Starting phenix.real_space_refine on Tue May 20 14:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfl_33792/05_2025/7yfl_33792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfl_33792/05_2025/7yfl_33792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfl_33792/05_2025/7yfl_33792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfl_33792/05_2025/7yfl_33792.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfl_33792/05_2025/7yfl_33792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfl_33792/05_2025/7yfl_33792.cif" } resolution = 3.9 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= 0.006 sd= 0.062 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 90 5.16 5 C 12720 2.51 5 N 3436 2.21 5 O 3722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19968 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5036 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 30, 'TRANS': 677} Chain breaks: 13 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 4807 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 31, 'TRANS': 647} Chain breaks: 12 Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 15, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 340 Chain: "C" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5036 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 30, 'TRANS': 677} Chain breaks: 13 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 351 Chain: "D" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 4807 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 31, 'TRANS': 647} Chain breaks: 12 Unresolved non-hydrogen bonds: 535 Unresolved non-hydrogen angles: 676 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 15, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 340 Chain: "E" 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: "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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.93, per 1000 atoms: 0.60 Number of scatterers: 19968 At special positions: 0 Unit cell: (117.66, 143.1, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3722 8.00 N 3436 7.00 C 12720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.02 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 902 " - " ASN A 61 " " NAG A 903 " - " ASN A 471 " " NAG A 904 " - " ASN A 440 " " NAG A 905 " - " ASN A 368 " " NAG A 906 " - " ASN A 203 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG C 904 " - " ASN C 440 " " NAG C 905 " - " ASN C 61 " " NAG C 906 " - " ASN C 471 " " NAG E 1 " - " ASN A 771 " " NAG F 1 " - " ASN B 715 " " NAG G 1 " - " ASN C 771 " " NAG H 1 " - " ASN D 715 " Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.8 seconds 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5188 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 24 sheets defined 43.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.782A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.409A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.768A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.636A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.915A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.793A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.639A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.806A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.550A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.675A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 580 removed outlier: 7.543A pdb=" N SER A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.646A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 656 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 693 Processing helix chain 'A' and resid 694 through 695 No H-bonds generated for 'chain 'A' and resid 694 through 695' Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 3.774A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.566A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.265A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 782 removed outlier: 4.757A pdb=" N ASN A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.980A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.844A pdb=" N ALA B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.620A pdb=" N LEU B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 230 through 239 removed outlier: 4.046A pdb=" N VAL B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 removed outlier: 4.045A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 315 through 338 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 582 through 593 removed outlier: 4.492A pdb=" N TRP B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS B 593 " --> pdb=" O MET B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.532A pdb=" N ASN B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 3.900A pdb=" N MET B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 717 through 726 Processing helix chain 'B' and resid 730 through 734 removed outlier: 4.133A pdb=" N VAL B 734 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 750 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 799 through 813 removed outlier: 3.714A pdb=" N ASP B 804 " --> pdb=" O LYS B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 840 through 853 Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.782A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 84 Processing helix chain 'C' and resid 103 through 115 removed outlier: 4.311A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.790A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.631A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.755A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.794A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.640A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.784A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.551A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.675A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 580 removed outlier: 3.909A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 613 removed outlier: 3.645A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 656 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 693 Processing helix chain 'C' and resid 694 through 695 No H-bonds generated for 'chain 'C' and resid 694 through 695' Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 709 removed outlier: 3.773A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 removed outlier: 3.553A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 744 removed outlier: 4.266A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 782 removed outlier: 4.770A pdb=" N ASN C 771 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.983A pdb=" N LEU D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.879A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.622A pdb=" N LEU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.043A pdb=" N VAL D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 263 removed outlier: 4.045A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 315 through 338 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 487 through 500 Processing helix chain 'D' and resid 522 through 530 Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 582 through 593 removed outlier: 4.491A pdb=" N TRP D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYS D 593 " --> pdb=" O MET D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.536A pdb=" N ASN D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 682 removed outlier: 3.930A pdb=" N MET D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 717 through 726 Processing helix chain 'D' and resid 730 through 734 removed outlier: 4.133A pdb=" N VAL D 734 " --> pdb=" O SER D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 750 Processing helix chain 'D' and resid 761 through 766 Processing helix chain 'D' and resid 799 through 813 removed outlier: 3.718A pdb=" N ASP D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 Processing helix chain 'D' and resid 840 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.370A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 197 removed outlier: 6.312A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.228A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 513 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 761 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.696A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 489 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.744A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.134A pdb=" N ILE B 141 " --> pdb=" O LEU B 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.523A pdb=" N ARG B 244 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TRP B 272 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL B 307 " --> pdb=" O TRP B 272 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N MET B 274 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N SER B 309 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU B 304 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 391 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 400 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 369 Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 434 removed outlier: 6.973A pdb=" N VAL B 434 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 505 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 463 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 755 through 758 removed outlier: 3.745A pdb=" N LEU B 775 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 755 through 758 removed outlier: 4.960A pdb=" N ILE B 561 " --> pdb=" O ALA B 785 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA B 785 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.386A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.306A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.229A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 513 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 761 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.723A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AB9, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.742A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.131A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 243 through 246 removed outlier: 6.522A pdb=" N ARG D 244 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TRP D 272 " --> pdb=" O PHE D 305 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL D 307 " --> pdb=" O TRP D 272 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET D 274 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N SER D 309 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 391 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 400 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 367 through 369 Processing sheet with id=AC4, first strand: chain 'D' and resid 433 through 434 removed outlier: 6.972A pdb=" N VAL D 434 " --> pdb=" O TYR D 506 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 505 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 463 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 755 through 758 removed outlier: 3.745A pdb=" N LEU D 775 " --> pdb=" O VAL D 565 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 755 through 758 removed outlier: 4.943A pdb=" N ILE D 561 " --> pdb=" O ALA D 785 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA D 785 " --> pdb=" O ILE D 561 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.49 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6555 1.34 - 1.47: 4868 1.47 - 1.59: 8783 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 20350 Sorted by residual: bond pdb=" N GLU A 662 " pdb=" CA GLU A 662 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.34e+00 bond pdb=" N GLU C 661 " pdb=" CA GLU C 661 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.13e-02 7.83e+03 5.35e+00 bond pdb=" CA THR C 665 " pdb=" C THR C 665 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.31e-02 5.83e+03 4.75e+00 bond pdb=" N GLU C 662 " pdb=" CA GLU C 662 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.33e+00 bond pdb=" C1 NAG C 904 " pdb=" O5 NAG C 904 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 20345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 27158 1.85 - 3.70: 504 3.70 - 5.55: 73 5.55 - 7.40: 38 7.40 - 9.25: 5 Bond angle restraints: 27778 Sorted by residual: angle pdb=" C ASP A 441 " pdb=" CA ASP A 441 " pdb=" CB ASP A 441 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.61e+01 angle pdb=" C TRP A 56 " pdb=" CA TRP A 56 " pdb=" CB TRP A 56 " ideal model delta sigma weight residual 115.79 110.29 5.50 1.19e+00 7.06e-01 2.14e+01 angle pdb=" CA LYS B 782 " pdb=" CB LYS B 782 " pdb=" CG LYS B 782 " ideal model delta sigma weight residual 114.10 122.39 -8.29 2.00e+00 2.50e-01 1.72e+01 angle pdb=" CA TRP C 636 " pdb=" CB TRP C 636 " pdb=" CG TRP C 636 " ideal model delta sigma weight residual 113.60 120.90 -7.30 1.90e+00 2.77e-01 1.48e+01 angle pdb=" CA TRP A 636 " pdb=" CB TRP A 636 " pdb=" CG TRP A 636 " ideal model delta sigma weight residual 113.60 120.81 -7.21 1.90e+00 2.77e-01 1.44e+01 ... (remaining 27773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 10969 21.17 - 42.34: 995 42.34 - 63.50: 212 63.50 - 84.67: 24 84.67 - 105.84: 12 Dihedral angle restraints: 12212 sinusoidal: 4220 harmonic: 7992 Sorted by residual: dihedral pdb=" CB CYS D 462 " pdb=" SG CYS D 462 " pdb=" SG CYS D 484 " pdb=" CB CYS D 484 " ideal model delta sinusoidal sigma weight residual -86.00 -174.19 88.19 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS B 462 " pdb=" SG CYS B 462 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual -86.00 -173.97 87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS D 455 " pdb=" SG CYS D 455 " pdb=" SG CYS D 483 " pdb=" CB CYS D 483 " ideal model delta sinusoidal sigma weight residual 93.00 154.50 -61.50 1 1.00e+01 1.00e-02 5.02e+01 ... (remaining 12209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3072 0.081 - 0.162: 259 0.162 - 0.243: 1 0.243 - 0.324: 4 0.324 - 0.404: 2 Chirality restraints: 3338 Sorted by residual: chirality pdb=" C1 NAG C 904 " pdb=" ND2 ASN C 440 " pdb=" C2 NAG C 904 " pdb=" O5 NAG C 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C1 NAG C 905 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C 905 " pdb=" O5 NAG C 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CG LEU D 670 " pdb=" CB LEU D 670 " pdb=" CD1 LEU D 670 " pdb=" CD2 LEU D 670 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3335 not shown) Planarity restraints: 3564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 440 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO B 441 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 441 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 441 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 440 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO D 441 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO D 441 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 441 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 636 " -0.031 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP C 636 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP C 636 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 636 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 636 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 636 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 636 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 636 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 636 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 636 " 0.000 2.00e-02 2.50e+03 ... (remaining 3561 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4924 2.79 - 3.32: 19190 3.32 - 3.84: 31379 3.84 - 4.37: 32286 4.37 - 4.90: 56166 Nonbonded interactions: 143945 Sorted by model distance: nonbonded pdb=" NH2 ARG A 397 " pdb=" OE1 GLU A 475 " model vdw 2.260 3.120 nonbonded pdb=" NH2 ARG C 397 " pdb=" OE1 GLU C 475 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR C 114 " pdb=" O CYS C 308 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" O CYS A 308 " model vdw 2.267 3.040 nonbonded pdb=" O SER C 446 " pdb=" OG SER C 446 " model vdw 2.277 3.040 ... (remaining 143940 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.130 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.210 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.005 0.046 20382 Z= 0.203 Angle : 0.657 16.961 27860 Z= 0.330 Chirality : 0.044 0.404 3338 Planarity : 0.005 0.121 3550 Dihedral : 16.695 105.838 6982 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.88 % Favored : 91.79 % Rotamer: Outliers : 0.34 % Allowed : 31.71 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2666 helix: 1.78 (0.17), residues: 1048 sheet: -1.63 (0.36), residues: 242 loop : -1.86 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP C 636 HIS 0.006 0.001 HIS C 780 PHE 0.019 0.002 PHE A 113 TYR 0.020 0.001 TYR B 673 ARG 0.005 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 14) link_NAG-ASN : angle 3.87244 ( 42) link_BETA1-4 : bond 0.00361 ( 4) link_BETA1-4 : angle 1.98661 ( 12) hydrogen bonds : bond 0.14207 ( 830) hydrogen bonds : angle 6.41996 ( 2442) SS BOND : bond 0.00372 ( 14) SS BOND : angle 1.31379 ( 28) covalent geometry : bond 0.00452 (20350) covalent geometry : angle 0.63824 (27778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 2.314 Fit side-chains REVERT: C 679 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.6190 (t80) outliers start: 6 outliers final: 4 residues processed: 173 average time/residue: 0.2613 time to fit residues: 75.3542 Evaluate side-chains 168 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain D residue 520 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 70 optimal weight: 0.0050 chunk 140 optimal weight: 50.0000 chunk 110 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 GLN B 465 GLN B 497 HIS B 725 ASN C 796 GLN D 465 GLN D 725 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.164835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136671 restraints weight = 41766.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126459 restraints weight = 56722.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.125408 restraints weight = 60125.418| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20382 Z= 0.103 Angle : 0.566 16.212 27860 Z= 0.278 Chirality : 0.043 0.404 3338 Planarity : 0.004 0.077 3550 Dihedral : 5.809 71.016 3284 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.05 % Favored : 92.72 % Rotamer: Outliers : 2.32 % Allowed : 30.35 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2666 helix: 1.85 (0.16), residues: 1088 sheet: -1.61 (0.35), residues: 242 loop : -1.82 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 636 HIS 0.003 0.001 HIS B 431 PHE 0.009 0.001 PHE C 533 TYR 0.018 0.001 TYR B 705 ARG 0.004 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00790 ( 14) link_NAG-ASN : angle 3.66586 ( 42) link_BETA1-4 : bond 0.00344 ( 4) link_BETA1-4 : angle 1.86856 ( 12) hydrogen bonds : bond 0.03019 ( 830) hydrogen bonds : angle 4.93542 ( 2442) SS BOND : bond 0.00546 ( 14) SS BOND : angle 1.07099 ( 28) covalent geometry : bond 0.00226 (20350) covalent geometry : angle 0.54580 (27778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 2.207 Fit side-chains REVERT: A 502 MET cc_start: 0.8927 (mmm) cc_final: 0.8612 (mmt) REVERT: B 829 HIS cc_start: 0.7575 (m90) cc_final: 0.7368 (m90) REVERT: D 829 HIS cc_start: 0.7593 (m90) cc_final: 0.7387 (m90) outliers start: 41 outliers final: 26 residues processed: 208 average time/residue: 0.2543 time to fit residues: 88.0921 Evaluate side-chains 192 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 177 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 218 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 147 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.164432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.136466 restraints weight = 41487.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125661 restraints weight = 54251.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.124823 restraints weight = 57990.607| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20382 Z= 0.108 Angle : 0.542 15.610 27860 Z= 0.266 Chirality : 0.042 0.409 3338 Planarity : 0.004 0.075 3550 Dihedral : 4.623 53.571 3280 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.71 % Favored : 93.06 % Rotamer: Outliers : 3.34 % Allowed : 29.05 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2666 helix: 1.99 (0.16), residues: 1078 sheet: -1.65 (0.33), residues: 262 loop : -1.77 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 636 HIS 0.003 0.001 HIS A 780 PHE 0.015 0.001 PHE A 113 TYR 0.014 0.001 TYR D 705 ARG 0.005 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00769 ( 14) link_NAG-ASN : angle 3.59824 ( 42) link_BETA1-4 : bond 0.00415 ( 4) link_BETA1-4 : angle 1.74425 ( 12) hydrogen bonds : bond 0.02886 ( 830) hydrogen bonds : angle 4.67017 ( 2442) SS BOND : bond 0.00309 ( 14) SS BOND : angle 1.16386 ( 28) covalent geometry : bond 0.00248 (20350) covalent geometry : angle 0.52196 (27778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 2.003 Fit side-chains REVERT: A 679 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.5484 (t80) REVERT: A 726 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7657 (tt) REVERT: B 829 HIS cc_start: 0.7653 (m90) cc_final: 0.7450 (m90) REVERT: C 726 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7628 (tt) REVERT: D 829 HIS cc_start: 0.7676 (m90) cc_final: 0.7474 (m90) outliers start: 59 outliers final: 43 residues processed: 222 average time/residue: 0.2335 time to fit residues: 88.1647 Evaluate side-chains 214 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 189 optimal weight: 8.9990 chunk 51 optimal weight: 50.0000 chunk 128 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 142 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 725 ASN C 59 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS D 725 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.161971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.131463 restraints weight = 41894.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120815 restraints weight = 62016.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118496 restraints weight = 65856.500| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20382 Z= 0.195 Angle : 0.593 15.384 27860 Z= 0.293 Chirality : 0.044 0.395 3338 Planarity : 0.004 0.073 3550 Dihedral : 4.469 53.627 3280 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.14 % Favored : 91.75 % Rotamer: Outliers : 4.25 % Allowed : 29.05 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2666 helix: 1.96 (0.16), residues: 1074 sheet: -1.81 (0.33), residues: 262 loop : -1.83 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP C 636 HIS 0.006 0.001 HIS C 780 PHE 0.018 0.002 PHE A 113 TYR 0.015 0.001 TYR D 705 ARG 0.004 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 14) link_NAG-ASN : angle 3.57466 ( 42) link_BETA1-4 : bond 0.00400 ( 4) link_BETA1-4 : angle 1.71793 ( 12) hydrogen bonds : bond 0.03139 ( 830) hydrogen bonds : angle 4.73745 ( 2442) SS BOND : bond 0.00618 ( 14) SS BOND : angle 1.36472 ( 28) covalent geometry : bond 0.00462 (20350) covalent geometry : angle 0.57430 (27778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 2.352 Fit side-chains REVERT: A 679 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5937 (t80) outliers start: 75 outliers final: 57 residues processed: 235 average time/residue: 0.2481 time to fit residues: 99.3460 Evaluate side-chains 224 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 73 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 0.0270 chunk 85 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 overall best weight: 2.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131372 restraints weight = 41832.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121807 restraints weight = 58129.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120556 restraints weight = 55461.773| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20382 Z= 0.177 Angle : 0.582 15.118 27860 Z= 0.287 Chirality : 0.043 0.393 3338 Planarity : 0.004 0.072 3550 Dihedral : 4.540 58.058 3280 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.54 % Favored : 92.35 % Rotamer: Outliers : 4.81 % Allowed : 29.28 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2666 helix: 1.84 (0.16), residues: 1090 sheet: -1.92 (0.33), residues: 262 loop : -1.78 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP C 636 HIS 0.004 0.001 HIS A 780 PHE 0.017 0.001 PHE A 533 TYR 0.018 0.001 TYR B 506 ARG 0.002 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 14) link_NAG-ASN : angle 3.48185 ( 42) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 1.70581 ( 12) hydrogen bonds : bond 0.02936 ( 830) hydrogen bonds : angle 4.70061 ( 2442) SS BOND : bond 0.00453 ( 14) SS BOND : angle 1.27347 ( 28) covalent geometry : bond 0.00422 (20350) covalent geometry : angle 0.56442 (27778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 171 time to evaluate : 2.101 Fit side-chains REVERT: A 477 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.8628 (p90) REVERT: A 679 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6111 (t80) REVERT: B 274 MET cc_start: 0.7862 (tmm) cc_final: 0.7647 (tmm) REVERT: C 125 MET cc_start: 0.7499 (mmm) cc_final: 0.7162 (mtt) REVERT: C 477 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8574 (p90) REVERT: D 274 MET cc_start: 0.7849 (tmm) cc_final: 0.7631 (tmm) outliers start: 85 outliers final: 63 residues processed: 245 average time/residue: 0.2351 time to fit residues: 97.9455 Evaluate side-chains 236 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 153 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 168 optimal weight: 0.0370 chunk 203 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 209 optimal weight: 0.3980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 HIS B 725 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS D 725 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.164469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136511 restraints weight = 41796.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125670 restraints weight = 56611.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125411 restraints weight = 54723.287| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20382 Z= 0.093 Angle : 0.551 14.838 27860 Z= 0.268 Chirality : 0.043 0.406 3338 Planarity : 0.004 0.075 3550 Dihedral : 4.331 53.789 3280 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 3.34 % Allowed : 30.75 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2666 helix: 1.94 (0.16), residues: 1096 sheet: -1.85 (0.33), residues: 262 loop : -1.76 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP A 636 HIS 0.002 0.000 HIS B 497 PHE 0.012 0.001 PHE A 113 TYR 0.015 0.001 TYR C 114 ARG 0.007 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 14) link_NAG-ASN : angle 3.41264 ( 42) link_BETA1-4 : bond 0.00445 ( 4) link_BETA1-4 : angle 1.68616 ( 12) hydrogen bonds : bond 0.02517 ( 830) hydrogen bonds : angle 4.62614 ( 2442) SS BOND : bond 0.00313 ( 14) SS BOND : angle 1.39595 ( 28) covalent geometry : bond 0.00209 (20350) covalent geometry : angle 0.53305 (27778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 2.376 Fit side-chains REVERT: A 679 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5912 (t80) REVERT: B 782 LYS cc_start: 0.4713 (tptp) cc_final: 0.3985 (tptp) REVERT: C 125 MET cc_start: 0.7464 (mmm) cc_final: 0.7205 (mtt) REVERT: C 155 MET cc_start: 0.8542 (tmm) cc_final: 0.8268 (ttt) REVERT: C 340 PHE cc_start: 0.5495 (m-80) cc_final: 0.5226 (m-10) outliers start: 59 outliers final: 51 residues processed: 228 average time/residue: 0.2419 time to fit residues: 93.4169 Evaluate side-chains 223 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 228 optimal weight: 6.9990 chunk 222 optimal weight: 40.0000 chunk 257 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 chunk 61 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 142 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN B 725 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN D 725 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134213 restraints weight = 42067.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.125930 restraints weight = 64077.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.124802 restraints weight = 73394.312| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20382 Z= 0.313 Angle : 0.697 14.966 27860 Z= 0.349 Chirality : 0.046 0.379 3338 Planarity : 0.004 0.076 3550 Dihedral : 4.583 54.157 3276 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.89 % Favored : 91.00 % Rotamer: Outliers : 5.27 % Allowed : 29.33 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2666 helix: 1.65 (0.16), residues: 1090 sheet: -1.85 (0.37), residues: 220 loop : -1.85 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 636 HIS 0.011 0.002 HIS C 780 PHE 0.028 0.002 PHE A 533 TYR 0.020 0.002 TYR A 711 ARG 0.003 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00921 ( 14) link_NAG-ASN : angle 3.52173 ( 42) link_BETA1-4 : bond 0.00275 ( 4) link_BETA1-4 : angle 1.71451 ( 12) hydrogen bonds : bond 0.03643 ( 830) hydrogen bonds : angle 5.08010 ( 2442) SS BOND : bond 0.00646 ( 14) SS BOND : angle 1.95300 ( 28) covalent geometry : bond 0.00739 (20350) covalent geometry : angle 0.68065 (27778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 170 time to evaluate : 2.131 Fit side-chains REVERT: B 681 MET cc_start: 0.5378 (mmm) cc_final: 0.4953 (mmm) REVERT: C 155 MET cc_start: 0.8473 (tmm) cc_final: 0.8202 (ttt) REVERT: C 340 PHE cc_start: 0.5589 (m-80) cc_final: 0.5040 (m-10) outliers start: 93 outliers final: 76 residues processed: 253 average time/residue: 0.2320 time to fit residues: 99.6232 Evaluate side-chains 249 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 148 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 204 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 221 optimal weight: 0.1980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.163059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134635 restraints weight = 41910.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.125751 restraints weight = 59181.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124564 restraints weight = 58003.015| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20382 Z= 0.114 Angle : 0.589 14.624 27860 Z= 0.282 Chirality : 0.043 0.397 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.286 53.432 3276 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer: Outliers : 3.96 % Allowed : 31.09 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2666 helix: 1.85 (0.16), residues: 1090 sheet: -1.99 (0.33), residues: 262 loop : -1.80 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP C 636 HIS 0.002 0.001 HIS C 780 PHE 0.011 0.001 PHE A 113 TYR 0.014 0.001 TYR D 673 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 14) link_NAG-ASN : angle 3.38887 ( 42) link_BETA1-4 : bond 0.00448 ( 4) link_BETA1-4 : angle 1.72160 ( 12) hydrogen bonds : bond 0.02589 ( 830) hydrogen bonds : angle 4.66493 ( 2442) SS BOND : bond 0.00334 ( 14) SS BOND : angle 1.42222 ( 28) covalent geometry : bond 0.00266 (20350) covalent geometry : angle 0.57170 (27778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 2.124 Fit side-chains REVERT: A 340 PHE cc_start: 0.5351 (m-80) cc_final: 0.5065 (m-10) REVERT: A 641 MET cc_start: 0.7206 (tmm) cc_final: 0.6913 (mmp) REVERT: A 679 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5820 (t80) REVERT: B 681 MET cc_start: 0.5294 (mmm) cc_final: 0.4859 (mmm) REVERT: C 155 MET cc_start: 0.8467 (tmm) cc_final: 0.8185 (ttt) REVERT: C 340 PHE cc_start: 0.5389 (m-80) cc_final: 0.5145 (m-10) outliers start: 70 outliers final: 61 residues processed: 240 average time/residue: 0.2463 time to fit residues: 100.1443 Evaluate side-chains 237 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 114 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 91 optimal weight: 8.9990 chunk 237 optimal weight: 20.0000 chunk 100 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.134822 restraints weight = 41765.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.127817 restraints weight = 61592.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.125204 restraints weight = 53864.185| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20382 Z= 0.110 Angle : 0.577 14.458 27860 Z= 0.274 Chirality : 0.042 0.397 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.098 54.059 3276 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 3.85 % Allowed : 30.97 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2666 helix: 1.91 (0.16), residues: 1096 sheet: -1.91 (0.32), residues: 262 loop : -1.81 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP C 636 HIS 0.003 0.001 HIS A 780 PHE 0.010 0.001 PHE A 533 TYR 0.017 0.001 TYR B 705 ARG 0.004 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 14) link_NAG-ASN : angle 3.32991 ( 42) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 1.59924 ( 12) hydrogen bonds : bond 0.02480 ( 830) hydrogen bonds : angle 4.52740 ( 2442) SS BOND : bond 0.00252 ( 14) SS BOND : angle 1.30400 ( 28) covalent geometry : bond 0.00258 (20350) covalent geometry : angle 0.56049 (27778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 180 time to evaluate : 2.437 Fit side-chains REVERT: A 679 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.5625 (t80) REVERT: B 681 MET cc_start: 0.5088 (mmm) cc_final: 0.4784 (mmp) REVERT: C 155 MET cc_start: 0.8473 (tmm) cc_final: 0.8209 (ttt) outliers start: 68 outliers final: 61 residues processed: 238 average time/residue: 0.2493 time to fit residues: 100.6813 Evaluate side-chains 239 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 192 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 3 optimal weight: 40.0000 chunk 176 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 158 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.164230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.137338 restraints weight = 41923.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129807 restraints weight = 53161.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.127892 restraints weight = 56842.062| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20382 Z= 0.097 Angle : 0.573 14.240 27860 Z= 0.271 Chirality : 0.042 0.398 3338 Planarity : 0.004 0.078 3550 Dihedral : 3.993 53.771 3276 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.41 % Favored : 93.47 % Rotamer: Outliers : 3.57 % Allowed : 31.26 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2666 helix: 2.00 (0.16), residues: 1090 sheet: -1.86 (0.32), residues: 262 loop : -1.76 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP C 636 HIS 0.002 0.000 HIS A 780 PHE 0.010 0.001 PHE A 113 TYR 0.016 0.001 TYR D 673 ARG 0.006 0.000 ARG B 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 14) link_NAG-ASN : angle 3.29153 ( 42) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 1.55675 ( 12) hydrogen bonds : bond 0.02336 ( 830) hydrogen bonds : angle 4.43351 ( 2442) SS BOND : bond 0.00245 ( 14) SS BOND : angle 1.15638 ( 28) covalent geometry : bond 0.00223 (20350) covalent geometry : angle 0.55763 (27778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5332 Ramachandran restraints generated. 2666 Oldfield, 0 Emsley, 2666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 174 time to evaluate : 2.100 Fit side-chains REVERT: A 74 MET cc_start: 0.2939 (ptt) cc_final: 0.2514 (ptt) REVERT: A 502 MET cc_start: 0.8904 (mmm) cc_final: 0.8647 (mmt) REVERT: A 679 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5496 (t80) REVERT: B 212 LEU cc_start: 0.7435 (pt) cc_final: 0.7144 (pp) REVERT: B 681 MET cc_start: 0.5125 (mmm) cc_final: 0.4763 (mmp) REVERT: C 155 MET cc_start: 0.8410 (tmm) cc_final: 0.8107 (ttt) REVERT: C 502 MET cc_start: 0.8966 (mmm) cc_final: 0.8661 (mmt) REVERT: D 212 LEU cc_start: 0.7452 (pt) cc_final: 0.7160 (pp) outliers start: 63 outliers final: 58 residues processed: 231 average time/residue: 0.2553 time to fit residues: 99.0269 Evaluate side-chains 228 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 5 optimal weight: 40.0000 chunk 57 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 272 optimal weight: 0.0980 chunk 186 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 130 optimal weight: 0.0270 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.164168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.137868 restraints weight = 42383.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.130384 restraints weight = 59379.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.128672 restraints weight = 60800.740| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20382 Z= 0.128 Angle : 0.581 14.168 27860 Z= 0.277 Chirality : 0.043 0.392 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.018 53.904 3276 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.16 % Favored : 92.72 % Rotamer: Outliers : 3.74 % Allowed : 30.80 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2666 helix: 1.97 (0.16), residues: 1096 sheet: -1.86 (0.33), residues: 262 loop : -1.78 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP C 636 HIS 0.004 0.001 HIS C 780 PHE 0.013 0.001 PHE A 533 TYR 0.018 0.001 TYR B 705 ARG 0.005 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 14) link_NAG-ASN : angle 3.28337 ( 42) link_BETA1-4 : bond 0.00341 ( 4) link_BETA1-4 : angle 1.52555 ( 12) hydrogen bonds : bond 0.02511 ( 830) hydrogen bonds : angle 4.45736 ( 2442) SS BOND : bond 0.00271 ( 14) SS BOND : angle 1.25598 ( 28) covalent geometry : bond 0.00303 (20350) covalent geometry : angle 0.56514 (27778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5014.04 seconds wall clock time: 89 minutes 6.41 seconds (5346.41 seconds total)