Starting phenix.real_space_refine on Fri Jun 13 22:00:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cv7_45957/06_2025/9cv7_45957.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cv7_45957/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cv7_45957/06_2025/9cv7_45957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cv7_45957/06_2025/9cv7_45957.map" model { file = "/net/cci-nas-00/data/ceres_data/9cv7_45957/06_2025/9cv7_45957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cv7_45957/06_2025/9cv7_45957.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.10, per 1000 atoms: 0.66 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: 4.22 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.06 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: 5.12 Time building geometry restraints manager: 4.93 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 \ 659 or resid 701 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.380 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), 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 TRP 0.026 0.002 TRP B 628 HIS 0.024 0.002 HIS C 374 PHE 0.029 0.003 PHE D 233 TYR 0.049 0.003 TYR D 486 ARG 0.016 0.001 ARG L 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 34) link_NAG-ASN : angle 3.77338 ( 102) 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_ALPHA1-3 : bond 0.00334 ( 1) link_ALPHA1-3 : angle 4.09488 ( 3) hydrogen bonds : bond 0.13179 ( 505) hydrogen bonds : angle 6.89135 ( 1401) SS BOND : bond 0.03117 ( 34) SS BOND : angle 6.12217 ( 68) covalent geometry : bond 0.00569 (15602) covalent geometry : angle 1.07636 (21183) *********************** 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 : 1.615 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 156 ILE cc_start: 0.7784 (tp) cc_final: 0.7556 (pt) REVERT: B 232 THR cc_start: 0.8668 (p) cc_final: 0.8423 (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: 0.7224 (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: 0.7716 (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: 0.7712 (mt) REVERT: C 477 ASN cc_start: 0.8298 (m-40) cc_final: 0.7927 (m110) REVERT: C 644 ARG cc_start: 0.8515 (mmp80) cc_final: 0.8174 (mmp80) REVERT: D 115 SER cc_start: 0.9225 (m) cc_final: 0.8937 (p) REVERT: D 430 VAL cc_start: 0.8599 (m) cc_final: 0.8258 (p) REVERT: D 477 ASN cc_start: 0.9518 (m-40) cc_final: 0.8994 (m110) REVERT: D 486 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6391 (m-80) outliers start: 7 outliers final: 3 residues processed: 347 average time/residue: 0.2883 time to fit residues: 145.6633 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 : 2.003 ------------------------------------------------------------------------------- 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 155 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 167 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 478 ASN ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100EASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 377 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN C 620 ASN D 98 ASN D 249 HIS D 287 GLN D 653 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.098795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.085068 restraints weight = 58578.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.087158 restraints weight = 33938.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.088612 restraints weight = 22917.212| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15678 Z= 0.247 Angle : 0.862 11.458 21377 Z= 0.411 Chirality : 0.052 0.362 2522 Planarity : 0.005 0.045 2631 Dihedral : 10.933 107.803 2866 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.52 % Allowed : 20.54 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1825 helix: 1.12 (0.26), residues: 399 sheet: -1.21 (0.24), residues: 430 loop : -1.23 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 95 HIS 0.004 0.001 HIS C 138 PHE 0.028 0.003 PHE C 383 TYR 0.030 0.002 TYR L 94 ARG 0.004 0.001 ARG B 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 34) link_NAG-ASN : angle 3.71546 ( 102) link_ALPHA1-6 : bond 0.03510 ( 1) link_ALPHA1-6 : angle 4.71238 ( 3) link_BETA1-4 : bond 0.01088 ( 6) link_BETA1-4 : angle 3.40073 ( 18) link_ALPHA1-3 : bond 0.01042 ( 1) link_ALPHA1-3 : angle 1.69128 ( 3) hydrogen bonds : bond 0.05115 ( 505) hydrogen bonds : angle 6.45725 ( 1401) SS BOND : bond 0.00703 ( 34) SS BOND : angle 1.28837 ( 68) covalent geometry : bond 0.00540 (15602) covalent geometry : angle 0.81477 (21183) *********************** 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 324 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 249 time to evaluate : 1.663 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: 0.7763 (mm) cc_final: 0.7249 (mm) REVERT: B 201 ILE cc_start: 0.8521 (mm) cc_final: 0.8294 (mm) REVERT: B 232 THR cc_start: 0.8716 (p) cc_final: 0.8504 (t) REVERT: B 442 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6714 (p0) REVERT: H 81 LYS cc_start: 0.7544 (ttpp) cc_final: 0.7013 (mmtt) REVERT: H 98 TYR cc_start: 0.8009 (m-80) cc_final: 0.7723 (m-80) REVERT: H 100 PHE cc_start: 0.8730 (m-80) cc_final: 0.8501 (m-80) REVERT: H 103 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.5159 (m100) REVERT: L 47 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8254 (mm) REVERT: C 161 MET cc_start: 0.6016 (mtp) cc_final: 0.5753 (mtp) REVERT: C 423 ILE cc_start: 0.8484 (mt) cc_final: 0.8259 (mt) REVERT: C 427 TRP cc_start: 0.6521 (m100) cc_final: 0.6230 (m100) REVERT: C 477 ASN cc_start: 0.8238 (m-40) cc_final: 0.7746 (m110) REVERT: D 115 SER cc_start: 0.9356 (m) cc_final: 0.9075 (p) REVERT: D 161 MET cc_start: 0.8116 (tpp) cc_final: 0.7555 (tmm) REVERT: D 198 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (p) REVERT: D 475 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7734 (tpp) REVERT: D 477 ASN cc_start: 0.9498 (m-40) cc_final: 0.9121 (m110) REVERT: D 486 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: D 535 MET cc_start: 0.7654 (tpt) cc_final: 0.7368 (mmm) REVERT: D 588 LYS cc_start: 0.9273 (mttt) cc_final: 0.9039 (mmtt) outliers start: 75 outliers final: 43 residues processed: 298 average time/residue: 0.2608 time to fit residues: 116.5136 Evaluate side-chains 261 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 ASN 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 103 TRP Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 26 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 93 THR 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 242 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 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 390 LEU 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 536 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 113 ASP 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 475 MET Chi-restraints excluded: chain D residue 486 TYR 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 109 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- 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 B 339 ASN B 630 GLN ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 428 GLN C 540 GLN C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.084347 restraints weight = 58100.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.086496 restraints weight = 33435.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.087996 restraints weight = 22500.604| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15678 Z= 0.186 Angle : 0.783 11.278 21377 Z= 0.372 Chirality : 0.049 0.338 2522 Planarity : 0.004 0.057 2631 Dihedral : 10.913 113.884 2862 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.94 % Allowed : 20.84 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1825 helix: 1.33 (0.26), residues: 390 sheet: -1.12 (0.25), residues: 421 loop : -1.21 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 95 HIS 0.005 0.001 HIS C 105 PHE 0.030 0.002 PHE C 383 TYR 0.014 0.002 TYR C 643 ARG 0.007 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 34) link_NAG-ASN : angle 3.54799 ( 102) link_ALPHA1-6 : bond 0.03370 ( 1) link_ALPHA1-6 : angle 5.00388 ( 3) link_BETA1-4 : bond 0.00904 ( 6) link_BETA1-4 : angle 3.33097 ( 18) link_ALPHA1-3 : bond 0.00922 ( 1) link_ALPHA1-3 : angle 1.68056 ( 3) hydrogen bonds : bond 0.04593 ( 505) hydrogen bonds : angle 6.17748 ( 1401) SS BOND : bond 0.00413 ( 34) SS BOND : angle 1.36093 ( 68) covalent geometry : bond 0.00413 (15602) covalent geometry : angle 0.73351 (21183) *********************** 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 331 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 249 time to evaluate : 1.614 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: 0.8377 (OUTLIER) cc_final: 0.8063 (pttt) REVERT: B 442 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.6742 (p0) REVERT: B 593 LEU cc_start: 0.9097 (mt) cc_final: 0.8673 (mm) REVERT: B 596 TRP cc_start: 0.7434 (m-10) cc_final: 0.7210 (m-90) REVERT: B 630 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: H 81 LYS cc_start: 0.7571 (ttpp) cc_final: 0.6958 (mmtt) REVERT: C 39 TYR cc_start: 0.8587 (m-80) cc_final: 0.8380 (m-80) REVERT: C 231 LYS cc_start: 0.8044 (mptt) cc_final: 0.7725 (mmtt) REVERT: C 423 ILE cc_start: 0.8275 (mt) cc_final: 0.8026 (mt) REVERT: C 425 ASN cc_start: 0.7505 (t0) cc_final: 0.7243 (t0) REVERT: C 477 ASN cc_start: 0.8171 (m-40) cc_final: 0.7652 (m110) REVERT: C 577 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8937 (tp40) REVERT: D 47 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7149 (p0) REVERT: D 161 MET cc_start: 0.8085 (tpp) cc_final: 0.7494 (tmm) REVERT: D 198 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8151 (p) REVERT: D 486 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6307 (m-80) REVERT: D 530 MET cc_start: 0.6867 (ptm) cc_final: 0.6291 (ptt) REVERT: D 535 MET cc_start: 0.7603 (tpt) cc_final: 0.7322 (mmm) REVERT: D 588 LYS cc_start: 0.9206 (mttt) cc_final: 0.8916 (mmtt) REVERT: D 596 TRP cc_start: 0.9154 (m-10) cc_final: 0.8226 (m-90) REVERT: D 638 HIS cc_start: 0.3772 (OUTLIER) cc_final: 0.2474 (m90) outliers start: 82 outliers final: 48 residues processed: 303 average time/residue: 0.2596 time to fit residues: 119.1907 Evaluate side-chains 280 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 283 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 545 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 MET 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 52 LEU Chi-restraints excluded: chain C residue 110 SER 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 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 390 LEU 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 591 GLN 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 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 468 PHE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 539 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.098593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.083897 restraints weight = 57101.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086191 restraints weight = 31482.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.087770 restraints weight = 20589.855| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15678 Z= 0.144 Angle : 0.743 11.143 21377 Z= 0.350 Chirality : 0.049 0.330 2522 Planarity : 0.004 0.067 2631 Dihedral : 10.585 113.122 2862 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.70 % Allowed : 22.35 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1825 helix: 1.61 (0.27), residues: 384 sheet: -1.01 (0.25), residues: 410 loop : -1.11 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 95 HIS 0.004 0.001 HIS D 374 PHE 0.027 0.002 PHE C 383 TYR 0.017 0.001 TYR H 98 ARG 0.007 0.000 ARG D 344 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 34) link_NAG-ASN : angle 3.43360 ( 102) link_ALPHA1-6 : bond 0.02870 ( 1) link_ALPHA1-6 : angle 5.01904 ( 3) link_BETA1-4 : bond 0.00888 ( 6) link_BETA1-4 : angle 3.28341 ( 18) link_ALPHA1-3 : bond 0.01002 ( 1) link_ALPHA1-3 : angle 1.73639 ( 3) hydrogen bonds : bond 0.04254 ( 505) hydrogen bonds : angle 5.90521 ( 1401) SS BOND : bond 0.00321 ( 34) SS BOND : angle 1.17134 ( 68) covalent geometry : bond 0.00322 (15602) covalent geometry : angle 0.69484 (21183) *********************** 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 326 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 1.656 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: 0.8513 (OUTLIER) cc_final: 0.8221 (pttt) REVERT: B 320 MET cc_start: 0.6651 (pmm) cc_final: 0.6395 (pmm) REVERT: B 442 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6798 (p0) REVERT: H 63 LEU cc_start: 0.9242 (mt) cc_final: 0.8769 (mp) REVERT: H 66 ARG cc_start: 0.5144 (mtm180) cc_final: 0.4467 (mtm180) REVERT: H 81 LYS cc_start: 0.7418 (ttpp) cc_final: 0.6777 (mmtt) REVERT: H 89 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7512 (pt) REVERT: L 69 ARG cc_start: 0.7170 (tpp-160) cc_final: 0.6819 (tpp-160) REVERT: C 39 TYR cc_start: 0.8699 (m-80) cc_final: 0.8405 (m-80) REVERT: C 231 LYS cc_start: 0.8060 (mptt) cc_final: 0.7695 (mmtt) REVERT: C 423 ILE cc_start: 0.8150 (mt) cc_final: 0.7930 (mt) REVERT: C 425 ASN cc_start: 0.7361 (t0) cc_final: 0.7141 (t0) REVERT: C 477 ASN cc_start: 0.8325 (m-40) cc_final: 0.7801 (m110) REVERT: C 629 MET cc_start: 0.6392 (mmp) cc_final: 0.5019 (mmp) REVERT: D 47 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7091 (p0) REVERT: D 100 MET cc_start: 0.8463 (mtt) cc_final: 0.7898 (mtm) REVERT: D 104 MET cc_start: 0.8855 (ttt) cc_final: 0.8536 (ttt) REVERT: D 192 ARG cc_start: 0.7446 (ptm-80) cc_final: 0.7167 (ptm-80) REVERT: D 198 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8088 (p) REVERT: D 477 ASN cc_start: 0.9545 (m-40) cc_final: 0.9002 (m110) REVERT: D 486 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: D 530 MET cc_start: 0.6643 (ptm) cc_final: 0.6138 (ptt) REVERT: D 535 MET cc_start: 0.7785 (tpt) cc_final: 0.7448 (mmm) REVERT: D 588 LYS cc_start: 0.9256 (mttt) cc_final: 0.8920 (mmtt) REVERT: D 596 TRP cc_start: 0.9230 (m-10) cc_final: 0.8400 (m-90) REVERT: D 635 ILE cc_start: 0.7107 (tt) cc_final: 0.6829 (tt) REVERT: D 638 HIS cc_start: 0.3628 (OUTLIER) cc_final: 0.2457 (m90) outliers start: 78 outliers final: 52 residues processed: 293 average time/residue: 0.2674 time to fit residues: 119.1437 Evaluate side-chains 277 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 156 ILE 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 442 ASN 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 58 VAL Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain C residue 88 ASN 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 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 390 LEU 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 530 MET Chi-restraints excluded: chain C residue 591 GLN Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 VAL 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 424 ILE Chi-restraints excluded: chain D residue 486 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 539 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 170 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 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 = 0.3885 r_free = 0.3885 target = 0.099218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.084608 restraints weight = 57652.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086877 restraints weight = 32095.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.088455 restraints weight = 21109.592| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15678 Z= 0.135 Angle : 0.732 11.134 21377 Z= 0.344 Chirality : 0.048 0.330 2522 Planarity : 0.004 0.044 2631 Dihedral : 10.194 112.199 2862 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.64 % Allowed : 23.13 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1825 helix: 1.71 (0.26), residues: 385 sheet: -0.89 (0.25), residues: 422 loop : -1.08 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 596 HIS 0.004 0.001 HIS D 374 PHE 0.026 0.002 PHE C 383 TYR 0.016 0.001 TYR H 98 ARG 0.007 0.000 ARG B 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 34) link_NAG-ASN : angle 3.32858 ( 102) link_ALPHA1-6 : bond 0.03198 ( 1) link_ALPHA1-6 : angle 4.81265 ( 3) link_BETA1-4 : bond 0.00852 ( 6) link_BETA1-4 : angle 3.21502 ( 18) link_ALPHA1-3 : bond 0.01043 ( 1) link_ALPHA1-3 : angle 1.92170 ( 3) hydrogen bonds : bond 0.04035 ( 505) hydrogen bonds : angle 5.70795 ( 1401) SS BOND : bond 0.00313 ( 34) SS BOND : angle 1.47599 ( 68) covalent geometry : bond 0.00304 (15602) covalent geometry : angle 0.68363 (21183) *********************** 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 329 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 252 time to evaluate : 1.777 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: 0.8477 (OUTLIER) cc_final: 0.8171 (pttt) REVERT: B 284 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7102 (mp) REVERT: B 320 MET cc_start: 0.6630 (pmm) cc_final: 0.6374 (pmm) REVERT: B 596 TRP cc_start: 0.7361 (m-90) cc_final: 0.7084 (m-90) REVERT: H 63 LEU cc_start: 0.9217 (mt) cc_final: 0.8867 (mp) REVERT: H 81 LYS cc_start: 0.7464 (ttpp) cc_final: 0.6938 (mmtt) REVERT: H 89 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7553 (pt) REVERT: L 89 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5435 (tt0) REVERT: C 39 TYR cc_start: 0.8684 (m-80) cc_final: 0.8379 (m-80) REVERT: C 231 LYS cc_start: 0.8133 (mptt) cc_final: 0.7807 (mmtt) REVERT: C 425 ASN cc_start: 0.7374 (t0) cc_final: 0.7165 (t0) REVERT: C 477 ASN cc_start: 0.8217 (m-40) cc_final: 0.7673 (m110) REVERT: C 530 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.4249 (mmp) REVERT: C 631 TRP cc_start: 0.7714 (t-100) cc_final: 0.7472 (t-100) REVERT: D 47 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7055 (p0) REVERT: D 104 MET cc_start: 0.8826 (ttt) cc_final: 0.8557 (ttt) REVERT: D 161 MET cc_start: 0.8173 (tpp) cc_final: 0.7830 (tpp) REVERT: D 198 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8044 (p) REVERT: D 486 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: D 530 MET cc_start: 0.6516 (ptm) cc_final: 0.6002 (ptt) REVERT: D 535 MET cc_start: 0.7744 (tpt) cc_final: 0.7449 (mmm) REVERT: D 574 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8920 (mtpt) REVERT: D 588 LYS cc_start: 0.9237 (mttt) cc_final: 0.8870 (mmtt) REVERT: D 596 TRP cc_start: 0.9218 (m-10) cc_final: 0.8374 (m-90) REVERT: D 635 ILE cc_start: 0.6969 (tt) cc_final: 0.6702 (tt) REVERT: D 638 HIS cc_start: 0.3617 (OUTLIER) cc_final: 0.2521 (m90) outliers start: 77 outliers final: 49 residues processed: 301 average time/residue: 0.2621 time to fit residues: 118.9495 Evaluate side-chains 286 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 156 ILE 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 333 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 82 SER Chi-restraints excluded: chain H residue 89 ILE 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 89 GLN Chi-restraints excluded: chain L residue 92 TYR 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 123 THR Chi-restraints excluded: chain C residue 239 CYS 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 333 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain D residue 47 ASP 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 318 TYR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 424 ILE 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 574 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 B 442 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.097833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083215 restraints weight = 57537.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085425 restraints weight = 32572.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.086978 restraints weight = 21638.500| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15678 Z= 0.156 Angle : 0.740 11.303 21377 Z= 0.348 Chirality : 0.048 0.323 2522 Planarity : 0.004 0.045 2631 Dihedral : 10.056 111.915 2862 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.30 % Allowed : 23.31 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1825 helix: 1.60 (0.26), residues: 389 sheet: -0.89 (0.25), residues: 417 loop : -1.13 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 95 HIS 0.005 0.001 HIS D 374 PHE 0.026 0.002 PHE C 383 TYR 0.015 0.001 TYR C 435 ARG 0.006 0.000 ARG L 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 34) link_NAG-ASN : angle 3.26817 ( 102) link_ALPHA1-6 : bond 0.03479 ( 1) link_ALPHA1-6 : angle 4.72592 ( 3) link_BETA1-4 : bond 0.00786 ( 6) link_BETA1-4 : angle 3.15807 ( 18) link_ALPHA1-3 : bond 0.00799 ( 1) link_ALPHA1-3 : angle 2.06675 ( 3) hydrogen bonds : bond 0.04056 ( 505) hydrogen bonds : angle 5.68991 ( 1401) SS BOND : bond 0.00411 ( 34) SS BOND : angle 1.46388 ( 68) covalent geometry : bond 0.00348 (15602) covalent geometry : angle 0.69452 (21183) *********************** 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 330 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 242 time to evaluate : 1.757 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: 0.8492 (OUTLIER) cc_final: 0.8207 (pttt) REVERT: B 442 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6574 (p0) REVERT: B 596 TRP cc_start: 0.7483 (m-10) cc_final: 0.7132 (m-90) REVERT: H 63 LEU cc_start: 0.9234 (mt) cc_final: 0.8893 (mp) REVERT: H 81 LYS cc_start: 0.7393 (ttpp) cc_final: 0.6854 (mmtt) REVERT: H 89 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7540 (pt) REVERT: L 4 MET cc_start: 0.7689 (tpp) cc_final: 0.6998 (mmt) REVERT: L 69 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6723 (tpp-160) REVERT: L 89 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.5790 (tt0) REVERT: C 39 TYR cc_start: 0.8690 (m-80) cc_final: 0.8391 (m-80) REVERT: C 231 LYS cc_start: 0.8150 (mptt) cc_final: 0.7782 (mmtt) REVERT: C 477 ASN cc_start: 0.8207 (m-40) cc_final: 0.7655 (m110) REVERT: C 631 TRP cc_start: 0.7855 (t-100) cc_final: 0.7435 (t-100) REVERT: C 648 ASP cc_start: 0.9146 (p0) cc_final: 0.8932 (p0) REVERT: D 47 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7076 (p0) REVERT: D 95 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: D 104 MET cc_start: 0.8880 (ttt) cc_final: 0.8549 (ttt) REVERT: D 161 MET cc_start: 0.8196 (tpp) cc_final: 0.7784 (tpp) REVERT: D 198 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (p) REVERT: D 477 ASN cc_start: 0.9538 (m-40) cc_final: 0.9143 (m110) REVERT: D 486 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: D 535 MET cc_start: 0.7774 (tpt) cc_final: 0.7466 (mmm) REVERT: D 588 LYS cc_start: 0.9239 (mttt) cc_final: 0.8875 (mmtt) REVERT: D 596 TRP cc_start: 0.9212 (m-10) cc_final: 0.8257 (m-90) REVERT: D 635 ILE cc_start: 0.7005 (tt) cc_final: 0.6738 (tt) REVERT: D 638 HIS cc_start: 0.3652 (OUTLIER) cc_final: 0.2533 (m90) outliers start: 88 outliers final: 62 residues processed: 298 average time/residue: 0.3001 time to fit residues: 134.7393 Evaluate side-chains 289 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 123 THR 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 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 442 ASN 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 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 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 123 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 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 390 LEU 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 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 95 MET 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 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 370 GLU 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 494 LEU Chi-restraints excluded: chain D residue 539 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 166 optimal weight: 0.3980 chunk 146 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 3 optimal weight: 0.0170 chunk 148 optimal weight: 6.9990 overall best weight: 1.2420 ------------------------------------------------------------------------------- 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 B 442 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.097961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.083484 restraints weight = 57565.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085723 restraints weight = 32322.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087282 restraints weight = 21299.969| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15678 Z= 0.151 Angle : 0.747 12.882 21377 Z= 0.349 Chirality : 0.048 0.322 2522 Planarity : 0.004 0.044 2631 Dihedral : 9.999 111.780 2862 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.82 % Allowed : 23.92 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 1825 helix: 1.64 (0.26), residues: 389 sheet: -0.93 (0.25), residues: 406 loop : -1.16 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 95 HIS 0.005 0.001 HIS D 374 PHE 0.029 0.002 PHE C 383 TYR 0.016 0.001 TYR H 59 ARG 0.014 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 34) link_NAG-ASN : angle 3.20197 ( 102) link_ALPHA1-6 : bond 0.03181 ( 1) link_ALPHA1-6 : angle 4.52795 ( 3) link_BETA1-4 : bond 0.00780 ( 6) link_BETA1-4 : angle 3.20769 ( 18) link_ALPHA1-3 : bond 0.00949 ( 1) link_ALPHA1-3 : angle 2.16710 ( 3) hydrogen bonds : bond 0.03966 ( 505) hydrogen bonds : angle 5.62303 ( 1401) SS BOND : bond 0.00367 ( 34) SS BOND : angle 1.29541 ( 68) covalent geometry : bond 0.00343 (15602) covalent geometry : angle 0.70479 (21183) *********************** 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 317 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 1.650 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: 0.8460 (OUTLIER) cc_final: 0.8153 (pttt) REVERT: B 154 MET cc_start: 0.7808 (mmm) cc_final: 0.7484 (mmm) REVERT: B 442 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6894 (p0) REVERT: B 479 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.6978 (m100) REVERT: B 596 TRP cc_start: 0.7571 (m-10) cc_final: 0.7209 (m-90) REVERT: H 63 LEU cc_start: 0.9183 (mt) cc_final: 0.8834 (mp) REVERT: H 81 LYS cc_start: 0.7326 (ttpp) cc_final: 0.6880 (mmmt) REVERT: H 89 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7501 (pt) REVERT: L 89 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.5524 (tt0) REVERT: C 39 TYR cc_start: 0.8662 (m-80) cc_final: 0.8374 (m-80) REVERT: C 91 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 231 LYS cc_start: 0.8163 (mptt) cc_final: 0.7817 (mmtt) REVERT: C 477 ASN cc_start: 0.8198 (m-40) cc_final: 0.7604 (m110) REVERT: C 596 TRP cc_start: 0.8274 (m-10) cc_final: 0.7742 (m-90) REVERT: C 631 TRP cc_start: 0.7790 (t-100) cc_final: 0.7470 (t-100) REVERT: C 648 ASP cc_start: 0.9144 (p0) cc_final: 0.8937 (p0) REVERT: D 47 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7091 (p0) REVERT: D 104 MET cc_start: 0.8885 (ttt) cc_final: 0.8589 (ttt) REVERT: D 193 LEU cc_start: 0.8860 (mm) cc_final: 0.8484 (tp) REVERT: D 198 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8107 (p) REVERT: D 477 ASN cc_start: 0.9536 (m-40) cc_final: 0.9135 (m110) REVERT: D 486 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: D 535 MET cc_start: 0.7807 (tpt) cc_final: 0.7488 (mmm) REVERT: D 588 LYS cc_start: 0.9218 (mttt) cc_final: 0.8890 (mmtt) REVERT: D 596 TRP cc_start: 0.9172 (m-10) cc_final: 0.8255 (m-90) REVERT: D 635 ILE cc_start: 0.6961 (tt) cc_final: 0.6680 (tt) REVERT: D 638 HIS cc_start: 0.3695 (OUTLIER) cc_final: 0.2579 (m90) outliers start: 80 outliers final: 62 residues processed: 289 average time/residue: 0.2391 time to fit residues: 107.1202 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 : 1.756 ------------------------------------------------------------------------------- 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 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 479 TRP 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 82 SER Chi-restraints excluded: chain H residue 89 ILE 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 89 GLN Chi-restraints excluded: chain L residue 92 TYR 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 123 THR Chi-restraints excluded: chain C residue 179 LEU 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 286 VAL 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 390 LEU 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 530 MET 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 95 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 VAL 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 370 GLU 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 539 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.099150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.084543 restraints weight = 56736.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.086832 restraints weight = 31872.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088425 restraints weight = 20967.882| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15678 Z= 0.129 Angle : 0.733 12.858 21377 Z= 0.342 Chirality : 0.048 0.327 2522 Planarity : 0.004 0.042 2631 Dihedral : 9.848 111.695 2862 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.10 % Allowed : 25.00 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1825 helix: 1.64 (0.26), residues: 396 sheet: -0.72 (0.26), residues: 391 loop : -1.07 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 95 HIS 0.004 0.001 HIS L 27 PHE 0.026 0.001 PHE C 383 TYR 0.019 0.001 TYR H 59 ARG 0.010 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 34) link_NAG-ASN : angle 3.12502 ( 102) link_ALPHA1-6 : bond 0.02905 ( 1) link_ALPHA1-6 : angle 4.37117 ( 3) link_BETA1-4 : bond 0.00803 ( 6) link_BETA1-4 : angle 3.21049 ( 18) link_ALPHA1-3 : bond 0.01104 ( 1) link_ALPHA1-3 : angle 2.28350 ( 3) hydrogen bonds : bond 0.03772 ( 505) hydrogen bonds : angle 5.46726 ( 1401) SS BOND : bond 0.00315 ( 34) SS BOND : angle 1.19979 ( 68) covalent geometry : bond 0.00292 (15602) covalent geometry : angle 0.69202 (21183) *********************** 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 315 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 2.185 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: B 52 LEU cc_start: 0.7869 (mm) cc_final: 0.7379 (mm) REVERT: B 97 LYS cc_start: 0.8310 (mmmt) cc_final: 0.8105 (mmmt) REVERT: B 152 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8281 (mmmt) REVERT: B 154 MET cc_start: 0.7741 (mmm) cc_final: 0.7480 (mmm) REVERT: B 442 ASN cc_start: 0.7210 (OUTLIER) cc_final: 0.6545 (p0) REVERT: B 479 TRP cc_start: 0.8979 (OUTLIER) cc_final: 0.6853 (m100) REVERT: B 596 TRP cc_start: 0.7573 (m-10) cc_final: 0.7314 (m-90) REVERT: H 63 LEU cc_start: 0.9192 (mt) cc_final: 0.8849 (mp) REVERT: H 81 LYS cc_start: 0.7390 (ttpp) cc_final: 0.6826 (mmtt) REVERT: H 89 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7316 (pt) REVERT: H 91 TYR cc_start: 0.6937 (m-80) cc_final: 0.6668 (m-80) REVERT: L 89 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.5411 (tt0) REVERT: C 39 TYR cc_start: 0.8675 (m-80) cc_final: 0.8358 (m-80) REVERT: C 91 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7044 (mm-30) REVERT: C 425 ASN cc_start: 0.7398 (t0) cc_final: 0.7169 (t0) REVERT: C 434 MET cc_start: 0.5467 (ptp) cc_final: 0.5030 (ptp) REVERT: C 477 ASN cc_start: 0.8242 (m-40) cc_final: 0.7720 (m110) REVERT: C 596 TRP cc_start: 0.8292 (m-10) cc_final: 0.7749 (m-90) REVERT: C 631 TRP cc_start: 0.7812 (t-100) cc_final: 0.7522 (t-100) REVERT: C 648 ASP cc_start: 0.9162 (p0) cc_final: 0.8955 (p0) REVERT: D 47 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.6810 (p0) REVERT: D 104 MET cc_start: 0.8911 (ttt) cc_final: 0.8608 (ttt) REVERT: D 161 MET cc_start: 0.8104 (tpp) cc_final: 0.7687 (tpp) REVERT: D 166 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8419 (mtt180) REVERT: D 192 ARG cc_start: 0.7419 (ptm-80) cc_final: 0.6977 (ptm160) REVERT: D 193 LEU cc_start: 0.8857 (mm) cc_final: 0.8375 (tp) REVERT: D 198 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8017 (p) REVERT: D 320 MET cc_start: 0.4857 (mmt) cc_final: 0.4024 (mmp) REVERT: D 477 ASN cc_start: 0.9520 (m-40) cc_final: 0.9102 (m110) REVERT: D 535 MET cc_start: 0.7982 (tpt) cc_final: 0.7602 (mmm) REVERT: D 588 LYS cc_start: 0.9233 (mttt) cc_final: 0.8925 (mmtt) REVERT: D 596 TRP cc_start: 0.9170 (m-10) cc_final: 0.8249 (m-90) REVERT: D 638 HIS cc_start: 0.3635 (OUTLIER) cc_final: 0.2485 (m90) outliers start: 68 outliers final: 53 residues processed: 290 average time/residue: 0.2533 time to fit residues: 112.6590 Evaluate side-chains 293 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 333 ILE Chi-restraints excluded: chain B residue 442 ASN 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 24 VAL Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 108 LEU 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 89 GLN Chi-restraints excluded: chain L residue 92 TYR 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 123 THR Chi-restraints excluded: chain C residue 179 LEU 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 286 VAL 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 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 217 TYR 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 393 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 539 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 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 = 0.3874 r_free = 0.3874 target = 0.098682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084123 restraints weight = 57440.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.086387 restraints weight = 32269.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.087981 restraints weight = 21308.473| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15678 Z= 0.137 Angle : 0.734 12.808 21377 Z= 0.343 Chirality : 0.048 0.322 2522 Planarity : 0.004 0.042 2631 Dihedral : 9.715 111.741 2860 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.16 % Allowed : 24.88 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1825 helix: 1.65 (0.26), residues: 396 sheet: -0.72 (0.26), residues: 381 loop : -1.10 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 95 HIS 0.004 0.001 HIS L 27 PHE 0.025 0.002 PHE C 383 TYR 0.015 0.001 TYR C 435 ARG 0.010 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 34) link_NAG-ASN : angle 3.12413 ( 102) link_ALPHA1-6 : bond 0.02792 ( 1) link_ALPHA1-6 : angle 4.22052 ( 3) link_BETA1-4 : bond 0.00709 ( 6) link_BETA1-4 : angle 3.24039 ( 18) link_ALPHA1-3 : bond 0.01006 ( 1) link_ALPHA1-3 : angle 2.41583 ( 3) hydrogen bonds : bond 0.03831 ( 505) hydrogen bonds : angle 5.49755 ( 1401) SS BOND : bond 0.00473 ( 34) SS BOND : angle 1.15420 ( 68) covalent geometry : bond 0.00313 (15602) covalent geometry : angle 0.69245 (21183) *********************** 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 309 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LEU cc_start: 0.8022 (mm) cc_final: 0.7627 (mm) REVERT: B 97 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8140 (mmmt) REVERT: B 152 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8283 (mmmt) REVERT: B 154 MET cc_start: 0.7721 (mmm) cc_final: 0.7474 (mmm) REVERT: B 479 TRP cc_start: 0.8971 (OUTLIER) cc_final: 0.6958 (m100) REVERT: B 596 TRP cc_start: 0.7650 (m-10) cc_final: 0.7350 (m-90) REVERT: H 63 LEU cc_start: 0.9230 (mt) cc_final: 0.8861 (mp) REVERT: H 81 LYS cc_start: 0.7370 (ttpp) cc_final: 0.6825 (mmmt) REVERT: H 89 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7348 (pt) REVERT: H 91 TYR cc_start: 0.7001 (m-80) cc_final: 0.6749 (m-80) REVERT: L 4 MET cc_start: 0.7738 (tpp) cc_final: 0.7013 (mmt) REVERT: L 89 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.5492 (tt0) REVERT: C 39 TYR cc_start: 0.8654 (m-80) cc_final: 0.8354 (m-80) REVERT: C 477 ASN cc_start: 0.8243 (m-40) cc_final: 0.7717 (m110) REVERT: C 530 MET cc_start: 0.3509 (mmp) cc_final: 0.3265 (mmp) REVERT: C 596 TRP cc_start: 0.8338 (m-10) cc_final: 0.7676 (m-90) REVERT: D 47 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6824 (p0) REVERT: D 104 MET cc_start: 0.8871 (ttt) cc_final: 0.8559 (ttt) REVERT: D 192 ARG cc_start: 0.7474 (ptm-80) cc_final: 0.7214 (ptm160) REVERT: D 198 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8064 (p) REVERT: D 320 MET cc_start: 0.4683 (mmt) cc_final: 0.4184 (mmp) REVERT: D 388 SER cc_start: 0.1865 (OUTLIER) cc_final: 0.1313 (p) REVERT: D 477 ASN cc_start: 0.9544 (m-40) cc_final: 0.9133 (m110) REVERT: D 535 MET cc_start: 0.8023 (tpt) cc_final: 0.7655 (mmm) REVERT: D 588 LYS cc_start: 0.9237 (mttt) cc_final: 0.8932 (mmtt) REVERT: D 635 ILE cc_start: 0.6916 (tt) cc_final: 0.6600 (tt) REVERT: D 638 HIS cc_start: 0.3674 (OUTLIER) cc_final: 0.2584 (m90) outliers start: 69 outliers final: 57 residues processed: 285 average time/residue: 0.2706 time to fit residues: 116.2396 Evaluate side-chains 296 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 229 ASN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 333 ILE 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 89 ILE 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 89 GLN Chi-restraints excluded: chain L residue 92 TYR 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 123 THR Chi-restraints excluded: chain C residue 179 LEU 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 286 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 309 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 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 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 VAL 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 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 496 ILE Chi-restraints excluded: chain D residue 539 VAL 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 98 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 105 HIS B 241 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.096577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.082128 restraints weight = 58009.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.084385 restraints weight = 32154.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.085972 restraints weight = 21100.542| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15678 Z= 0.186 Angle : 0.776 12.350 21377 Z= 0.363 Chirality : 0.048 0.312 2522 Planarity : 0.004 0.044 2631 Dihedral : 9.896 113.394 2860 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.28 % Allowed : 25.00 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1825 helix: 1.56 (0.26), residues: 396 sheet: -0.95 (0.26), residues: 373 loop : -1.15 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP H 95 HIS 0.006 0.001 HIS L 27 PHE 0.027 0.002 PHE C 383 TYR 0.014 0.002 TYR C 435 ARG 0.009 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 34) link_NAG-ASN : angle 3.19830 ( 102) link_ALPHA1-6 : bond 0.03088 ( 1) link_ALPHA1-6 : angle 4.39566 ( 3) link_BETA1-4 : bond 0.00687 ( 6) link_BETA1-4 : angle 3.22654 ( 18) link_ALPHA1-3 : bond 0.00794 ( 1) link_ALPHA1-3 : angle 2.40768 ( 3) hydrogen bonds : bond 0.04144 ( 505) hydrogen bonds : angle 5.71352 ( 1401) SS BOND : bond 0.00450 ( 34) SS BOND : angle 1.18830 ( 68) covalent geometry : bond 0.00418 (15602) covalent geometry : angle 0.73562 (21183) ********************** 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 296 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 1.639 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 52 LEU cc_start: 0.7960 (mm) cc_final: 0.7486 (mm) REVERT: B 97 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8280 (mmmt) REVERT: B 152 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8274 (mmmt) REVERT: B 201 ILE cc_start: 0.8279 (mm) cc_final: 0.7938 (mm) REVERT: B 479 TRP cc_start: 0.9061 (OUTLIER) cc_final: 0.7137 (m100) REVERT: B 596 TRP cc_start: 0.7770 (m-10) cc_final: 0.7297 (m-90) REVERT: H 63 LEU cc_start: 0.9213 (mt) cc_final: 0.8848 (mp) REVERT: H 81 LYS cc_start: 0.7259 (ttpp) cc_final: 0.6658 (mmtt) REVERT: L 4 MET cc_start: 0.7909 (tpp) cc_final: 0.7215 (mmt) REVERT: L 89 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.5666 (tt0) REVERT: C 39 TYR cc_start: 0.8676 (m-80) cc_final: 0.8359 (m-80) REVERT: C 320 MET cc_start: 0.4594 (ptp) cc_final: 0.4046 (ptp) REVERT: C 477 ASN cc_start: 0.8223 (m-40) cc_final: 0.7639 (m110) REVERT: C 596 TRP cc_start: 0.8444 (m-10) cc_final: 0.7725 (m-90) REVERT: D 47 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7024 (p0) REVERT: D 104 MET cc_start: 0.8910 (ttt) cc_final: 0.8564 (ttt) REVERT: D 198 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8230 (p) REVERT: D 388 SER cc_start: 0.2139 (OUTLIER) cc_final: 0.1716 (p) REVERT: D 477 ASN cc_start: 0.9589 (m-40) cc_final: 0.9222 (m110) REVERT: D 535 MET cc_start: 0.7918 (tpt) cc_final: 0.7618 (mmm) REVERT: D 588 LYS cc_start: 0.9261 (mttt) cc_final: 0.8903 (mmtt) REVERT: D 596 TRP cc_start: 0.9140 (m-10) cc_final: 0.8293 (m-90) REVERT: D 635 ILE cc_start: 0.7112 (tt) cc_final: 0.6835 (tt) REVERT: D 638 HIS cc_start: 0.3861 (OUTLIER) cc_final: 0.2731 (m90) outliers start: 71 outliers final: 59 residues processed: 273 average time/residue: 0.2484 time to fit residues: 103.6521 Evaluate side-chains 281 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 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 333 ILE 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 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 89 GLN 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 123 THR 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 286 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 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 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 581 LEU Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 127 VAL 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 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 496 ILE Chi-restraints excluded: chain D residue 539 VAL 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 161 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.096842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.082459 restraints weight = 57364.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.084729 restraints weight = 31692.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.086310 restraints weight = 20770.963| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15678 Z= 0.169 Angle : 0.779 12.585 21377 Z= 0.362 Chirality : 0.049 0.313 2522 Planarity : 0.004 0.042 2631 Dihedral : 9.905 113.256 2860 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.22 % Allowed : 25.00 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1825 helix: 1.58 (0.26), residues: 396 sheet: -0.95 (0.26), residues: 378 loop : -1.12 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP H 95 HIS 0.005 0.001 HIS D 374 PHE 0.026 0.002 PHE C 383 TYR 0.014 0.002 TYR H 59 ARG 0.008 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 34) link_NAG-ASN : angle 3.15433 ( 102) link_ALPHA1-6 : bond 0.02855 ( 1) link_ALPHA1-6 : angle 4.18449 ( 3) link_BETA1-4 : bond 0.00698 ( 6) link_BETA1-4 : angle 3.24168 ( 18) link_ALPHA1-3 : bond 0.00872 ( 1) link_ALPHA1-3 : angle 2.35640 ( 3) hydrogen bonds : bond 0.04008 ( 505) hydrogen bonds : angle 5.67701 ( 1401) SS BOND : bond 0.00381 ( 34) SS BOND : angle 1.15857 ( 68) covalent geometry : bond 0.00386 (15602) covalent geometry : angle 0.74018 (21183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.01 seconds wall clock time: 93 minutes 55.79 seconds (5635.79 seconds total)