68) hydrogen bonds : bond 0.04504 ( 505) hydrogen bonds : angle 6.01723 ( 1401) link_ALPHA1-3 : bond 0.00566 ( 1) link_ALPHA1-3 : angle 2.14218 ( 3) link_ALPHA1-6 : bond 0.03417 ( 1) link_ALPHA1-6 : angle 4.89559 ( 3) link_BETA1-4 : bond 0.00630 ( 6) link_BETA1-4 : angle 3.28323 ( 18) link_NAG-ASN : bond 0.00569 ( 34) link_NAG-ASN : angle 3.45171 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 218 time to evaluate : 0.600 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: B 152 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7959 (pttt) REVERT: B 284 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7202 (mp) REVERT: B 427 TRP cc_start: 0.7732 (OUTLIER) cc_final: 0.7456 (m100) REVERT: B 479 TRP cc_start: 0.8901 (OUTLIER) cc_final: 0.7017 (m100) REVERT: B 544 LEU cc_start: 0.7166 (mt) cc_final: 0.6703 (mt) REVERT: B 596 TRP cc_start: 0.7871 (m-10) cc_final: 0.7480 (m-90) REVERT: H 63 LEU cc_start: 0.9178 (mt) cc_final: 0.8808 (mp) REVERT: H 81 LYS cc_start: 0.7504 (ttpp) cc_final: 0.6835 (mmtt) REVERT: H 89 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7862 (mt) REVERT: L 89 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.5813 (tt0) REVERT: C 39 TYR cc_start: 0.8540 (m-80) cc_final: 0.8079 (m-80) REVERT: C 223 TYR cc_start: 0.6915 (m-80) cc_final: 0.6635 (m-80) REVERT: C 320 MET cc_start: 0.4932 (ptp) cc_final: 0.4385 (ptp) REVERT: C 434 MET cc_start: 0.5015 (ptp) cc_final: 0.4692 (ptp) REVERT: C 477 ASN cc_start: 0.8032 (m-40) cc_final: 0.7565 (m-40) REVERT: C 596 TRP cc_start: 0.8198 (m-10) cc_final: 0.7665 (m-90) REVERT: C 643 TYR cc_start: 0.8819 (m-80) cc_final: 0.8550 (m-80) REVERT: C 644 ARG cc_start: 0.8641 (mmp80) cc_final: 0.8392 (mmp80) REVERT: D 47 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7361 (p0) REVERT: D 69 TRP cc_start: 0.6324 (OUTLIER) cc_final: 0.5344 (m100) REVERT: D 104 MET cc_start: 0.8621 (ttt) cc_final: 0.8265 (tmm) REVERT: D 129 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7401 (mt) REVERT: D 166 ARG cc_start: 0.8502 (mmt90) cc_final: 0.8260 (mtt90) REVERT: D 198 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8483 (p) REVERT: D 320 MET cc_start: 0.4952 (mmt) cc_final: 0.4201 (mmp) REVERT: D 388 SER cc_start: 0.2565 (OUTLIER) cc_final: 0.2108 (p) REVERT: D 475 MET cc_start: 0.8434 (mmm) cc_final: 0.7563 (mmm) REVERT: D 486 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: D 535 MET cc_start: 0.7630 (tpt) cc_final: 0.7382 (mmm) REVERT: D 588 LYS cc_start: 0.9152 (mttt) cc_final: 0.8864 (mmtt) REVERT: D 638 HIS cc_start: 0.4143 (OUTLIER) cc_final: 0.2904 (m90) outliers start: 101 outliers final: 82 residues processed: 286 average time/residue: 0.1088 time to fit residues: 48.7163 Evaluate side-chains 303 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 208 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 479 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 32 ASN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 318 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 73 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 164 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 100EASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 249 HIS D 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.083455 restraints weight = 58448.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.085639 restraints weight = 33488.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.087157 restraints weight = 22412.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.088190 restraints weight = 16619.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.088945 restraints weight = 13290.676| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15678 Z= 0.146 Angle : 0.778 11.930 21377 Z= 0.363 Chirality : 0.049 0.303 2522 Planarity : 0.004 0.047 2631 Dihedral : 10.239 111.598 2862 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.82 % Allowed : 25.84 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.19), residues: 1825 helix: 1.50 (0.26), residues: 391 sheet: -1.26 (0.25), residues: 412 loop : -1.24 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 298 TYR 0.016 0.001 TYR C 435 PHE 0.031 0.002 PHE C 383 TRP 0.041 0.002 TRP H 95 HIS 0.004 0.001 HIS L 27 Details of bonding type rmsd covalent geometry : bond 0.00334 (15602) covalent geometry : angle 0.73529 (21183) SS BOND : bond 0.00399 ( 34) SS BOND : angle 1.23122 ( 68) hydrogen bonds : bond 0.03977 ( 505) hydrogen bonds : angle 5.77852 ( 1401) link_ALPHA1-3 : bond 0.00953 ( 1) link_ALPHA1-3 : angle 2.15961 ( 3) link_ALPHA1-6 : bond 0.03043 ( 1) link_ALPHA1-6 : angle 4.50897 ( 3) link_BETA1-4 : bond 0.00774 ( 6) link_BETA1-4 : angle 3.26818 ( 18) link_NAG-ASN : bond 0.00472 ( 34) link_NAG-ASN : angle 3.29991 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 230 time to evaluate : 0.609 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: B 52 LEU cc_start: 0.7852 (mm) cc_final: 0.7388 (mm) REVERT: B 152 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7919 (pttt) REVERT: B 427 TRP cc_start: 0.7634 (OUTLIER) cc_final: 0.7364 (m100) REVERT: B 479 TRP cc_start: 0.8833 (OUTLIER) cc_final: 0.6987 (m100) REVERT: B 596 TRP cc_start: 0.7683 (m-10) cc_final: 0.7381 (m-90) REVERT: H 63 LEU cc_start: 0.9103 (mt) cc_final: 0.8752 (mp) REVERT: H 81 LYS cc_start: 0.7530 (ttpp) cc_final: 0.6977 (mmtt) REVERT: H 89 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (mt) REVERT: L 69 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6327 (mmp80) REVERT: L 77 ASN cc_start: 0.7955 (t0) cc_final: 0.7665 (p0) REVERT: L 89 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.5567 (tt0) REVERT: C 39 TYR cc_start: 0.8479 (m-80) cc_final: 0.7992 (m-80) REVERT: C 223 TYR cc_start: 0.6760 (m-80) cc_final: 0.6487 (m-80) REVERT: C 434 MET cc_start: 0.4167 (ptp) cc_final: 0.3929 (ptp) REVERT: C 477 ASN cc_start: 0.8111 (m-40) cc_final: 0.7536 (m110) REVERT: C 596 TRP cc_start: 0.8267 (m-10) cc_final: 0.7690 (m-90) REVERT: C 643 TYR cc_start: 0.8772 (m-80) cc_final: 0.8564 (m-80) REVERT: C 648 ASP cc_start: 0.9082 (p0) cc_final: 0.8874 (p0) REVERT: D 47 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7248 (p0) REVERT: D 69 TRP cc_start: 0.6303 (OUTLIER) cc_final: 0.5492 (m100) REVERT: D 104 MET cc_start: 0.8541 (ttt) cc_final: 0.8231 (tmm) REVERT: D 129 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7299 (mt) REVERT: D 166 ARG cc_start: 0.8502 (mmt90) cc_final: 0.7918 (mtt180) REVERT: D 198 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8358 (p) REVERT: D 211 ASP cc_start: 0.8178 (t0) cc_final: 0.7930 (t0) REVERT: D 320 MET cc_start: 0.4648 (mmt) cc_final: 0.4419 (mmp) REVERT: D 475 MET cc_start: 0.8390 (mmm) cc_final: 0.7482 (mmm) REVERT: D 535 MET cc_start: 0.7661 (tpt) cc_final: 0.7430 (mmm) REVERT: D 588 LYS cc_start: 0.9072 (mttt) cc_final: 0.8837 (mmtt) REVERT: D 638 HIS cc_start: 0.4132 (OUTLIER) cc_final: 0.2894 (m90) outliers start: 80 outliers final: 60 residues processed: 285 average time/residue: 0.1186 time to fit residues: 51.9377 Evaluate side-chains 291 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 479 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 58 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100EASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.083593 restraints weight = 59050.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085804 restraints weight = 33733.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.087332 restraints weight = 22470.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.088312 restraints weight = 16588.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089114 restraints weight = 13332.352| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 15678 Z= 0.238 Angle : 1.068 59.102 21377 Z= 0.586 Chirality : 0.053 0.682 2522 Planarity : 0.004 0.061 2631 Dihedral : 10.235 111.981 2860 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.64 % Allowed : 26.02 % Favored : 69.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.19), residues: 1825 helix: 1.48 (0.26), residues: 391 sheet: -1.26 (0.25), residues: 412 loop : -1.25 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 298 TYR 0.016 0.002 TYR C 435 PHE 0.045 0.002 PHE C 383 TRP 0.050 0.003 TRP D 571 HIS 0.014 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00562 (15602) covalent geometry : angle 1.03957 (21183) SS BOND : bond 0.00362 ( 34) SS BOND : angle 1.12805 ( 68) hydrogen bonds : bond 0.04002 ( 505) hydrogen bonds : angle 5.78960 ( 1401) link_ALPHA1-3 : bond 0.00692 ( 1) link_ALPHA1-3 : angle 2.19403 ( 3) link_ALPHA1-6 : bond 0.03149 ( 1) link_ALPHA1-6 : angle 4.63682 ( 3) link_BETA1-4 : bond 0.00573 ( 6) link_BETA1-4 : angle 3.32780 ( 18) link_NAG-ASN : bond 0.00473 ( 34) link_NAG-ASN : angle 3.29907 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 220 time to evaluate : 0.611 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: B 52 LEU cc_start: 0.7860 (mm) cc_final: 0.7387 (mm) REVERT: B 152 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7926 (pttt) REVERT: B 427 TRP cc_start: 0.7615 (OUTLIER) cc_final: 0.7363 (m100) REVERT: B 479 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.6980 (m100) REVERT: B 596 TRP cc_start: 0.7738 (m-10) cc_final: 0.7367 (m-90) REVERT: H 63 LEU cc_start: 0.9103 (mt) cc_final: 0.8761 (mp) REVERT: H 81 LYS cc_start: 0.7526 (ttpp) cc_final: 0.6980 (mmtt) REVERT: H 89 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7712 (mt) REVERT: L 69 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6323 (mmp80) REVERT: L 77 ASN cc_start: 0.7946 (t0) cc_final: 0.7666 (p0) REVERT: L 89 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.5557 (tt0) REVERT: C 39 TYR cc_start: 0.8474 (m-80) cc_final: 0.7988 (m-80) REVERT: C 223 TYR cc_start: 0.6762 (m-80) cc_final: 0.6496 (m-80) REVERT: C 434 MET cc_start: 0.4297 (ptp) cc_final: 0.4074 (ptp) REVERT: C 477 ASN cc_start: 0.8106 (m-40) cc_final: 0.7530 (m110) REVERT: C 596 TRP cc_start: 0.8263 (m-10) cc_final: 0.7691 (m-90) REVERT: C 648 ASP cc_start: 0.9074 (p0) cc_final: 0.8866 (p0) REVERT: D 47 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7249 (p0) REVERT: D 69 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.5486 (m100) REVERT: D 104 MET cc_start: 0.8526 (ttt) cc_final: 0.8215 (tmm) REVERT: D 129 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7297 (mt) REVERT: D 166 ARG cc_start: 0.8496 (mmt90) cc_final: 0.7905 (mtt180) REVERT: D 198 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8360 (p) REVERT: D 211 ASP cc_start: 0.8176 (t0) cc_final: 0.7930 (t0) REVERT: D 320 MET cc_start: 0.4646 (mmt) cc_final: 0.4286 (mmp) REVERT: D 388 SER cc_start: 0.2122 (OUTLIER) cc_final: 0.1541 (p) REVERT: D 475 MET cc_start: 0.8391 (mmm) cc_final: 0.7475 (mmm) REVERT: D 535 MET cc_start: 0.7648 (tpt) cc_final: 0.7425 (mmm) REVERT: D 588 LYS cc_start: 0.9071 (mttt) cc_final: 0.8834 (mmtt) REVERT: D 638 HIS cc_start: 0.4115 (OUTLIER) cc_final: 0.2878 (m90) outliers start: 77 outliers final: 61 residues processed: 274 average time/residue: 0.1081 time to fit residues: 46.7390 Evaluate side-chains 292 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 479 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 638 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100EASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083905 restraints weight = 58762.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.086015 restraints weight = 34154.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087491 restraints weight = 23034.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.088423 restraints weight = 17121.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089183 restraints weight = 13875.146| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 15678 Z= 0.253 Angle : 1.048 46.794 21377 Z= 0.617 Chirality : 0.053 0.756 2522 Planarity : 0.005 0.100 2631 Dihedral : 10.234 111.925 2860 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.46 % Allowed : 26.08 % Favored : 69.46 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.19), residues: 1825 helix: 1.48 (0.26), residues: 391 sheet: -1.26 (0.25), residues: 412 loop : -1.25 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 298 TYR 0.016 0.002 TYR C 435 PHE 0.045 0.002 PHE C 383 TRP 0.050 0.003 TRP D 571 HIS 0.014 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00589 (15602) covalent geometry : angle 1.01908 (21183) SS BOND : bond 0.00361 ( 34) SS BOND : angle 1.12727 ( 68) hydrogen bonds : bond 0.04002 ( 505) hydrogen bonds : angle 5.78958 ( 1401) link_ALPHA1-3 : bond 0.00717 ( 1) link_ALPHA1-3 : angle 2.19571 ( 3) link_ALPHA1-6 : bond 0.03109 ( 1) link_ALPHA1-6 : angle 4.62195 ( 3) link_BETA1-4 : bond 0.00587 ( 6) link_BETA1-4 : angle 3.31967 ( 18) link_NAG-ASN : bond 0.00473 ( 34) link_NAG-ASN : angle 3.29906 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.35 seconds wall clock time: 49 minutes 3.96 seconds (2943.96 seconds total)