Starting phenix.real_space_refine on Mon Aug 25 12:24:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj1_36337/08_2025/8jj1_36337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj1_36337/08_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_36337/08_2025/8jj1_36337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj1_36337/08_2025/8jj1_36337.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj1_36337/08_2025/8jj1_36337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj1_36337/08_2025/8jj1_36337.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.29, per 1000 atoms: 0.19 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: 2.03 Conformation dependent library (CDL) restraints added in 905.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.90 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: 5.63 Time building geometry restraints manager: 2.66 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 901)) selection = (chain 'C' and (resid 34 through 540 or resid 546 through 796 or resid 813 throu \ gh 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (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 ARG 0.001 0.000 ARG A 49 TYR 0.006 0.001 TYR A 281 PHE 0.012 0.001 PHE B 817 TRP 0.017 0.001 TRP C 55 HIS 0.002 0.000 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00172 (28676) covalent geometry : angle 0.41064 (38903) SS BOND : bond 0.00119 ( 16) SS BOND : angle 0.61401 ( 32) hydrogen bonds : bond 0.15708 ( 1199) hydrogen bonds : angle 5.98744 ( 3399) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 0.83704 ( 3) link_NAG-ASN : bond 0.00388 ( 12) link_NAG-ASN : angle 1.08727 ( 36) *********************** 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 : 0.848 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: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7624 (mt) cc_final: 0.7296 (mm) REVERT: H 116 LEU cc_start: 0.8574 (tp) cc_final: 0.7842 (pp) REVERT: A 324 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6775 (mpp) REVERT: A 517 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: A 641 PHE cc_start: 0.3526 (OUTLIER) cc_final: 0.3302 (t80) REVERT: A 653 MET cc_start: 0.4402 (mtp) cc_final: 0.2383 (tpt) REVERT: A 828 MET cc_start: 0.3487 (tpt) cc_final: 0.3008 (tmm) REVERT: B 57 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7985 (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: 0.1667 (tpt-90) REVERT: B 607 MET cc_start: 0.5317 (pp-130) cc_final: 0.4919 (tpp) REVERT: B 639 PHE cc_start: 0.7403 (t80) cc_final: 0.6837 (t80) REVERT: B 702 MET cc_start: 0.7183 (ppp) cc_final: 0.6164 (ppp) REVERT: C 39 MET cc_start: 0.7675 (mtp) cc_final: 0.7217 (mtp) REVERT: C 138 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7318 (mtmt) REVERT: C 252 ASP cc_start: 0.8059 (p0) cc_final: 0.7819 (p0) REVERT: C 560 MET cc_start: 0.2030 (ppp) cc_final: 0.1319 (ttm) REVERT: C 653 MET cc_start: 0.5870 (ppp) cc_final: 0.4505 (mmt) REVERT: D 326 MET cc_start: 0.8638 (mpt) cc_final: 0.8427 (mmm) REVERT: D 354 MET cc_start: 0.7536 (mmm) cc_final: 0.7324 (mmm) REVERT: G 2 ILE cc_start: 0.6681 (mp) cc_final: 0.5855 (mm) outliers start: 110 outliers final: 24 residues processed: 512 average time/residue: 0.1809 time to fit residues: 141.5189 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 : 1.097 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0470 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 overall best weight: 6.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 218 GLN A 671 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A 766 GLN B 38 HIS B 48 GLN B 134 HIS B 146 HIS B 270 GLN B 293 HIS B 300 ASN 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 404 ASN C 451 ASN C 485 HIS 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 280 HIS D 487 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 42 GLN F 55 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.048887 restraints weight = 159946.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.050286 restraints weight = 95273.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050422 restraints weight = 63412.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050615 restraints weight = 62289.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.050591 restraints weight = 52775.719| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 28705 Z= 0.371 Angle : 0.804 15.320 38974 Z= 0.417 Chirality : 0.050 0.447 4403 Planarity : 0.005 0.077 4911 Dihedral : 6.215 90.108 4127 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 3.83 % Allowed : 11.59 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 3489 helix: 1.41 (0.15), residues: 1232 sheet: 0.40 (0.22), residues: 621 loop : -0.55 (0.17), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 523 TYR 0.032 0.003 TYR C 230 PHE 0.028 0.003 PHE A 115 TRP 0.034 0.002 TRP B 160 HIS 0.012 0.002 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00831 (28676) covalent geometry : angle 0.79887 (38903) SS BOND : bond 0.00526 ( 16) SS BOND : angle 1.99999 ( 32) hydrogen bonds : bond 0.04132 ( 1199) hydrogen bonds : angle 5.38634 ( 3399) link_BETA1-4 : bond 0.00172 ( 1) link_BETA1-4 : angle 1.55447 ( 3) link_NAG-ASN : bond 0.00662 ( 12) link_NAG-ASN : angle 2.60124 ( 36) *********************** 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 322 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 205 time to evaluate : 0.683 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 4 LEU cc_start: 0.7922 (mt) cc_final: 0.7713 (mm) REVERT: H 116 LEU cc_start: 0.8992 (tp) cc_final: 0.8729 (tt) REVERT: A 230 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.5916 (t80) REVERT: A 306 MET cc_start: 0.7836 (ttt) cc_final: 0.7545 (tpp) REVERT: A 324 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7239 (mmt) REVERT: A 653 MET cc_start: 0.4576 (mtp) cc_final: 0.4344 (mtt) REVERT: A 828 MET cc_start: 0.3619 (tpt) cc_final: 0.3142 (ttp) REVERT: B 35 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 57 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8158 (tptt) REVERT: B 58 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8336 (mm) REVERT: B 72 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8396 (mt) REVERT: B 154 MET cc_start: 0.8480 (mtp) cc_final: 0.8267 (mtp) REVERT: B 548 ARG cc_start: 0.3816 (mtm-85) cc_final: 0.1516 (ttt180) REVERT: B 639 PHE cc_start: 0.7312 (t80) cc_final: 0.6754 (t80) REVERT: B 697 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.7070 (p) REVERT: B 702 MET cc_start: 0.7563 (ppp) cc_final: 0.7239 (ppp) REVERT: B 736 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8450 (mp) REVERT: C 74 MET cc_start: 0.8432 (pmm) cc_final: 0.7893 (pmm) REVERT: C 138 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7458 (mtmt) REVERT: C 143 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8203 (t) REVERT: C 158 MET cc_start: 0.8160 (mtm) cc_final: 0.7926 (mtm) REVERT: C 321 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.5191 (p90) REVERT: C 419 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8587 (p) REVERT: C 653 MET cc_start: 0.6146 (ppp) cc_final: 0.5217 (mmm) REVERT: D 36 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7560 (mmm160) REVERT: D 74 MET cc_start: 0.8903 (ttm) cc_final: 0.8662 (tpp) REVERT: D 354 MET cc_start: 0.8010 (mmm) cc_final: 0.7712 (mmm) REVERT: E 3 GLN cc_start: 0.7420 (tm-30) cc_final: 0.6744 (tm-30) REVERT: G 50 MET cc_start: 0.8077 (mmm) cc_final: 0.7780 (mmm) outliers start: 117 outliers final: 52 residues processed: 312 average time/residue: 0.1619 time to fit residues: 80.2467 Evaluate side-chains 234 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 203 VAL Chi-restraints excluded: chain A residue 230 TYR 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 720 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 665 THR 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 B residue 736 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU 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 308 CYS 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 701 THR Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 737 GLU Chi-restraints excluded: chain D residue 751 GLU Chi-restraints excluded: chain E residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 16 optimal weight: 5.9990 chunk 346 optimal weight: 20.0000 chunk 265 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 282 optimal weight: 0.0770 chunk 143 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 239 optimal weight: 30.0000 chunk 254 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- 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 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN C 153 GLN C 404 ASN ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 HIS ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 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 = 0.3810 r_free = 0.3810 target = 0.068635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051960 restraints weight = 158498.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051762 restraints weight = 92413.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052482 restraints weight = 76130.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052756 restraints weight = 60474.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.052857 restraints weight = 58549.780| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28705 Z= 0.143 Angle : 0.581 13.722 38974 Z= 0.297 Chirality : 0.044 0.368 4403 Planarity : 0.004 0.038 4911 Dihedral : 5.143 51.379 4112 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 2.98 % Allowed : 12.50 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 3489 helix: 1.61 (0.15), residues: 1222 sheet: 0.46 (0.22), residues: 615 loop : -0.55 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 437 TYR 0.020 0.002 TYR A 822 PHE 0.031 0.001 PHE D 42 TRP 0.019 0.001 TRP B 160 HIS 0.004 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00319 (28676) covalent geometry : angle 0.57131 (38903) SS BOND : bond 0.00366 ( 16) SS BOND : angle 3.02752 ( 32) hydrogen bonds : bond 0.03359 ( 1199) hydrogen bonds : angle 4.96548 ( 3399) link_BETA1-4 : bond 0.00823 ( 1) link_BETA1-4 : angle 1.44504 ( 3) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 1.95541 ( 36) *********************** 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 269 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 178 time to evaluate : 1.091 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: 0.8998 (tp) cc_final: 0.8723 (tt) REVERT: A 74 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6552 (pmt) REVERT: A 306 MET cc_start: 0.7699 (ttt) cc_final: 0.7395 (tpp) REVERT: A 324 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7208 (mmm) REVERT: A 653 MET cc_start: 0.4686 (mtp) cc_final: 0.4458 (mtt) REVERT: A 828 MET cc_start: 0.3496 (tpt) cc_final: 0.2877 (ttp) REVERT: B 58 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8512 (pt) REVERT: B 72 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8102 (mt) REVERT: B 546 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.4483 (pt) REVERT: B 548 ARG cc_start: 0.3733 (mtm-85) cc_final: 0.1708 (tpt-90) REVERT: B 555 MET cc_start: 0.3962 (ptp) cc_final: 0.3540 (ptm) REVERT: B 639 PHE cc_start: 0.7185 (t80) cc_final: 0.6688 (t80) REVERT: B 702 MET cc_start: 0.7666 (ppp) cc_final: 0.7287 (ppp) REVERT: C 112 MET cc_start: 0.8498 (mmm) cc_final: 0.8148 (tpp) REVERT: C 138 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7383 (mttm) REVERT: C 143 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8241 (t) REVERT: C 200 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8084 (tpt) REVERT: C 653 MET cc_start: 0.6055 (ppp) cc_final: 0.5142 (mmm) REVERT: C 705 MET cc_start: 0.8279 (tpp) cc_final: 0.7925 (mpp) REVERT: D 354 MET cc_start: 0.7998 (mmm) cc_final: 0.7657 (mmm) REVERT: D 576 MET cc_start: 0.2357 (ttp) cc_final: 0.1974 (tmm) REVERT: E 3 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7275 (tm-30) REVERT: G 50 MET cc_start: 0.8171 (mmm) cc_final: 0.7708 (mmm) outliers start: 91 outliers final: 37 residues processed: 254 average time/residue: 0.1733 time to fit residues: 70.4334 Evaluate side-chains 211 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 LEU 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 355 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 416 SER 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 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 143 THR Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 430 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 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 634 MET Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 133 optimal weight: 9.9990 chunk 147 optimal weight: 30.0000 chunk 83 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 693 ASN A 710 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.068125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.051514 restraints weight = 157255.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.051314 restraints weight = 94188.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.052017 restraints weight = 73934.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.052377 restraints weight = 58620.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052470 restraints weight = 56027.401| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28705 Z= 0.155 Angle : 0.573 11.735 38974 Z= 0.291 Chirality : 0.044 0.368 4403 Planarity : 0.004 0.060 4911 Dihedral : 4.816 45.685 4100 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 3.08 % Allowed : 13.26 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 3489 helix: 1.63 (0.15), residues: 1233 sheet: -0.05 (0.21), residues: 652 loop : -0.55 (0.17), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 386 TYR 0.024 0.001 TYR A 165 PHE 0.045 0.001 PHE D 42 TRP 0.017 0.001 TRP A 609 HIS 0.003 0.001 HIS B 780 Details of bonding type rmsd covalent geometry : bond 0.00349 (28676) covalent geometry : angle 0.56775 (38903) SS BOND : bond 0.00485 ( 16) SS BOND : angle 1.60598 ( 32) hydrogen bonds : bond 0.03164 ( 1199) hydrogen bonds : angle 4.82321 ( 3399) link_BETA1-4 : bond 0.00085 ( 1) link_BETA1-4 : angle 1.42061 ( 3) link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 2.18721 ( 36) *********************** 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 262 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 168 time to evaluate : 0.830 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: H 46 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7865 (mm-30) REVERT: H 116 LEU cc_start: 0.8964 (tp) cc_final: 0.8683 (tt) REVERT: A 74 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6109 (pmt) REVERT: A 181 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7046 (mmt-90) REVERT: A 306 MET cc_start: 0.7749 (ttt) cc_final: 0.7405 (tpp) REVERT: A 321 TYR cc_start: 0.4866 (m-80) cc_final: 0.4656 (t80) REVERT: A 324 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7293 (mmm) REVERT: A 653 MET cc_start: 0.4826 (mtp) cc_final: 0.4514 (mtt) REVERT: A 828 MET cc_start: 0.3351 (tpt) cc_final: 0.2784 (ttp) REVERT: B 58 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8519 (pt) REVERT: B 330 TYR cc_start: 0.4931 (m-80) cc_final: 0.3992 (m-10) REVERT: B 548 ARG cc_start: 0.3304 (mtm-85) cc_final: 0.1544 (tpt-90) REVERT: B 555 MET cc_start: 0.4214 (ptp) cc_final: 0.3775 (ptm) REVERT: B 607 MET cc_start: 0.5012 (tmm) cc_final: 0.4700 (tmm) REVERT: B 639 PHE cc_start: 0.7249 (t80) cc_final: 0.6753 (t80) REVERT: B 702 MET cc_start: 0.7600 (ppp) cc_final: 0.7173 (ppp) REVERT: C 138 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7460 (mttm) REVERT: C 143 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8224 (t) REVERT: C 170 PHE cc_start: 0.8353 (m-10) cc_final: 0.8102 (m-10) REVERT: C 175 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9068 (p) REVERT: C 480 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8912 (p) REVERT: C 653 MET cc_start: 0.6044 (ppp) cc_final: 0.5073 (mmm) REVERT: D 354 MET cc_start: 0.7982 (mmm) cc_final: 0.7674 (mmm) REVERT: D 632 LEU cc_start: -0.0932 (OUTLIER) cc_final: -0.1184 (tt) REVERT: E 3 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7572 (tm-30) REVERT: G 42 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: G 50 MET cc_start: 0.8197 (mmm) cc_final: 0.7770 (mmm) outliers start: 94 outliers final: 49 residues processed: 248 average time/residue: 0.1625 time to fit residues: 66.1278 Evaluate side-chains 222 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 299 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 720 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 416 SER Chi-restraints excluded: chain B residue 436 CYS 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 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 143 THR 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 169 VAL Chi-restraints excluded: chain C residue 175 THR 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 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 632 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL 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 232 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 258 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 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 = 0.3793 r_free = 0.3793 target = 0.067966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051318 restraints weight = 156928.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051218 restraints weight = 93212.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051878 restraints weight = 72595.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.052109 restraints weight = 58224.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052179 restraints weight = 56132.672| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28705 Z= 0.147 Angle : 0.563 11.925 38974 Z= 0.285 Chirality : 0.043 0.364 4403 Planarity : 0.003 0.042 4911 Dihedral : 4.684 44.968 4100 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 2.98 % Allowed : 13.98 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3489 helix: 1.56 (0.15), residues: 1248 sheet: -0.07 (0.21), residues: 641 loop : -0.55 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 386 TYR 0.020 0.001 TYR A 165 PHE 0.053 0.001 PHE D 42 TRP 0.023 0.001 TRP A 609 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00331 (28676) covalent geometry : angle 0.55724 (38903) SS BOND : bond 0.00269 ( 16) SS BOND : angle 1.85334 ( 32) hydrogen bonds : bond 0.03076 ( 1199) hydrogen bonds : angle 4.73842 ( 3399) link_BETA1-4 : bond 0.00036 ( 1) link_BETA1-4 : angle 1.35662 ( 3) link_NAG-ASN : bond 0.00299 ( 12) link_NAG-ASN : angle 2.10511 ( 36) *********************** 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 263 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 1.103 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 46 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7842 (mm-30) REVERT: H 116 LEU cc_start: 0.8944 (tp) cc_final: 0.8655 (tt) REVERT: A 74 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6025 (pmt) REVERT: A 181 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7045 (mmt-90) REVERT: A 306 MET cc_start: 0.7728 (ttt) cc_final: 0.7456 (tpp) REVERT: A 653 MET cc_start: 0.4835 (mtp) cc_final: 0.4531 (mtt) REVERT: A 828 MET cc_start: 0.3296 (tpt) cc_final: 0.2629 (tmm) REVERT: B 58 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8549 (pt) REVERT: B 546 ILE cc_start: 0.5480 (OUTLIER) cc_final: 0.4463 (pt) REVERT: B 548 ARG cc_start: 0.3299 (mtm-85) cc_final: 0.1470 (tpt-90) REVERT: B 555 MET cc_start: 0.4213 (ptp) cc_final: 0.3838 (ptm) REVERT: B 639 PHE cc_start: 0.7275 (t80) cc_final: 0.6772 (t80) REVERT: B 702 MET cc_start: 0.7450 (ppp) cc_final: 0.7038 (ppp) REVERT: C 138 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7477 (mttm) REVERT: C 175 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9105 (p) REVERT: C 480 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8930 (p) REVERT: C 653 MET cc_start: 0.6078 (ppp) cc_final: 0.5082 (mmm) REVERT: D 354 MET cc_start: 0.7934 (mmm) cc_final: 0.7635 (mmm) REVERT: D 635 VAL cc_start: 0.4952 (OUTLIER) cc_final: 0.4571 (t) REVERT: F 58 VAL cc_start: 0.6089 (t) cc_final: 0.5833 (t) REVERT: G 42 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: G 50 MET cc_start: 0.8246 (mmm) cc_final: 0.7830 (mmm) outliers start: 91 outliers final: 53 residues processed: 245 average time/residue: 0.1587 time to fit residues: 63.0886 Evaluate side-chains 221 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 GLN Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 720 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 416 SER 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 721 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 39 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 169 VAL Chi-restraints excluded: chain C residue 175 THR 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 65 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 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 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 635 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 304 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 233 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 375 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS 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 = 0.3767 r_free = 0.3767 target = 0.067056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.050077 restraints weight = 157405.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.050030 restraints weight = 99159.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050313 restraints weight = 80855.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050785 restraints weight = 65463.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.050752 restraints weight = 61443.044| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28705 Z= 0.208 Angle : 0.611 11.870 38974 Z= 0.312 Chirality : 0.045 0.397 4403 Planarity : 0.004 0.061 4911 Dihedral : 4.892 45.064 4097 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.53 % Rotamer: Outliers : 3.08 % Allowed : 14.14 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3489 helix: 1.45 (0.15), residues: 1244 sheet: -0.30 (0.21), residues: 647 loop : -0.62 (0.17), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 52 TYR 0.023 0.002 TYR A 165 PHE 0.051 0.002 PHE D 42 TRP 0.027 0.001 TRP A 609 HIS 0.006 0.001 HIS B 705 Details of bonding type rmsd covalent geometry : bond 0.00468 (28676) covalent geometry : angle 0.60541 (38903) SS BOND : bond 0.00287 ( 16) SS BOND : angle 1.81216 ( 32) hydrogen bonds : bond 0.03270 ( 1199) hydrogen bonds : angle 4.84148 ( 3399) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.53846 ( 3) link_NAG-ASN : bond 0.00310 ( 12) link_NAG-ASN : angle 2.31380 ( 36) *********************** 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 256 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 162 time to evaluate : 1.027 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: symmetry clash REVERT: H 46 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7861 (mm-30) REVERT: H 98 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.7050 (ttp-110) REVERT: H 116 LEU cc_start: 0.8987 (tp) cc_final: 0.8727 (tt) REVERT: A 74 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6011 (pmt) REVERT: A 181 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6832 (mmt-90) REVERT: A 306 MET cc_start: 0.7837 (ttt) cc_final: 0.7437 (tpp) REVERT: A 653 MET cc_start: 0.4596 (mtp) cc_final: 0.4348 (mtt) REVERT: A 823 MET cc_start: 0.3235 (ttp) cc_final: 0.2973 (ttm) REVERT: A 828 MET cc_start: 0.3375 (tpt) cc_final: 0.2777 (ttp) REVERT: B 58 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8519 (pt) REVERT: B 548 ARG cc_start: 0.3607 (mtm-85) cc_final: 0.1428 (tpt-90) REVERT: B 555 MET cc_start: 0.4207 (ptp) cc_final: 0.3896 (ptm) REVERT: B 607 MET cc_start: 0.5047 (tmm) cc_final: 0.4670 (tmm) REVERT: B 639 PHE cc_start: 0.7277 (t80) cc_final: 0.6782 (t80) REVERT: B 702 MET cc_start: 0.7511 (ppp) cc_final: 0.6509 (ppp) REVERT: C 138 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7554 (mttm) REVERT: C 153 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8625 (mp10) REVERT: C 653 MET cc_start: 0.6165 (ppp) cc_final: 0.5165 (mmm) REVERT: D 36 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7526 (mmm160) REVERT: D 354 MET cc_start: 0.7951 (mmm) cc_final: 0.7626 (mmm) REVERT: D 632 LEU cc_start: -0.0894 (OUTLIER) cc_final: -0.1108 (tt) REVERT: E 70 MET cc_start: 0.8225 (mtm) cc_final: 0.7860 (ptm) REVERT: G 42 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: G 50 MET cc_start: 0.8323 (mmm) cc_final: 0.7960 (mmm) outliers start: 94 outliers final: 62 residues processed: 242 average time/residue: 0.1682 time to fit residues: 66.3194 Evaluate side-chains 224 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 154 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 720 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 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 39 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 169 VAL Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 365 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 564 MET Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 65 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 197 PHE 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 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 632 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 330 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 702 HIS ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 GLN ** D 705 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.066108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.048035 restraints weight = 156888.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048858 restraints weight = 95434.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.049032 restraints weight = 69512.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.049289 restraints weight = 64101.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.049314 restraints weight = 53408.360| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 28705 Z= 0.264 Angle : 0.668 13.175 38974 Z= 0.341 Chirality : 0.046 0.437 4403 Planarity : 0.004 0.049 4911 Dihedral : 5.186 45.250 4096 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.90 % Rotamer: Outliers : 3.14 % Allowed : 14.63 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 3489 helix: 1.28 (0.15), residues: 1245 sheet: -0.51 (0.21), residues: 645 loop : -0.75 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 94 TYR 0.026 0.002 TYR B 330 PHE 0.057 0.002 PHE D 42 TRP 0.036 0.002 TRP A 609 HIS 0.005 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00591 (28676) covalent geometry : angle 0.66189 (38903) SS BOND : bond 0.00357 ( 16) SS BOND : angle 1.91553 ( 32) hydrogen bonds : bond 0.03492 ( 1199) hydrogen bonds : angle 4.97290 ( 3399) link_BETA1-4 : bond 0.00039 ( 1) link_BETA1-4 : angle 1.75459 ( 3) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.58804 ( 36) *********************** 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 255 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 159 time to evaluate : 0.875 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: H 46 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7847 (tm-30) REVERT: H 98 ARG cc_start: 0.7213 (ttp-170) cc_final: 0.7013 (ttp-110) REVERT: A 74 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.5946 (pmt) REVERT: A 153 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: A 181 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6601 (mmt-90) REVERT: A 306 MET cc_start: 0.7777 (ttt) cc_final: 0.7393 (tpp) REVERT: A 653 MET cc_start: 0.4677 (mtp) cc_final: 0.4418 (mtt) REVERT: A 823 MET cc_start: 0.3209 (ttp) cc_final: 0.2962 (ttm) REVERT: A 828 MET cc_start: 0.3334 (tpt) cc_final: 0.2699 (tmm) REVERT: B 58 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8656 (mm) REVERT: B 555 MET cc_start: 0.4238 (ptp) cc_final: 0.3924 (ptm) REVERT: B 607 MET cc_start: 0.5155 (tmm) cc_final: 0.4809 (tmm) REVERT: B 639 PHE cc_start: 0.7224 (t80) cc_final: 0.6645 (t80) REVERT: B 702 MET cc_start: 0.7768 (ppp) cc_final: 0.7490 (ppp) REVERT: C 138 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7468 (mttm) REVERT: C 153 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8654 (mp10) REVERT: C 653 MET cc_start: 0.6048 (ppp) cc_final: 0.5168 (mmm) REVERT: D 36 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7497 (mmm160) REVERT: D 354 MET cc_start: 0.7933 (mmm) cc_final: 0.7574 (mmm) REVERT: D 361 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9111 (mt) REVERT: E 70 MET cc_start: 0.8317 (mtm) cc_final: 0.7990 (ptm) REVERT: G 42 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: G 50 MET cc_start: 0.8367 (mmm) cc_final: 0.7998 (mmm) outliers start: 96 outliers final: 63 residues processed: 242 average time/residue: 0.1538 time to fit residues: 61.7576 Evaluate side-chains 225 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 153 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS 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 721 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 39 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 169 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE 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 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 329 LYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 426 VAL 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 D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 91 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 144 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 188 optimal weight: 0.1980 chunk 255 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 320 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS B 375 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS D 147 GLN D 162 HIS ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN G 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.066983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.050034 restraints weight = 157002.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.050058 restraints weight = 94509.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.050673 restraints weight = 74513.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.050674 restraints weight = 62584.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050850 restraints weight = 58005.203| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28705 Z= 0.148 Angle : 0.595 13.320 38974 Z= 0.302 Chirality : 0.044 0.384 4403 Planarity : 0.004 0.041 4911 Dihedral : 4.949 44.217 4095 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.55 % Allowed : 15.45 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3489 helix: 1.35 (0.15), residues: 1247 sheet: -0.49 (0.21), residues: 642 loop : -0.73 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.031 0.001 TYR G 49 PHE 0.061 0.001 PHE D 42 TRP 0.033 0.001 TRP A 609 HIS 0.006 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00333 (28676) covalent geometry : angle 0.59021 (38903) SS BOND : bond 0.00233 ( 16) SS BOND : angle 1.51813 ( 32) hydrogen bonds : bond 0.03198 ( 1199) hydrogen bonds : angle 4.85650 ( 3399) link_BETA1-4 : bond 0.00156 ( 1) link_BETA1-4 : angle 1.62686 ( 3) link_NAG-ASN : bond 0.00256 ( 12) link_NAG-ASN : angle 2.26352 ( 36) *********************** 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 238 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 160 time to evaluate : 0.951 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: H 46 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7842 (tm-30) REVERT: H 86 LEU cc_start: 0.8295 (mp) cc_final: 0.7881 (pt) REVERT: A 90 MET cc_start: 0.8431 (tpt) cc_final: 0.8223 (tpt) REVERT: A 181 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6751 (mmt-90) REVERT: A 321 TYR cc_start: 0.5153 (m-80) cc_final: 0.4603 (t80) REVERT: A 653 MET cc_start: 0.4560 (mtp) cc_final: 0.4325 (mtt) REVERT: A 823 MET cc_start: 0.3057 (ttp) cc_final: 0.2849 (ttm) REVERT: A 828 MET cc_start: 0.3316 (tpt) cc_final: 0.2745 (tmm) REVERT: B 58 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8561 (pt) REVERT: B 555 MET cc_start: 0.4260 (ptp) cc_final: 0.3920 (ptm) REVERT: B 607 MET cc_start: 0.5157 (tmm) cc_final: 0.4786 (tmm) REVERT: B 639 PHE cc_start: 0.7179 (t80) cc_final: 0.6740 (t80) REVERT: B 702 MET cc_start: 0.7789 (ppp) cc_final: 0.6712 (ppp) REVERT: B 706 MET cc_start: 0.8560 (ppp) cc_final: 0.8199 (ppp) REVERT: C 138 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7567 (mttm) REVERT: C 158 MET cc_start: 0.7934 (mtt) cc_final: 0.7601 (mtt) REVERT: C 653 MET cc_start: 0.6052 (ppp) cc_final: 0.5150 (mmm) REVERT: D 36 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7484 (mmm160) REVERT: D 354 MET cc_start: 0.7899 (mmm) cc_final: 0.7560 (mmm) REVERT: D 361 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9076 (mt) REVERT: D 576 MET cc_start: 0.1503 (tmm) cc_final: 0.0986 (ptt) REVERT: E 70 MET cc_start: 0.8156 (mtm) cc_final: 0.7942 (ptm) REVERT: G 42 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: G 50 MET cc_start: 0.8337 (mmm) cc_final: 0.8025 (mmm) REVERT: G 89 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6578 (tm-30) outliers start: 78 outliers final: 56 residues processed: 227 average time/residue: 0.1608 time to fit residues: 59.9621 Evaluate side-chains 214 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 720 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 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS 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 B residue 824 ILE Chi-restraints excluded: chain C residue 39 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 163 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 THR 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 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 65 VAL 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 197 PHE 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 329 LYS Chi-restraints excluded: chain D residue 361 LEU 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 D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 289 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 291 optimal weight: 0.8980 chunk 50 optimal weight: 0.0030 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.067114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.050375 restraints weight = 156263.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.050104 restraints weight = 100697.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.050885 restraints weight = 76984.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.050776 restraints weight = 64103.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051061 restraints weight = 58192.154| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 28705 Z= 0.139 Angle : 0.597 13.137 38974 Z= 0.302 Chirality : 0.044 0.369 4403 Planarity : 0.003 0.040 4911 Dihedral : 4.878 44.170 4092 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 2.32 % Allowed : 16.17 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.15), residues: 3489 helix: 1.31 (0.15), residues: 1248 sheet: -0.47 (0.21), residues: 642 loop : -0.72 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 94 TYR 0.031 0.001 TYR G 49 PHE 0.067 0.001 PHE D 42 TRP 0.041 0.001 TRP A 609 HIS 0.005 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00317 (28676) covalent geometry : angle 0.59234 (38903) SS BOND : bond 0.00211 ( 16) SS BOND : angle 1.44855 ( 32) hydrogen bonds : bond 0.03177 ( 1199) hydrogen bonds : angle 4.83186 ( 3399) link_BETA1-4 : bond 0.00582 ( 1) link_BETA1-4 : angle 1.52669 ( 3) link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.15483 ( 36) *********************** 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 227 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 0.843 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 46 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7852 (tm-30) REVERT: A 181 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6857 (mmt-90) REVERT: A 473 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.2978 (m-80) REVERT: A 653 MET cc_start: 0.4546 (mtp) cc_final: 0.4325 (mtt) REVERT: A 828 MET cc_start: 0.3295 (tpt) cc_final: 0.2725 (tmm) REVERT: B 58 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8544 (pt) REVERT: B 555 MET cc_start: 0.4247 (ptp) cc_final: 0.3884 (ptm) REVERT: B 607 MET cc_start: 0.5213 (tmm) cc_final: 0.4853 (tmm) REVERT: B 639 PHE cc_start: 0.7181 (t80) cc_final: 0.6590 (t80) REVERT: B 702 MET cc_start: 0.7820 (ppp) cc_final: 0.7071 (ppp) REVERT: B 706 MET cc_start: 0.8577 (ppp) cc_final: 0.8296 (ppp) REVERT: C 138 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7559 (mttm) REVERT: C 653 MET cc_start: 0.6049 (ppp) cc_final: 0.5138 (mmm) REVERT: D 354 MET cc_start: 0.7883 (mmm) cc_final: 0.7556 (mmm) REVERT: D 361 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9072 (mt) REVERT: D 576 MET cc_start: 0.1651 (tmm) cc_final: 0.1137 (ptt) REVERT: D 607 MET cc_start: 0.5922 (ptt) cc_final: 0.5660 (ppp) REVERT: G 42 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: G 50 MET cc_start: 0.8462 (mmm) cc_final: 0.8180 (mmm) outliers start: 71 outliers final: 56 residues processed: 214 average time/residue: 0.1525 time to fit residues: 54.0906 Evaluate side-chains 212 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 720 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 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS 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 C residue 39 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 163 GLN Chi-restraints excluded: chain C residue 169 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 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE 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 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 329 LYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL 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 220 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.065548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047293 restraints weight = 157544.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047837 restraints weight = 98948.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.048281 restraints weight = 72036.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048406 restraints weight = 66772.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.048489 restraints weight = 57185.477| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 28705 Z= 0.302 Angle : 0.730 13.980 38974 Z= 0.373 Chirality : 0.047 0.465 4403 Planarity : 0.004 0.060 4911 Dihedral : 5.428 47.307 4092 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.25 % Favored : 93.72 % Rotamer: Outliers : 2.42 % Allowed : 16.20 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.15), residues: 3489 helix: 1.00 (0.15), residues: 1258 sheet: -0.72 (0.21), residues: 640 loop : -0.94 (0.17), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG G 24 TYR 0.034 0.002 TYR C 230 PHE 0.066 0.002 PHE D 42 TRP 0.048 0.002 TRP A 609 HIS 0.007 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00677 (28676) covalent geometry : angle 0.72386 (38903) SS BOND : bond 0.00398 ( 16) SS BOND : angle 1.85092 ( 32) hydrogen bonds : bond 0.03733 ( 1199) hydrogen bonds : angle 5.15865 ( 3399) link_BETA1-4 : bond 0.00182 ( 1) link_BETA1-4 : angle 1.85076 ( 3) link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 2.67888 ( 36) ********************** 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 225 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 151 time to evaluate : 1.067 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: H 46 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7896 (tm-30) REVERT: A 153 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: A 181 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6254 (mmt-90) REVERT: A 705 MET cc_start: 0.6850 (mmt) cc_final: 0.6535 (tpp) REVERT: A 828 MET cc_start: 0.3358 (tpt) cc_final: 0.2722 (tmm) REVERT: B 416 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8810 (p) REVERT: B 555 MET cc_start: 0.4190 (ptp) cc_final: 0.3893 (ptm) REVERT: B 607 MET cc_start: 0.5233 (tmm) cc_final: 0.4904 (tmm) REVERT: B 702 MET cc_start: 0.7873 (ppp) cc_final: 0.7273 (ppp) REVERT: C 138 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7612 (mttm) REVERT: C 286 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6550 (t80) REVERT: C 653 MET cc_start: 0.5991 (ppp) cc_final: 0.5123 (mmp) REVERT: C 705 MET cc_start: 0.8284 (mmm) cc_final: 0.7976 (mmm) REVERT: D 354 MET cc_start: 0.7920 (mmm) cc_final: 0.7532 (mmm) REVERT: D 576 MET cc_start: 0.1786 (tmm) cc_final: 0.1249 (ptt) REVERT: D 607 MET cc_start: 0.6119 (ptt) cc_final: 0.5848 (ppp) REVERT: G 42 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: G 50 MET cc_start: 0.8465 (mmm) cc_final: 0.8166 (mmm) outliers start: 74 outliers final: 55 residues processed: 213 average time/residue: 0.1565 time to fit residues: 55.5390 Evaluate side-chains 209 residues out of total 3060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 203 VAL 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 393 TYR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 416 SER 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 39 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 163 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE 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 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 329 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 19 VAL 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 226 optimal weight: 10.0000 chunk 233 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 347 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.050597 restraints weight = 155678.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.050469 restraints weight = 96661.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.051209 restraints weight = 71988.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.051083 restraints weight = 63041.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051272 restraints weight = 56985.956| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28705 Z= 0.117 Angle : 0.606 14.046 38974 Z= 0.306 Chirality : 0.044 0.346 4403 Planarity : 0.004 0.040 4911 Dihedral : 4.953 45.055 4090 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 1.87 % Allowed : 16.60 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 3489 helix: 1.15 (0.15), residues: 1253 sheet: -0.59 (0.21), residues: 645 loop : -0.78 (0.17), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.000 ARG F 24 TYR 0.033 0.001 TYR G 49 PHE 0.059 0.001 PHE D 42 TRP 0.045 0.001 TRP A 609 HIS 0.005 0.001 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00260 (28676) covalent geometry : angle 0.60149 (38903) SS BOND : bond 0.00180 ( 16) SS BOND : angle 1.37799 ( 32) hydrogen bonds : bond 0.03202 ( 1199) hydrogen bonds : angle 4.88676 ( 3399) link_BETA1-4 : bond 0.00134 ( 1) link_BETA1-4 : angle 1.46274 ( 3) link_NAG-ASN : bond 0.00340 ( 12) link_NAG-ASN : angle 2.11430 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4147.32 seconds wall clock time: 72 minutes 48.98 seconds (4368.98 seconds total)