Starting phenix.real_space_refine on Tue Jun 24 03:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj1_36337/06_2025/8jj1_36337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj1_36337/06_2025/8jj1_36337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jj1_36337/06_2025/8jj1_36337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj1_36337/06_2025/8jj1_36337.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj1_36337/06_2025/8jj1_36337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj1_36337/06_2025/8jj1_36337.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 158 5.16 5 C 17933 2.51 5 N 4689 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28026 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "A" Number of atoms: 6033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6033 Classifications: {'peptide': 763} Link IDs: {'PTRANS': 31, 'TRANS': 731} Chain breaks: 5 Chain: "B" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6153 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 745} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 6004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6004 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 730} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 6158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6158 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 747} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "I" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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 Time building chain proxies: 15.79, per 1000 atoms: 0.56 Number of scatterers: 28026 At special positions: 0 Unit cell: (167.4, 177.12, 176.04, 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 158 16.00 O 5246 8.00 N 4689 7.00 C 17933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 276 " " NAG B 902 " - " ASN B 368 " " NAG B 903 " - " ASN B 350 " " NAG B 904 " - " ASN B 771 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 368 " " NAG D 904 " - " ASN D 350 " " NAG D 905 " - " ASN D 771 " " NAG I 1 " - " ASN B 61 " Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 3.3 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6592 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 33 sheets defined 38.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.708A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.504A pdb=" N ARG A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.958A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.771A pdb=" N MET A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.735A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 4.085A pdb=" N PHE A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 232 through 247 Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.159A pdb=" N VAL A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.959A pdb=" N THR A 382 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.870A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 579 removed outlier: 4.200A pdb=" N LEU A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 610 removed outlier: 3.818A pdb=" N LEU A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 651 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 707 through 709 No H-bonds generated for 'chain 'A' and resid 707 through 709' Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.519A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 771 through 785 removed outlier: 3.752A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 814 through 837 Processing helix chain 'B' and resid 35 through 51 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.683A pdb=" N THR B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.758A pdb=" N TYR B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 130 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.857A pdb=" N VAL B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.645A pdb=" N LEU B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.593A pdb=" N HIS B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 582 removed outlier: 3.766A pdb=" N LEU B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 582 " --> pdb=" O TYR B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 615 Processing helix chain 'B' and resid 627 through 656 removed outlier: 3.509A pdb=" N VAL B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.958A pdb=" N HIS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 812 through 840 removed outlier: 3.545A pdb=" N PHE B 817 " --> pdb=" O MET B 813 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 832 " --> pdb=" O ILE B 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.987A pdb=" N ARG C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.536A pdb=" N ALA C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.893A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.620A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 removed outlier: 3.884A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.995A pdb=" N SER C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.893A pdb=" N VAL C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 560 through 579 removed outlier: 3.708A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 4.209A pdb=" N ILE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE C 613 " --> pdb=" O TRP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 Processing helix chain 'C' and resid 633 through 653 removed outlier: 4.109A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.575A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.772A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 707 through 709 No H-bonds generated for 'chain 'C' and resid 707 through 709' Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 732 through 742 Processing helix chain 'C' and resid 771 through 785 removed outlier: 4.175A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 796 removed outlier: 3.733A pdb=" N LEU C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 837 removed outlier: 3.719A pdb=" N MET C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 51 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 4.033A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 removed outlier: 3.935A pdb=" N GLU D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 276 through 299 removed outlier: 3.525A pdb=" N HIS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 583 removed outlier: 4.262A pdb=" N LEU D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 654 removed outlier: 3.711A pdb=" N TRP D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA D 637 " --> pdb=" O GLY D 633 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 638 " --> pdb=" O MET D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.906A pdb=" N ASP D 658 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG D 659 " --> pdb=" O VAL D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 669 through 674 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.563A pdb=" N HIS D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.594A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 837 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.707A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.713A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.700A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 94 No H-bonds generated for 'chain 'G' and resid 92 through 94' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.674A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 73 removed outlier: 7.184A pdb=" N LEU A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 removed outlier: 3.681A pdb=" N VAL A 173 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 227 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.896A pdb=" N MET A 507 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 409 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 418 through 420 removed outlier: 3.545A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA9, first strand: chain 'A' and resid 727 through 731 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 66 removed outlier: 6.279A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.378A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP B 247 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU B 269 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 249 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N LEU B 271 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 478 removed outlier: 3.905A pdb=" N MET B 512 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 413 removed outlier: 3.783A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.077A pdb=" N LYS B 534 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 682 removed outlier: 6.972A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N ASP B 732 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.576A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.574A pdb=" N TRP C 255 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 279 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL C 257 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 363 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 446 through 456 removed outlier: 8.516A pdb=" N GLU C 448 " --> pdb=" O ILE C 442 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 442 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU C 477 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE C 439 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 406 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR C 478 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER C 407 " --> pdb=" O MET C 507 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AC2, first strand: chain 'C' and resid 682 through 683 removed outlier: 6.299A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.445A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU D 119 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.618A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP D 247 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU D 269 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL D 249 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU D 271 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 266 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 351 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE D 366 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 353 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 329 through 330 Processing sheet with id=AC6, first strand: chain 'D' and resid 397 through 402 removed outlier: 6.375A pdb=" N LEU D 398 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS D 477 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 400 " --> pdb=" O HIS D 477 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE D 435 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU D 478 " --> pdb=" O ILE D 435 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR D 437 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 512 through 515 removed outlier: 4.874A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 681 through 682 removed outlier: 3.564A pdb=" N ALA D 682 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 730 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.725A pdb=" N VAL E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.551A pdb=" N ARG E 98 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.989A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.014A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 1206 hydrogen bonds defined for protein. 3399 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: 12.99 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8950 1.34 - 1.46: 6892 1.46 - 1.58: 12562 1.58 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 28676 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" CA GLN D 686 " pdb=" CB GLN D 686 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.21e-02 6.83e+03 2.18e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 28671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 38372 1.40 - 2.81: 430 2.81 - 4.21: 77 4.21 - 5.61: 18 5.61 - 7.02: 6 Bond angle restraints: 38903 Sorted by residual: angle pdb=" N SER G 93 " pdb=" CA SER G 93 " pdb=" C SER G 93 " ideal model delta sigma weight residual 114.75 109.09 5.66 1.26e+00 6.30e-01 2.02e+01 angle pdb=" CA SER G 93 " pdb=" C SER G 93 " pdb=" N TYR G 94 " ideal model delta sigma weight residual 119.80 115.98 3.82 1.34e+00 5.57e-01 8.15e+00 angle pdb=" CA SER G 93 " pdb=" C SER G 93 " pdb=" O SER G 93 " ideal model delta sigma weight residual 118.47 120.80 -2.33 1.14e+00 7.69e-01 4.17e+00 angle pdb=" N TYR C 286 " pdb=" CA TYR C 286 " pdb=" C TYR C 286 " ideal model delta sigma weight residual 108.34 111.01 -2.67 1.31e+00 5.83e-01 4.14e+00 angle pdb=" C THR D 550 " pdb=" N LEU D 551 " pdb=" CA LEU D 551 " ideal model delta sigma weight residual 121.54 125.42 -3.88 1.91e+00 2.74e-01 4.14e+00 ... (remaining 38898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 16378 17.51 - 35.02: 627 35.02 - 52.54: 151 52.54 - 70.05: 11 70.05 - 87.56: 8 Dihedral angle restraints: 17175 sinusoidal: 6942 harmonic: 10233 Sorted by residual: dihedral pdb=" CA LYS G 92 " pdb=" C LYS G 92 " pdb=" N SER G 93 " pdb=" CA SER G 93 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG D 52 " pdb=" CB ARG D 52 " pdb=" CG ARG D 52 " pdb=" CD ARG D 52 " ideal model delta sinusoidal sigma weight residual 180.00 120.47 59.53 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN D 59 " pdb=" CA GLN D 59 " pdb=" CB GLN D 59 " pdb=" CG GLN D 59 " ideal model delta sinusoidal sigma weight residual 60.00 2.19 57.81 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 17172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3504 0.045 - 0.090: 609 0.090 - 0.135: 288 0.135 - 0.180: 1 0.180 - 0.225: 1 Chirality restraints: 4403 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 687 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1 NAG D 905 " pdb=" ND2 ASN D 771 " pdb=" C2 NAG D 905 " pdb=" O5 NAG D 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE B 546 " pdb=" N ILE B 546 " pdb=" C ILE B 546 " pdb=" CB ILE B 546 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 4400 not shown) Planarity restraints: 4923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 318 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D 319 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 318 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 319 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 546 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO D 547 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " 0.017 5.00e-02 4.00e+02 ... (remaining 4920 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3184 2.75 - 3.29: 28420 3.29 - 3.83: 47298 3.83 - 4.36: 53647 4.36 - 4.90: 93090 Nonbonded interactions: 225639 Sorted by model distance: nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.217 3.040 nonbonded pdb=" ND2 ASN B 70 " pdb=" O TYR C 321 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP A 45 " pdb=" OG1 THR A 47 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP B 283 " pdb=" OG1 THR B 335 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP D 417 " pdb=" OG1 THR D 419 " model vdw 2.249 3.040 ... (remaining 225634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 540 or resid 546 through 613 or (resid 614 and \ (name N or name CA or name C or name O or name CB )) or resid 625 through 837 or \ resid 901)) selection = (chain 'C' and (resid 34 through 540 or resid 546 through 796 or resid 813 throu \ gh 837 or resid 901)) } ncs_group { reference = (chain 'B' and (resid 25 through 658 or (resid 659 and (name N or name CA or nam \ e C or name O or name CB )) or resid 660 through 837 or resid 901 through 904)) selection = (chain 'D' and (resid 25 through 584 or resid 604 through 796 or resid 811 throu \ gh 837 or resid 902 through 905)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 62.780 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.002 0.037 28705 Z= 0.091 Angle : 0.412 7.015 38974 Z= 0.209 Chirality : 0.040 0.225 4403 Planarity : 0.003 0.034 4911 Dihedral : 9.548 87.562 10535 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 3.60 % Allowed : 7.59 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3489 helix: 2.29 (0.15), residues: 1216 sheet: 1.05 (0.23), residues: 604 loop : -0.30 (0.17), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 55 HIS 0.002 0.000 HIS B 134 PHE 0.012 0.001 PHE B 817 TYR 0.006 0.001 TYR A 281 ARG 0.001 0.000 ARG A 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 12) link_NAG-ASN : angle 1.08727 ( 36) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 0.83704 ( 3) hydrogen bonds : bond 0.15708 ( 1199) hydrogen bonds : angle 5.98744 ( 3399) SS BOND : bond 0.00119 ( 16) SS BOND : angle 0.61401 ( 32) covalent geometry : bond 0.00172 (28676) covalent geometry : angle 0.41064 (38903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 420 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7624 (mt) cc_final: 0.7299 (mm) REVERT: H 116 LEU cc_start: 0.8574 (tp) cc_final: 0.8118 (mp) REVERT: A 324 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6777 (mpp) REVERT: A 517 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: A 641 PHE cc_start: 0.3526 (OUTLIER) cc_final: 0.3301 (t80) REVERT: A 653 MET cc_start: 0.4402 (mtp) cc_final: 0.2376 (tpt) REVERT: A 828 MET cc_start: 0.3487 (tpt) cc_final: 0.3009 (tmm) REVERT: B 57 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7986 (tppt) REVERT: B 58 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 548 ARG cc_start: 0.2666 (mtm-85) cc_final: 0.1664 (tpt-90) REVERT: B 607 MET cc_start: 0.5317 (pp-130) cc_final: 0.4917 (tpp) REVERT: B 639 PHE cc_start: 0.7403 (t80) cc_final: 0.6835 (t80) REVERT: B 702 MET cc_start: 0.7183 (ppp) cc_final: 0.6154 (ppp) REVERT: C 39 MET cc_start: 0.7675 (mtp) cc_final: 0.7216 (mtp) REVERT: C 138 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7319 (mtmt) REVERT: C 252 ASP cc_start: 0.8059 (p0) cc_final: 0.7851 (p0) REVERT: C 475 TYR cc_start: 0.5038 (m-80) cc_final: 0.4500 (m-80) REVERT: C 560 MET cc_start: 0.2030 (ppp) cc_final: 0.1320 (ttm) REVERT: C 653 MET cc_start: 0.5870 (ppp) cc_final: 0.4512 (mmt) REVERT: D 354 MET cc_start: 0.7536 (mmm) cc_final: 0.7323 (mmm) REVERT: G 2 ILE cc_start: 0.6681 (mp) cc_final: 0.5956 (mm) outliers start: 110 outliers final: 24 residues processed: 512 average time/residue: 0.4528 time to fit residues: 351.7503 Evaluate side-chains 242 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 636 PHE Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 703 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 204 optimal weight: 0.0070 chunk 318 optimal weight: 0.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 451 ASN A 671 GLN A 766 GLN B 48 GLN B 134 HIS B 270 GLN B 293 HIS B 371 HIS B 477 HIS B 509 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 812 ASN C 59 GLN C 152 GLN C 380 ASN C 490 ASN ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 487 GLN D 556 GLN E 65 GLN F 27 GLN F 42 GLN F 55 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.071557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.055576 restraints weight = 161365.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.055778 restraints weight = 93652.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.056206 restraints weight = 80889.520| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28705 Z= 0.148 Angle : 0.555 10.208 38974 Z= 0.287 Chirality : 0.043 0.296 4403 Planarity : 0.004 0.040 4911 Dihedral : 5.430 88.519 4127 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 2.91 % Allowed : 11.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.15), residues: 3489 helix: 2.01 (0.15), residues: 1234 sheet: 0.81 (0.22), residues: 626 loop : -0.36 (0.17), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 160 HIS 0.005 0.001 HIS A 44 PHE 0.040 0.001 PHE A 183 TYR 0.022 0.001 TYR A 321 ARG 0.005 0.000 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 12) link_NAG-ASN : angle 1.39268 ( 36) link_BETA1-4 : bond 0.00974 ( 1) link_BETA1-4 : angle 0.94618 ( 3) hydrogen bonds : bond 0.03333 ( 1199) hydrogen bonds : angle 5.03502 ( 3399) SS BOND : bond 0.00631 ( 16) SS BOND : angle 2.10285 ( 32) covalent geometry : bond 0.00323 (28676) covalent geometry : angle 0.55053 (38903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 217 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6963 (pmm) REVERT: A 324 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7382 (mpp) REVERT: A 331 MET cc_start: 0.6904 (pmm) cc_final: 0.6690 (tmm) REVERT: A 507 MET cc_start: 0.7959 (ttm) cc_final: 0.7698 (mtp) REVERT: A 653 MET cc_start: 0.4678 (mtp) cc_final: 0.2564 (tpt) REVERT: A 697 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8450 (t0) REVERT: A 828 MET cc_start: 0.3486 (tpt) cc_final: 0.2922 (tmm) REVERT: B 57 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8051 (tppt) REVERT: B 58 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8173 (pt) REVERT: B 154 MET cc_start: 0.8265 (mtp) cc_final: 0.8010 (mtp) REVERT: B 548 ARG cc_start: 0.3234 (mtm-85) cc_final: 0.1770 (ttt180) REVERT: B 607 MET cc_start: 0.5517 (pp-130) cc_final: 0.5134 (tpp) REVERT: B 639 PHE cc_start: 0.7221 (t80) cc_final: 0.6708 (t80) REVERT: B 702 MET cc_start: 0.7620 (ppp) cc_final: 0.7070 (ppp) REVERT: C 138 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7497 (mtmt) REVERT: C 162 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: C 331 MET cc_start: 0.2941 (ptm) cc_final: 0.2263 (ptm) REVERT: C 653 MET cc_start: 0.6187 (ppp) cc_final: 0.4785 (mmm) REVERT: D 555 MET cc_start: 0.6651 (tmm) cc_final: 0.6343 (ppp) REVERT: G 2 ILE cc_start: 0.6512 (mp) cc_final: 0.6304 (mm) REVERT: G 42 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7022 (mp10) outliers start: 89 outliers final: 35 residues processed: 296 average time/residue: 0.4209 time to fit residues: 198.4662 Evaluate side-chains 220 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 697 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 47 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 179 optimal weight: 0.1980 chunk 189 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 HIS C 503 GLN ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.071402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055601 restraints weight = 160525.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.055385 restraints weight = 97191.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.055950 restraints weight = 79177.046| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28705 Z= 0.105 Angle : 0.518 8.910 38974 Z= 0.264 Chirality : 0.042 0.271 4403 Planarity : 0.003 0.037 4911 Dihedral : 5.114 89.151 4118 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 2.13 % Allowed : 11.62 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3489 helix: 1.95 (0.15), residues: 1231 sheet: 0.69 (0.22), residues: 605 loop : -0.38 (0.17), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 609 HIS 0.004 0.001 HIS A 44 PHE 0.051 0.001 PHE B 817 TYR 0.019 0.001 TYR A 822 ARG 0.005 0.000 ARG D 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 12) link_NAG-ASN : angle 1.64459 ( 36) link_BETA1-4 : bond 0.00207 ( 1) link_BETA1-4 : angle 1.00312 ( 3) hydrogen bonds : bond 0.03033 ( 1199) hydrogen bonds : angle 4.79380 ( 3399) SS BOND : bond 0.00427 ( 16) SS BOND : angle 1.42422 ( 32) covalent geometry : bond 0.00231 (28676) covalent geometry : angle 0.51477 (38903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8893 (tp) cc_final: 0.8650 (tt) REVERT: A 74 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6910 (pmm) REVERT: A 306 MET cc_start: 0.7840 (ttt) cc_final: 0.7271 (tpp) REVERT: A 324 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7336 (mpp) REVERT: A 507 MET cc_start: 0.8027 (ttm) cc_final: 0.7708 (mtp) REVERT: A 653 MET cc_start: 0.4693 (mtp) cc_final: 0.2509 (tpt) REVERT: A 697 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8431 (t0) REVERT: A 705 MET cc_start: 0.6867 (mmt) cc_final: 0.6637 (mmt) REVERT: A 828 MET cc_start: 0.3391 (tpt) cc_final: 0.2769 (tmm) REVERT: B 57 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7996 (tppt) REVERT: B 58 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8204 (pt) REVERT: B 154 MET cc_start: 0.8258 (mtp) cc_final: 0.8045 (mtp) REVERT: B 416 SER cc_start: 0.8594 (m) cc_final: 0.7698 (t) REVERT: B 470 MET cc_start: 0.8501 (mtm) cc_final: 0.8233 (mtm) REVERT: B 546 ILE cc_start: 0.5234 (OUTLIER) cc_final: 0.4288 (pt) REVERT: B 548 ARG cc_start: 0.3111 (mtm-85) cc_final: 0.1634 (ttt180) REVERT: B 639 PHE cc_start: 0.7227 (t80) cc_final: 0.6679 (t80) REVERT: B 702 MET cc_start: 0.7427 (ppp) cc_final: 0.7057 (ppp) REVERT: C 138 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7490 (mtmt) REVERT: C 653 MET cc_start: 0.6155 (ppp) cc_final: 0.4813 (mmm) REVERT: D 354 MET cc_start: 0.8101 (mmm) cc_final: 0.7698 (mmm) REVERT: D 702 MET cc_start: 0.7881 (mmt) cc_final: 0.7675 (mmt) REVERT: G 42 GLN cc_start: 0.7768 (mt0) cc_final: 0.7186 (mp10) outliers start: 65 outliers final: 32 residues processed: 249 average time/residue: 0.4358 time to fit residues: 174.4798 Evaluate side-chains 211 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 697 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 703 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 105 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 148 optimal weight: 0.0060 chunk 257 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN B 38 HIS B 146 HIS B 293 HIS B 499 ASN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN C 674 HIS ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS F 27 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.069565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.053085 restraints weight = 160195.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.053141 restraints weight = 96160.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.053845 restraints weight = 74192.076| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28705 Z= 0.166 Angle : 0.563 8.016 38974 Z= 0.289 Chirality : 0.044 0.306 4403 Planarity : 0.004 0.042 4911 Dihedral : 5.131 89.610 4116 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.65 % Allowed : 12.14 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3489 helix: 1.80 (0.15), residues: 1237 sheet: 0.34 (0.22), residues: 632 loop : -0.39 (0.17), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 609 HIS 0.006 0.001 HIS D 280 PHE 0.043 0.002 PHE D 42 TYR 0.016 0.001 TYR A 230 ARG 0.005 0.000 ARG B 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 1.93758 ( 36) link_BETA1-4 : bond 0.00243 ( 1) link_BETA1-4 : angle 1.26426 ( 3) hydrogen bonds : bond 0.03095 ( 1199) hydrogen bonds : angle 4.67010 ( 3399) SS BOND : bond 0.00273 ( 16) SS BOND : angle 1.49735 ( 32) covalent geometry : bond 0.00370 (28676) covalent geometry : angle 0.55839 (38903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 187 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8828 (tp) cc_final: 0.8578 (tt) REVERT: A 74 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6490 (pmt) REVERT: A 112 MET cc_start: 0.8606 (mmm) cc_final: 0.8334 (mmt) REVERT: A 183 PHE cc_start: 0.4964 (m-80) cc_final: 0.4646 (m-80) REVERT: A 306 MET cc_start: 0.7630 (ttt) cc_final: 0.7175 (tpp) REVERT: A 324 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7353 (mmm) REVERT: A 653 MET cc_start: 0.4759 (mtp) cc_final: 0.4514 (mtt) REVERT: A 828 MET cc_start: 0.3458 (tpt) cc_final: 0.2875 (ttp) REVERT: B 57 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.7996 (tppt) REVERT: B 58 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8117 (mm) REVERT: B 74 MET cc_start: 0.8056 (tpp) cc_final: 0.7855 (tpp) REVERT: B 416 SER cc_start: 0.8597 (m) cc_final: 0.8296 (p) REVERT: B 546 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4325 (pt) REVERT: B 548 ARG cc_start: 0.3300 (mtm-85) cc_final: 0.1490 (ttt180) REVERT: B 639 PHE cc_start: 0.7226 (t80) cc_final: 0.6679 (t80) REVERT: B 702 MET cc_start: 0.7661 (ppp) cc_final: 0.7367 (ppp) REVERT: C 138 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7475 (mtmt) REVERT: C 653 MET cc_start: 0.6067 (ppp) cc_final: 0.4880 (mmm) REVERT: D 41 MET cc_start: 0.6444 (ppp) cc_final: 0.6002 (ppp) REVERT: D 555 MET cc_start: 0.6571 (tmm) cc_final: 0.6279 (ppp) REVERT: E 32 TYR cc_start: 0.7961 (m-80) cc_final: 0.7753 (m-80) REVERT: E 98 ARG cc_start: 0.8063 (tmm-80) cc_final: 0.7838 (tmm-80) REVERT: G 2 ILE cc_start: 0.6732 (mm) cc_final: 0.5955 (pt) REVERT: G 42 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7215 (mp10) outliers start: 81 outliers final: 43 residues processed: 254 average time/residue: 0.4169 time to fit residues: 169.8773 Evaluate side-chains 219 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 136 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 288 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 277 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 293 HIS ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** 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 = 0.3831 r_free = 0.3831 target = 0.069387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.053086 restraints weight = 158271.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052685 restraints weight = 101584.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.053283 restraints weight = 80550.294| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28705 Z= 0.143 Angle : 0.549 10.442 38974 Z= 0.278 Chirality : 0.043 0.310 4403 Planarity : 0.003 0.039 4911 Dihedral : 4.662 45.703 4105 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 2.78 % Allowed : 12.77 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3489 helix: 1.77 (0.15), residues: 1238 sheet: 0.33 (0.21), residues: 640 loop : -0.44 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 609 HIS 0.005 0.001 HIS D 280 PHE 0.053 0.001 PHE D 42 TYR 0.022 0.001 TYR A 393 ARG 0.011 0.000 ARG B 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 1.88328 ( 36) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 1.33744 ( 3) hydrogen bonds : bond 0.02988 ( 1199) hydrogen bonds : angle 4.62202 ( 3399) SS BOND : bond 0.00406 ( 16) SS BOND : angle 1.67961 ( 32) covalent geometry : bond 0.00318 (28676) covalent geometry : angle 0.54419 (38903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8826 (tp) cc_final: 0.8575 (tt) REVERT: A 74 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6448 (pmt) REVERT: A 183 PHE cc_start: 0.4957 (m-80) cc_final: 0.4731 (m-80) REVERT: A 455 CYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6500 (m) REVERT: A 630 MET cc_start: 0.6639 (mtt) cc_final: 0.6428 (mtp) REVERT: A 653 MET cc_start: 0.4747 (mtp) cc_final: 0.4521 (mtt) REVERT: A 823 MET cc_start: 0.3270 (ttp) cc_final: 0.2976 (ttm) REVERT: A 828 MET cc_start: 0.3352 (tpt) cc_final: 0.2775 (ttp) REVERT: B 58 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8415 (pt) REVERT: B 416 SER cc_start: 0.8694 (m) cc_final: 0.8459 (p) REVERT: B 546 ILE cc_start: 0.5378 (OUTLIER) cc_final: 0.4358 (pt) REVERT: B 548 ARG cc_start: 0.3205 (mtm-85) cc_final: 0.1547 (tpt-90) REVERT: B 639 PHE cc_start: 0.7362 (t80) cc_final: 0.6754 (t80) REVERT: B 702 MET cc_start: 0.7643 (ppp) cc_final: 0.7274 (ppp) REVERT: C 138 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7330 (mtmt) REVERT: C 653 MET cc_start: 0.6125 (ppp) cc_final: 0.5108 (mmm) REVERT: D 72 ILE cc_start: 0.9045 (mm) cc_final: 0.8708 (mp) REVERT: D 326 MET cc_start: 0.8798 (mmm) cc_final: 0.8574 (mmm) REVERT: F 50 MET cc_start: 0.6555 (tpp) cc_final: 0.6271 (tpp) REVERT: G 42 GLN cc_start: 0.7698 (mt0) cc_final: 0.7404 (mp10) outliers start: 85 outliers final: 47 residues processed: 257 average time/residue: 0.3859 time to fit residues: 159.9809 Evaluate side-chains 217 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 50 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 335 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 HIS A 710 GLN B 293 HIS ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.069425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052959 restraints weight = 158724.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.053034 restraints weight = 94440.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.053622 restraints weight = 77029.394| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28705 Z= 0.118 Angle : 0.545 12.012 38974 Z= 0.275 Chirality : 0.043 0.302 4403 Planarity : 0.003 0.039 4911 Dihedral : 4.545 45.222 4102 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 2.29 % Allowed : 13.49 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3489 helix: 1.73 (0.15), residues: 1243 sheet: 0.19 (0.21), residues: 650 loop : -0.42 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 609 HIS 0.004 0.001 HIS D 280 PHE 0.058 0.001 PHE D 42 TYR 0.019 0.001 TYR H 32 ARG 0.005 0.000 ARG C 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 12) link_NAG-ASN : angle 1.81162 ( 36) link_BETA1-4 : bond 0.00004 ( 1) link_BETA1-4 : angle 1.20394 ( 3) hydrogen bonds : bond 0.02829 ( 1199) hydrogen bonds : angle 4.57207 ( 3399) SS BOND : bond 0.00258 ( 16) SS BOND : angle 1.49214 ( 32) covalent geometry : bond 0.00263 (28676) covalent geometry : angle 0.54092 (38903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8813 (tp) cc_final: 0.8550 (tt) REVERT: A 74 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6243 (pmt) REVERT: A 183 PHE cc_start: 0.4919 (m-80) cc_final: 0.4693 (m-80) REVERT: A 207 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: A 306 MET cc_start: 0.7783 (ttt) cc_final: 0.7358 (tpp) REVERT: A 331 MET cc_start: 0.6533 (tmm) cc_final: 0.6005 (tmm) REVERT: A 653 MET cc_start: 0.4978 (mtp) cc_final: 0.4684 (mtt) REVERT: A 823 MET cc_start: 0.3282 (ttp) cc_final: 0.3019 (ttm) REVERT: A 828 MET cc_start: 0.3363 (tpt) cc_final: 0.2703 (tmm) REVERT: B 58 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8467 (pt) REVERT: B 416 SER cc_start: 0.8656 (m) cc_final: 0.8420 (p) REVERT: B 546 ILE cc_start: 0.5394 (OUTLIER) cc_final: 0.4369 (pt) REVERT: B 548 ARG cc_start: 0.3243 (mtm-85) cc_final: 0.1560 (tpt-90) REVERT: B 639 PHE cc_start: 0.7291 (t80) cc_final: 0.6681 (t80) REVERT: B 702 MET cc_start: 0.7630 (ppp) cc_final: 0.6966 (ppp) REVERT: C 138 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7375 (mtmt) REVERT: C 653 MET cc_start: 0.6131 (ppp) cc_final: 0.5086 (mmm) REVERT: D 326 MET cc_start: 0.8830 (mmm) cc_final: 0.8584 (mmm) REVERT: D 555 MET cc_start: 0.6717 (tmm) cc_final: 0.6443 (ppp) REVERT: G 42 GLN cc_start: 0.7708 (mt0) cc_final: 0.7427 (mp10) REVERT: G 50 MET cc_start: 0.7622 (mmm) cc_final: 0.7318 (mmm) outliers start: 70 outliers final: 46 residues processed: 235 average time/residue: 0.3816 time to fit residues: 145.4389 Evaluate side-chains 216 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 701 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 200 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 150 optimal weight: 0.0270 chunk 102 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 145 optimal weight: 40.0000 chunk 290 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.069300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.052835 restraints weight = 158141.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052937 restraints weight = 94096.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.053487 restraints weight = 77244.137| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28705 Z= 0.118 Angle : 0.545 12.769 38974 Z= 0.274 Chirality : 0.043 0.304 4403 Planarity : 0.003 0.039 4911 Dihedral : 4.481 45.117 4100 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 2.42 % Allowed : 13.45 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3489 helix: 1.76 (0.15), residues: 1230 sheet: 0.17 (0.21), residues: 647 loop : -0.46 (0.17), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 55 HIS 0.004 0.001 HIS D 280 PHE 0.052 0.001 PHE D 42 TYR 0.018 0.001 TYR D 681 ARG 0.006 0.000 ARG E 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 12) link_NAG-ASN : angle 1.77521 ( 36) link_BETA1-4 : bond 0.00192 ( 1) link_BETA1-4 : angle 1.27613 ( 3) hydrogen bonds : bond 0.02789 ( 1199) hydrogen bonds : angle 4.53896 ( 3399) SS BOND : bond 0.00347 ( 16) SS BOND : angle 1.45727 ( 32) covalent geometry : bond 0.00265 (28676) covalent geometry : angle 0.54132 (38903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 170 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8819 (tp) cc_final: 0.8557 (tt) REVERT: A 74 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6185 (pmt) REVERT: A 183 PHE cc_start: 0.4918 (m-80) cc_final: 0.4700 (m-80) REVERT: A 207 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: A 306 MET cc_start: 0.7733 (ttt) cc_final: 0.7245 (tpp) REVERT: A 331 MET cc_start: 0.6449 (tmm) cc_final: 0.6143 (tmm) REVERT: A 653 MET cc_start: 0.4956 (mtp) cc_final: 0.4684 (mtt) REVERT: A 823 MET cc_start: 0.3621 (ttp) cc_final: 0.3388 (ttm) REVERT: A 828 MET cc_start: 0.3335 (tpt) cc_final: 0.2677 (tmm) REVERT: B 58 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8441 (pt) REVERT: B 416 SER cc_start: 0.8667 (m) cc_final: 0.8432 (p) REVERT: B 546 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.4397 (pt) REVERT: B 548 ARG cc_start: 0.3251 (mtm-85) cc_final: 0.1412 (ttt180) REVERT: B 639 PHE cc_start: 0.7261 (t80) cc_final: 0.6742 (t80) REVERT: C 138 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7360 (mttm) REVERT: C 653 MET cc_start: 0.6101 (ppp) cc_final: 0.5041 (mmm) REVERT: D 326 MET cc_start: 0.8828 (mmm) cc_final: 0.8551 (mmm) REVERT: F 50 MET cc_start: 0.6916 (tpp) cc_final: 0.6705 (tpp) REVERT: G 42 GLN cc_start: 0.7734 (mt0) cc_final: 0.7445 (mp10) REVERT: G 50 MET cc_start: 0.7694 (mmm) cc_final: 0.7332 (mmm) outliers start: 74 outliers final: 51 residues processed: 232 average time/residue: 0.3898 time to fit residues: 147.3851 Evaluate side-chains 220 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 701 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 171 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 HIS ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS E 65 GLN F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.068059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051312 restraints weight = 157705.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051171 restraints weight = 95551.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051882 restraints weight = 75079.604| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28705 Z= 0.193 Angle : 0.620 13.353 38974 Z= 0.313 Chirality : 0.044 0.350 4403 Planarity : 0.004 0.053 4911 Dihedral : 4.779 45.944 4100 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.53 % Rotamer: Outliers : 2.13 % Allowed : 13.94 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3489 helix: 1.62 (0.15), residues: 1235 sheet: 0.04 (0.22), residues: 607 loop : -0.58 (0.17), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 55 HIS 0.006 0.001 HIS D 280 PHE 0.060 0.002 PHE D 42 TYR 0.023 0.002 TYR A 393 ARG 0.011 0.001 ARG E 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.10935 ( 36) link_BETA1-4 : bond 0.00007 ( 1) link_BETA1-4 : angle 1.39706 ( 3) hydrogen bonds : bond 0.03119 ( 1199) hydrogen bonds : angle 4.71132 ( 3399) SS BOND : bond 0.00417 ( 16) SS BOND : angle 1.52744 ( 32) covalent geometry : bond 0.00435 (28676) covalent geometry : angle 0.61590 (38903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 165 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8119 (mp) REVERT: H 116 LEU cc_start: 0.8907 (tp) cc_final: 0.8654 (tt) REVERT: A 74 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6112 (pmt) REVERT: A 112 MET cc_start: 0.8713 (mmt) cc_final: 0.8513 (mmt) REVERT: A 306 MET cc_start: 0.7689 (ttt) cc_final: 0.7275 (tpp) REVERT: A 331 MET cc_start: 0.6426 (tmm) cc_final: 0.6081 (tmm) REVERT: A 653 MET cc_start: 0.4877 (mtp) cc_final: 0.4572 (mtt) REVERT: A 828 MET cc_start: 0.2779 (tpt) cc_final: 0.2192 (tmm) REVERT: B 58 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8447 (pt) REVERT: B 546 ILE cc_start: 0.5496 (OUTLIER) cc_final: 0.4476 (pt) REVERT: B 548 ARG cc_start: 0.3402 (mtm-85) cc_final: 0.1441 (tmt170) REVERT: B 639 PHE cc_start: 0.7276 (t80) cc_final: 0.6767 (t80) REVERT: C 138 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7347 (mttm) REVERT: C 653 MET cc_start: 0.6081 (ppp) cc_final: 0.5068 (mmm) REVERT: D 41 MET cc_start: 0.6632 (ppp) cc_final: 0.6352 (ppp) REVERT: E 3 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7796 (tm-30) REVERT: F 58 VAL cc_start: 0.6208 (t) cc_final: 0.5958 (t) REVERT: G 42 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: G 50 MET cc_start: 0.7827 (mmm) cc_final: 0.7459 (mmm) outliers start: 65 outliers final: 47 residues processed: 219 average time/residue: 0.4063 time to fit residues: 144.7558 Evaluate side-chains 212 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 344 optimal weight: 30.0000 chunk 174 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 284 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** G 89 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.069027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.052204 restraints weight = 156687.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.052420 restraints weight = 88476.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.053083 restraints weight = 70820.969| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28705 Z= 0.109 Angle : 0.581 14.287 38974 Z= 0.291 Chirality : 0.043 0.310 4403 Planarity : 0.004 0.109 4911 Dihedral : 4.547 44.311 4099 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 1.80 % Allowed : 14.60 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 3489 helix: 1.56 (0.15), residues: 1236 sheet: 0.01 (0.21), residues: 656 loop : -0.53 (0.17), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 609 HIS 0.003 0.001 HIS A 44 PHE 0.064 0.001 PHE D 42 TYR 0.014 0.001 TYR A 393 ARG 0.006 0.000 ARG C 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 12) link_NAG-ASN : angle 1.83026 ( 36) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.33327 ( 3) hydrogen bonds : bond 0.02947 ( 1199) hydrogen bonds : angle 4.61111 ( 3399) SS BOND : bond 0.00276 ( 16) SS BOND : angle 1.30048 ( 32) covalent geometry : bond 0.00243 (28676) covalent geometry : angle 0.57792 (38903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8923 (tp) cc_final: 0.8683 (tt) REVERT: A 74 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6141 (pmt) REVERT: A 306 MET cc_start: 0.7719 (ttt) cc_final: 0.7266 (tpp) REVERT: A 331 MET cc_start: 0.6406 (tmm) cc_final: 0.6178 (tmm) REVERT: A 653 MET cc_start: 0.5032 (mtp) cc_final: 0.4792 (mtt) REVERT: A 828 MET cc_start: 0.2702 (tpt) cc_final: 0.2059 (tmm) REVERT: B 58 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8467 (pt) REVERT: B 546 ILE cc_start: 0.5313 (OUTLIER) cc_final: 0.4295 (pt) REVERT: B 548 ARG cc_start: 0.3163 (mtm-85) cc_final: 0.1353 (tmt170) REVERT: B 639 PHE cc_start: 0.7208 (t80) cc_final: 0.6676 (t80) REVERT: C 138 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7269 (mttm) REVERT: C 175 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9121 (p) REVERT: C 653 MET cc_start: 0.6075 (ppp) cc_final: 0.5050 (mmm) REVERT: D 41 MET cc_start: 0.6828 (ppp) cc_final: 0.6407 (ppp) REVERT: D 813 MET cc_start: -0.3652 (mtp) cc_final: -0.3934 (mmt) REVERT: E 3 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7739 (tm-30) REVERT: G 42 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: G 50 MET cc_start: 0.7909 (mmm) cc_final: 0.7630 (mmm) outliers start: 55 outliers final: 36 residues processed: 215 average time/residue: 0.4496 time to fit residues: 156.3424 Evaluate side-chains 204 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 335 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 477 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN E 35 HIS E 65 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.066358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048179 restraints weight = 157639.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.048857 restraints weight = 103917.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.049205 restraints weight = 72244.758| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 28705 Z= 0.301 Angle : 0.737 14.464 38974 Z= 0.375 Chirality : 0.048 0.449 4403 Planarity : 0.005 0.107 4911 Dihedral : 5.251 45.468 4094 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 1.83 % Allowed : 15.06 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3489 helix: 1.24 (0.15), residues: 1239 sheet: -0.53 (0.21), residues: 651 loop : -0.75 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 609 HIS 0.007 0.001 HIS A 674 PHE 0.071 0.002 PHE D 42 TYR 0.040 0.002 TYR A 393 ARG 0.023 0.001 ARG C 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.63184 ( 36) link_BETA1-4 : bond 0.00686 ( 1) link_BETA1-4 : angle 1.77405 ( 3) hydrogen bonds : bond 0.03705 ( 1199) hydrogen bonds : angle 4.98833 ( 3399) SS BOND : bond 0.00378 ( 16) SS BOND : angle 1.63820 ( 32) covalent geometry : bond 0.00679 (28676) covalent geometry : angle 0.73142 (38903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8953 (tp) cc_final: 0.8717 (tt) REVERT: A 74 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6107 (pmt) REVERT: A 90 MET cc_start: 0.8524 (tpt) cc_final: 0.8285 (tpt) REVERT: A 306 MET cc_start: 0.7883 (ttt) cc_final: 0.7427 (tpp) REVERT: A 653 MET cc_start: 0.4761 (mtp) cc_final: 0.4556 (mtt) REVERT: A 776 ASP cc_start: 0.7860 (p0) cc_final: 0.7648 (p0) REVERT: A 828 MET cc_start: 0.2454 (tpt) cc_final: 0.1865 (ttp) REVERT: B 58 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8626 (pt) REVERT: B 546 ILE cc_start: 0.5622 (OUTLIER) cc_final: 0.4512 (pt) REVERT: B 548 ARG cc_start: 0.3541 (mtm-85) cc_final: 0.1374 (tmt170) REVERT: B 702 MET cc_start: 0.7563 (ppp) cc_final: 0.7354 (ptp) REVERT: C 138 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7539 (mttm) REVERT: C 653 MET cc_start: 0.6031 (ppp) cc_final: 0.5089 (mmm) REVERT: D 41 MET cc_start: 0.6844 (ppp) cc_final: 0.6432 (ppp) REVERT: E 3 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8017 (tm-30) REVERT: G 42 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: G 50 MET cc_start: 0.8162 (mmm) cc_final: 0.7810 (mmm) outliers start: 56 outliers final: 40 residues processed: 206 average time/residue: 0.3966 time to fit residues: 134.3628 Evaluate side-chains 200 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 3.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 192 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 340 optimal weight: 7.9990 chunk 315 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.067944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051446 restraints weight = 156802.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.050909 restraints weight = 99742.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.051767 restraints weight = 78334.710| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28705 Z= 0.123 Angle : 0.599 14.442 38974 Z= 0.301 Chirality : 0.044 0.345 4403 Planarity : 0.004 0.096 4911 Dihedral : 4.777 46.066 4093 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 1.44 % Allowed : 15.22 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3489 helix: 1.40 (0.15), residues: 1238 sheet: -0.21 (0.21), residues: 641 loop : -0.67 (0.17), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 609 HIS 0.003 0.001 HIS B 780 PHE 0.065 0.001 PHE D 42 TYR 0.018 0.001 TYR A 393 ARG 0.022 0.000 ARG G 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 2.09414 ( 36) link_BETA1-4 : bond 0.00331 ( 1) link_BETA1-4 : angle 1.53505 ( 3) hydrogen bonds : bond 0.03115 ( 1199) hydrogen bonds : angle 4.72195 ( 3399) SS BOND : bond 0.00335 ( 16) SS BOND : angle 1.31354 ( 32) covalent geometry : bond 0.00277 (28676) covalent geometry : angle 0.59491 (38903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9891.96 seconds wall clock time: 177 minutes 40.92 seconds (10660.92 seconds total)