Starting phenix.real_space_refine on Thu Mar 5 06:40:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfl_33792/03_2026/7yfl_33792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfl_33792/03_2026/7yfl_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yfl_33792/03_2026/7yfl_33792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfl_33792/03_2026/7yfl_33792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yfl_33792/03_2026/7yfl_33792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfl_33792/03_2026/7yfl_33792.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 15, 'HIS:plan': 5, 'GLU:plan': 17, 'GLN:plan1': 7, 'PHE:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 14, 'TYR:plan': 2} 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: {'GLU:plan': 11, 'ARG:plan': 23, 'ASP:plan': 15, 'PHE:plan': 8, 'GLN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3} 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: {'ARG:plan': 15, 'HIS:plan': 5, 'GLU:plan': 17, 'GLN:plan1': 7, 'PHE:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 14, 'TYR:plan': 2} 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: {'GLU:plan': 11, 'ARG:plan': 23, 'ASP:plan': 15, 'PHE:plan': 8, 'GLN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3} 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: 4.56, per 1000 atoms: 0.23 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: 1.37 Conformation dependent library (CDL) restraints added in 1.0 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: 0.54 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: 3.44 Time building geometry restraints manager: 1.84 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: 0.02 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: 1.160 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.360 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- 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 : 8.93 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG B 821 TYR 0.020 0.001 TYR B 673 PHE 0.019 0.002 PHE A 113 TRP 0.068 0.001 TRP C 636 HIS 0.006 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00452 (20350) covalent geometry : angle 0.63824 (27778) SS BOND : bond 0.00372 ( 14) SS BOND : angle 1.31379 ( 28) hydrogen bonds : bond 0.14207 ( 830) hydrogen bonds : angle 6.41996 ( 2442) link_BETA1-4 : bond 0.00361 ( 4) link_BETA1-4 : angle 1.98661 ( 12) link_NAG-ASN : bond 0.00830 ( 14) link_NAG-ASN : angle 3.87244 ( 42) *********************** 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 : 0.790 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: 0.1182 time to fit residues: 34.4525 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 : 0.903 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** B 465 GLN B 497 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.162306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131985 restraints weight = 41665.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122892 restraints weight = 61894.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.120594 restraints weight = 59701.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.121125 restraints weight = 46368.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.121524 restraints weight = 36772.263| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20382 Z= 0.165 Angle : 0.592 16.210 27860 Z= 0.294 Chirality : 0.043 0.395 3338 Planarity : 0.004 0.076 3550 Dihedral : 6.014 72.472 3284 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.05 % Rotamer: Outliers : 3.45 % Allowed : 28.71 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2666 helix: 1.84 (0.16), residues: 1070 sheet: -1.69 (0.33), residues: 262 loop : -1.87 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 821 TYR 0.018 0.001 TYR B 705 PHE 0.015 0.001 PHE C 533 TRP 0.047 0.001 TRP A 636 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00385 (20350) covalent geometry : angle 0.57257 (27778) SS BOND : bond 0.00819 ( 14) SS BOND : angle 1.30169 ( 28) hydrogen bonds : bond 0.03425 ( 830) hydrogen bonds : angle 5.07915 ( 2442) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.93330 ( 12) link_NAG-ASN : bond 0.00803 ( 14) link_NAG-ASN : angle 3.68633 ( 42) *********************** 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 233 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 0.806 Fit side-chains REVERT: A 502 MET cc_start: 0.8952 (mmm) cc_final: 0.8629 (mmt) REVERT: A 679 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.5826 (t80) outliers start: 61 outliers final: 44 residues processed: 225 average time/residue: 0.1179 time to fit residues: 44.9530 Evaluate side-chains 211 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 679 PHE 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 172 LEU 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 520 VAL Chi-restraints excluded: chain B residue 670 LEU 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 197 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 747 VAL 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 456 ILE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 670 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 271 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 chunk 55 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 270 optimal weight: 0.0970 chunk 234 optimal weight: 0.0040 chunk 41 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 138 optimal weight: 50.0000 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 GLN B 497 HIS C 59 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN D 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.164348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136662 restraints weight = 41816.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125195 restraints weight = 56330.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125448 restraints weight = 53833.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.125760 restraints weight = 43009.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125738 restraints weight = 34120.570| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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= 0.107 Angle : 0.546 15.595 27860 Z= 0.268 Chirality : 0.042 0.410 3338 Planarity : 0.004 0.075 3550 Dihedral : 4.722 53.513 3281 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.75 % Favored : 93.02 % Rotamer: Outliers : 3.51 % Allowed : 28.82 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2666 helix: 1.92 (0.16), residues: 1080 sheet: -1.66 (0.33), residues: 262 loop : -1.80 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 821 TYR 0.013 0.001 TYR D 705 PHE 0.015 0.001 PHE C 113 TRP 0.043 0.001 TRP C 636 HIS 0.003 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00245 (20350) covalent geometry : angle 0.52595 (27778) SS BOND : bond 0.00299 ( 14) SS BOND : angle 1.16088 ( 28) hydrogen bonds : bond 0.02841 ( 830) hydrogen bonds : angle 4.69475 ( 2442) link_BETA1-4 : bond 0.00457 ( 4) link_BETA1-4 : angle 1.78788 ( 12) link_NAG-ASN : bond 0.00762 ( 14) link_NAG-ASN : angle 3.60913 ( 42) *********************** 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 240 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 0.592 Fit side-chains REVERT: A 679 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5451 (t80) REVERT: C 427 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7741 (p0) outliers start: 62 outliers final: 42 residues processed: 228 average time/residue: 0.1064 time to fit residues: 41.8034 Evaluate side-chains 216 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL 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 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 444 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 141 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 427 ASN 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 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 172 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 118 optimal weight: 0.0870 chunk 163 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 HIS ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.164344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.135426 restraints weight = 41954.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129141 restraints weight = 64959.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125969 restraints weight = 54912.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.125426 restraints weight = 49587.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.125569 restraints weight = 38601.061| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1058 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= 0.106 Angle : 0.540 15.330 27860 Z= 0.263 Chirality : 0.042 0.408 3338 Planarity : 0.004 0.075 3550 Dihedral : 4.345 53.812 3281 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 3.74 % Allowed : 29.84 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2666 helix: 2.01 (0.16), residues: 1080 sheet: -1.71 (0.33), residues: 262 loop : -1.77 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 821 TYR 0.015 0.001 TYR B 705 PHE 0.017 0.001 PHE A 113 TRP 0.051 0.001 TRP C 636 HIS 0.003 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00245 (20350) covalent geometry : angle 0.52094 (27778) SS BOND : bond 0.00252 ( 14) SS BOND : angle 1.10498 ( 28) hydrogen bonds : bond 0.02631 ( 830) hydrogen bonds : angle 4.53110 ( 2442) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 1.70374 ( 12) link_NAG-ASN : bond 0.00736 ( 14) link_NAG-ASN : angle 3.52646 ( 42) *********************** 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 238 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 0.642 Fit side-chains REVERT: A 679 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.5475 (t80) outliers start: 66 outliers final: 50 residues processed: 230 average time/residue: 0.1117 time to fit residues: 44.1220 Evaluate side-chains 220 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 699 LEU Chi-restraints excluded: chain A residue 709 HIS 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 185 THR Chi-restraints excluded: chain B residue 212 LEU 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 491 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 C residue 105 THR 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 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 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 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 491 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 84 optimal weight: 0.0040 chunk 252 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 187 optimal weight: 40.0000 chunk 85 optimal weight: 40.0000 chunk 232 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.163824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135469 restraints weight = 41593.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125937 restraints weight = 56387.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124063 restraints weight = 54573.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124187 restraints weight = 48045.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123741 restraints weight = 39944.136| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20382 Z= 0.122 Angle : 0.547 15.143 27860 Z= 0.266 Chirality : 0.042 0.405 3338 Planarity : 0.004 0.077 3550 Dihedral : 4.324 55.554 3281 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 4.36 % Allowed : 29.45 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2666 helix: 2.05 (0.16), residues: 1080 sheet: -1.75 (0.33), residues: 262 loop : -1.76 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 821 TYR 0.015 0.001 TYR D 705 PHE 0.015 0.001 PHE C 340 TRP 0.048 0.001 TRP A 636 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00286 (20350) covalent geometry : angle 0.52767 (27778) SS BOND : bond 0.00261 ( 14) SS BOND : angle 1.72475 ( 28) hydrogen bonds : bond 0.02660 ( 830) hydrogen bonds : angle 4.52062 ( 2442) link_BETA1-4 : bond 0.00406 ( 4) link_BETA1-4 : angle 1.65453 ( 12) link_NAG-ASN : bond 0.00729 ( 14) link_NAG-ASN : angle 3.44847 ( 42) *********************** 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 251 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 174 time to evaluate : 0.624 Fit side-chains REVERT: A 477 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8387 (p90) REVERT: A 679 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.5473 (t80) REVERT: C 477 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8434 (p90) outliers start: 77 outliers final: 64 residues processed: 242 average time/residue: 0.1095 time to fit residues: 45.7436 Evaluate side-chains 239 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 427 ASN 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 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 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 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 C residue 105 THR 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 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 273 optimal weight: 7.9990 chunk 140 optimal weight: 0.0470 chunk 260 optimal weight: 5.9990 chunk 212 optimal weight: 50.0000 chunk 191 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 267 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.163385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.134800 restraints weight = 41649.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125141 restraints weight = 57387.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124055 restraints weight = 56154.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124577 restraints weight = 45521.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124030 restraints weight = 38889.382| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20382 Z= 0.125 Angle : 0.551 14.884 27860 Z= 0.269 Chirality : 0.043 0.401 3338 Planarity : 0.004 0.077 3550 Dihedral : 4.337 58.262 3281 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.05 % Favored : 92.84 % Rotamer: Outliers : 4.47 % Allowed : 29.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2666 helix: 2.10 (0.16), residues: 1070 sheet: -1.80 (0.33), residues: 262 loop : -1.77 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 821 TYR 0.026 0.001 TYR A 578 PHE 0.012 0.001 PHE C 533 TRP 0.061 0.001 TRP A 636 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00295 (20350) covalent geometry : angle 0.53335 (27778) SS BOND : bond 0.00481 ( 14) SS BOND : angle 1.32357 ( 28) hydrogen bonds : bond 0.02578 ( 830) hydrogen bonds : angle 4.61357 ( 2442) link_BETA1-4 : bond 0.00407 ( 4) link_BETA1-4 : angle 1.63432 ( 12) link_NAG-ASN : bond 0.00723 ( 14) link_NAG-ASN : angle 3.40222 ( 42) *********************** 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 249 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 170 time to evaluate : 0.758 Fit side-chains REVERT: A 340 PHE cc_start: 0.5368 (m-80) cc_final: 0.5141 (m-10) REVERT: A 679 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.5567 (t80) REVERT: C 125 MET cc_start: 0.7310 (mmm) cc_final: 0.6950 (mtt) outliers start: 79 outliers final: 69 residues processed: 239 average time/residue: 0.1100 time to fit residues: 45.3063 Evaluate side-chains 240 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 170 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 197 PHE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 427 ASN 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 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 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 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 C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 78 optimal weight: 40.0000 chunk 76 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131817 restraints weight = 41814.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.121692 restraints weight = 57795.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119615 restraints weight = 61585.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.120287 restraints weight = 46653.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120464 restraints weight = 38107.805| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20382 Z= 0.186 Angle : 0.604 14.758 27860 Z= 0.296 Chirality : 0.044 0.390 3338 Planarity : 0.004 0.077 3550 Dihedral : 4.229 53.857 3277 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.64 % Rotamer: Outliers : 4.64 % Allowed : 29.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2666 helix: 1.85 (0.16), residues: 1104 sheet: -1.97 (0.34), residues: 242 loop : -1.75 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.017 0.001 TYR C 578 PHE 0.018 0.002 PHE C 533 TRP 0.063 0.001 TRP C 636 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00444 (20350) covalent geometry : angle 0.58638 (27778) SS BOND : bond 0.00312 ( 14) SS BOND : angle 1.63828 ( 28) hydrogen bonds : bond 0.02988 ( 830) hydrogen bonds : angle 4.73956 ( 2442) link_BETA1-4 : bond 0.00319 ( 4) link_BETA1-4 : angle 1.64826 ( 12) link_NAG-ASN : bond 0.00753 ( 14) link_NAG-ASN : angle 3.41371 ( 42) *********************** 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 250 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 168 time to evaluate : 0.761 Fit side-chains REVERT: A 679 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5831 (t80) REVERT: A 785 MET cc_start: 0.9035 (tpp) cc_final: 0.8824 (mmt) REVERT: B 274 MET cc_start: 0.7941 (tmm) cc_final: 0.7737 (tmm) REVERT: C 125 MET cc_start: 0.7474 (mmm) cc_final: 0.7147 (mtt) REVERT: C 155 MET cc_start: 0.8575 (tmm) cc_final: 0.8375 (ttt) REVERT: C 340 PHE cc_start: 0.5538 (m-80) cc_final: 0.5146 (m-10) REVERT: D 274 MET cc_start: 0.7934 (tmm) cc_final: 0.7734 (tmm) outliers start: 82 outliers final: 70 residues processed: 244 average time/residue: 0.1085 time to fit residues: 45.5136 Evaluate side-chains 238 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 167 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 718 THR 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 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 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 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 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 718 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 76 optimal weight: 0.8980 chunk 231 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 238 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 142 optimal weight: 50.0000 chunk 194 optimal weight: 20.0000 chunk 262 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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** B 497 HIS ** 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** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.162439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.134788 restraints weight = 42057.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127686 restraints weight = 67061.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.126143 restraints weight = 66961.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126535 restraints weight = 57701.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.125916 restraints weight = 48422.221| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20382 Z= 0.189 Angle : 0.604 14.574 27860 Z= 0.297 Chirality : 0.044 0.385 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.322 53.862 3277 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.09 % Rotamer: Outliers : 4.87 % Allowed : 29.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2666 helix: 1.84 (0.16), residues: 1090 sheet: -2.08 (0.32), residues: 266 loop : -1.83 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 523 TYR 0.015 0.001 TYR C 578 PHE 0.021 0.002 PHE A 340 TRP 0.059 0.001 TRP A 636 HIS 0.005 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00451 (20350) covalent geometry : angle 0.58710 (27778) SS BOND : bond 0.00394 ( 14) SS BOND : angle 1.53599 ( 28) hydrogen bonds : bond 0.02925 ( 830) hydrogen bonds : angle 4.73579 ( 2442) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 1.64614 ( 12) link_NAG-ASN : bond 0.00736 ( 14) link_NAG-ASN : angle 3.38513 ( 42) *********************** 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 257 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 0.721 Fit side-chains REVERT: A 679 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6145 (t80) REVERT: C 125 MET cc_start: 0.7482 (mmm) cc_final: 0.7248 (mtt) REVERT: C 155 MET cc_start: 0.8500 (tmm) cc_final: 0.8243 (ttt) outliers start: 86 outliers final: 73 residues processed: 250 average time/residue: 0.1049 time to fit residues: 44.8332 Evaluate side-chains 247 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE 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 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 718 THR Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 783 VAL 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 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 518 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 636 TRP 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 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 718 THR Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 152 optimal weight: 0.0050 chunk 154 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 265 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 overall best weight: 3.5800 ------------------------------------------------------------------------------- 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 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.161440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.134905 restraints weight = 41685.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126703 restraints weight = 61899.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124579 restraints weight = 63913.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124883 restraints weight = 56145.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.124323 restraints weight = 43334.110| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20382 Z= 0.225 Angle : 0.646 14.603 27860 Z= 0.317 Chirality : 0.044 0.381 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.515 54.056 3277 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.33 % Favored : 91.56 % Rotamer: Outliers : 4.59 % Allowed : 30.35 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2666 helix: 1.71 (0.16), residues: 1102 sheet: -2.23 (0.33), residues: 250 loop : -1.83 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 217 TYR 0.017 0.001 TYR D 705 PHE 0.022 0.002 PHE A 533 TRP 0.057 0.001 TRP C 636 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00535 (20350) covalent geometry : angle 0.63008 (27778) SS BOND : bond 0.00511 ( 14) SS BOND : angle 1.62890 ( 28) hydrogen bonds : bond 0.03163 ( 830) hydrogen bonds : angle 4.79952 ( 2442) link_BETA1-4 : bond 0.00330 ( 4) link_BETA1-4 : angle 1.63480 ( 12) link_NAG-ASN : bond 0.00785 ( 14) link_NAG-ASN : angle 3.41212 ( 42) *********************** 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 255 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 174 time to evaluate : 0.897 Fit side-chains REVERT: C 125 MET cc_start: 0.7506 (mmm) cc_final: 0.7298 (mtt) REVERT: C 155 MET cc_start: 0.8448 (tmm) cc_final: 0.8184 (ttt) REVERT: C 679 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6078 (t80) outliers start: 81 outliers final: 69 residues processed: 249 average time/residue: 0.1197 time to fit residues: 51.3043 Evaluate side-chains 243 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 450 THR 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 683 THR Chi-restraints excluded: chain A residue 699 LEU 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 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 718 THR 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 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 157 VAL Chi-restraints excluded: chain C residue 197 PHE 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 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 679 PHE Chi-restraints excluded: chain C residue 683 THR Chi-restraints excluded: chain C residue 699 LEU 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 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 718 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 233 optimal weight: 50.0000 chunk 78 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 141 optimal weight: 40.0000 chunk 225 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 75 optimal weight: 40.0000 chunk 19 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.161661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.135119 restraints weight = 42136.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.127285 restraints weight = 66624.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126493 restraints weight = 63922.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.126585 restraints weight = 56927.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.126621 restraints weight = 42797.201| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1709 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= 0.214 Angle : 0.644 14.540 27860 Z= 0.316 Chirality : 0.044 0.379 3338 Planarity : 0.004 0.078 3550 Dihedral : 4.572 54.069 3277 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.99 % Favored : 91.90 % Rotamer: Outliers : 4.08 % Allowed : 30.86 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2666 helix: 1.68 (0.16), residues: 1106 sheet: -2.22 (0.34), residues: 246 loop : -1.85 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 821 TYR 0.016 0.001 TYR B 673 PHE 0.019 0.002 PHE A 533 TRP 0.062 0.001 TRP A 636 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00510 (20350) covalent geometry : angle 0.62861 (27778) SS BOND : bond 0.00384 ( 14) SS BOND : angle 1.54563 ( 28) hydrogen bonds : bond 0.03072 ( 830) hydrogen bonds : angle 4.76280 ( 2442) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.67083 ( 12) link_NAG-ASN : bond 0.00771 ( 14) link_NAG-ASN : angle 3.39015 ( 42) ********************** 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 244 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 0.813 Fit side-chains REVERT: A 502 MET cc_start: 0.9065 (mmm) cc_final: 0.8718 (mmt) REVERT: C 155 MET cc_start: 0.8451 (tmm) cc_final: 0.8179 (ttt) REVERT: C 237 MET cc_start: 0.3752 (ptp) cc_final: 0.3427 (ptp) REVERT: C 502 MET cc_start: 0.9085 (mmm) cc_final: 0.8692 (mmt) outliers start: 72 outliers final: 68 residues processed: 236 average time/residue: 0.1151 time to fit residues: 47.0667 Evaluate side-chains 238 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE 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 683 THR Chi-restraints excluded: chain A residue 699 LEU 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 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 491 ILE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 718 THR 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 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 157 VAL Chi-restraints excluded: chain C residue 197 PHE 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 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 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 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 718 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 766 MET Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 95 optimal weight: 0.4980 chunk 263 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 405 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.164794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135449 restraints weight = 42077.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126713 restraints weight = 61087.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125152 restraints weight = 55646.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125134 restraints weight = 47287.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124648 restraints weight = 40514.938| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1745 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= 0.100 Angle : 0.591 14.161 27860 Z= 0.282 Chirality : 0.043 0.394 3338 Planarity : 0.004 0.079 3550 Dihedral : 4.258 53.454 3277 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.71 % Favored : 93.17 % Rotamer: Outliers : 2.66 % Allowed : 32.05 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2666 helix: 1.90 (0.16), residues: 1096 sheet: -2.02 (0.33), residues: 252 loop : -1.82 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 821 TYR 0.019 0.001 TYR D 705 PHE 0.024 0.001 PHE A 137 TRP 0.058 0.001 TRP A 636 HIS 0.002 0.000 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00227 (20350) covalent geometry : angle 0.57524 (27778) SS BOND : bond 0.00226 ( 14) SS BOND : angle 1.16074 ( 28) hydrogen bonds : bond 0.02436 ( 830) hydrogen bonds : angle 4.49739 ( 2442) link_BETA1-4 : bond 0.00474 ( 4) link_BETA1-4 : angle 1.64723 ( 12) link_NAG-ASN : bond 0.00716 ( 14) link_NAG-ASN : angle 3.31221 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.72 seconds wall clock time: 48 minutes 12.70 seconds (2892.70 seconds total)