Starting phenix.real_space_refine on Wed May 28 18:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jiz_36335/05_2025/8jiz_36335.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jiz_36335/05_2025/8jiz_36335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jiz_36335/05_2025/8jiz_36335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jiz_36335/05_2025/8jiz_36335.map" model { file = "/net/cci-nas-00/data/ceres_data/8jiz_36335/05_2025/8jiz_36335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jiz_36335/05_2025/8jiz_36335.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 170 5.16 5 C 19800 2.51 5 N 5177 2.21 5 O 5855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 1.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31002 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5950 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 30, 'TRANS': 730} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6120 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 32, 'TRANS': 749} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 5940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5940 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 28, 'TRANS': 727} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 6094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6094 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1708 Classifications: {'peptide': 228} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 214} Chain: "F" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1650 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1644 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} 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: "J" 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: "K" 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: "L" 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: "M" 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: 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: "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: 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 Time building chain proxies: 18.79, per 1000 atoms: 0.61 Number of scatterers: 31002 At special positions: 0 Unit cell: (180.36, 226.8, 201.96, 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 170 16.00 O 5855 8.00 N 5177 7.00 C 19800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " 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=2.04 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 E 151 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 900 " - " ASN A 687 " " NAG B 901 " - " ASN B 471 " " NAG B 902 " - " ASN B 203 " " NAG C 900 " - " ASN C 687 " " NAG D 901 " - " ASN D 368 " " NAG D 902 " - " ASN D 471 " " NAG D 903 " - " ASN D 771 " " NAG D 904 " - " ASN D 203 " " NAG I 1 " - " ASN B 61 " " NAG J 1 " - " ASN B 276 " " NAG K 1 " - " ASN B 771 " " NAG L 1 " - " ASN D 61 " " NAG M 1 " - " ASN D 276 " Time building additional restraints: 7.28 Conformation dependent library (CDL) restraints added in 3.6 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7372 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 49 sheets defined 36.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.733A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.984A pdb=" N PHE A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 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 522 removed outlier: 3.587A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.686A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.836A pdb=" N MET A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 653 removed outlier: 3.778A pdb=" N PHE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.571A pdb=" N ASN A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.559A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.415A pdb=" N ALA A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 144 through 159 Processing helix chain 'B' and resid 170 through 187 removed outlier: 3.656A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.246A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.525A pdb=" N GLU B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.514A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 Processing helix chain 'B' and resid 457 through 471 removed outlier: 3.876A pdb=" N ASP B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.727A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 628 through 654 removed outlier: 3.668A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 3.667A pdb=" N ARG B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 674' Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 708 removed outlier: 3.687A pdb=" N LYS B 708 " --> pdb=" O HIS B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.725A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 843 removed outlier: 3.765A pdb=" N ALA B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 57 through 60 removed outlier: 3.643A pdb=" N ALA C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.682A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.716A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 232 through 246 removed outlier: 3.626A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.789A pdb=" N THR C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.545A pdb=" N TYR C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 522 Processing helix chain 'C' and resid 559 through 579 Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 633 through 652 removed outlier: 3.966A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.799A 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 698 removed outlier: 3.546A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN C 697 " --> pdb=" O ASN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 708 removed outlier: 4.191A pdb=" N GLN C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 704 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 removed outlier: 3.739A pdb=" N ALA C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 742 through 745 Processing helix chain 'C' and resid 771 through 785 removed outlier: 4.153A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 793 Processing helix chain 'C' and resid 813 through 836 removed outlier: 4.102A pdb=" N MET C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 821 " --> pdb=" O MET C 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 52 removed outlier: 3.984A pdb=" N HIS D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 104 through 114 removed outlier: 4.261A pdb=" N TYR D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.074A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 237 removed outlier: 3.900A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.950A pdb=" N SER D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 276 through 299 removed outlier: 3.670A pdb=" N HIS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 457 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 561 through 584 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.901A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 3.777A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 699 through 706 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 removed outlier: 4.080A pdb=" N PHE D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 843 removed outlier: 3.599A pdb=" N PHE D 829 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.771A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 32 " --> pdb=" O LEU E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.906A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.646A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 121 through 126' Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.633A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 167 through 169 No H-bonds generated for 'chain 'G' and resid 167 through 169' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.637A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.890A pdb=" N VAL A 38 " --> pdb=" O LEU A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.531A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 207 removed outlier: 6.315A pdb=" N SER A 171 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR A 230 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL A 173 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 276 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 410 removed outlier: 6.461A pdb=" N ILE A 408 " --> pdb=" O TYR A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 508 removed outlier: 3.679A pdb=" N ASP A 523 " --> pdb=" O LEU A 765 " (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 729 through 731 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 62 removed outlier: 7.051A pdb=" N VAL B 27 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.355A pdb=" N ILE B 164 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 166 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.354A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'B' and resid 681 through 682 removed outlier: 6.931A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 73 removed outlier: 3.782A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU C 98 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.566A pdb=" N PHE C 170 " --> pdb=" O ASP C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 206 removed outlier: 3.711A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 365 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 456 removed outlier: 8.486A pdb=" N LEU C 479 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ARG C 437 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 507 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AC3, first strand: chain 'C' and resid 728 through 731 removed outlier: 3.530A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.787A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 194 through 197 removed outlier: 3.552A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 269 through 271 removed outlier: 3.541A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 366 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 373 " --> pdb=" O ILE D 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 330 through 333 removed outlier: 4.697A pdb=" N ASP D 332 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY D 336 " --> pdb=" O ASP D 332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 477 through 478 Processing sheet with id=AC9, first strand: chain 'D' and resid 412 through 413 removed outlier: 3.527A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD2, first strand: chain 'D' and resid 681 through 682 removed outlier: 6.708A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 747 " --> pdb=" O VAL D 542 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'E' and resid 45 through 51 removed outlier: 5.055A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 92 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL E 120 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 131 through 135 removed outlier: 3.780A pdb=" N GLY E 150 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER E 191 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR E 187 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 131 through 135 removed outlier: 3.780A pdb=" N GLY E 150 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER E 191 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR E 187 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 162 through 165 removed outlier: 4.255A pdb=" N TYR E 205 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.754A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.575A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.595A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.736A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.135A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR F 192 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE F 209 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.279A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 131 through 135 removed outlier: 4.300A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 131 through 135 removed outlier: 4.300A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 161 through 165 removed outlier: 3.953A pdb=" N TYR G 205 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.974A pdb=" N THR H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.690A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.690A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.929A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.382A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR H 192 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE H 209 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS H 194 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS H 207 " --> pdb=" O CYS H 194 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL H 196 " --> pdb=" O VAL H 205 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL H 205 " --> pdb=" O VAL H 196 " (cutoff:3.500A) 1277 hydrogen bonds defined for protein. 3588 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: 13.96 Time building geometry restraints manager: 8.52 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: 9902 1.34 - 1.46: 7610 1.46 - 1.58: 13909 1.58 - 1.70: 0 1.70 - 1.82: 285 Bond restraints: 31706 Sorted by residual: bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 31701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 42549 1.86 - 3.73: 438 3.73 - 5.59: 43 5.59 - 7.45: 7 7.45 - 9.31: 2 Bond angle restraints: 43039 Sorted by residual: angle pdb=" C ASP E 106 " pdb=" CA ASP E 106 " pdb=" CB ASP E 106 " ideal model delta sigma weight residual 117.23 109.58 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" C THR D 35 " pdb=" CA THR D 35 " pdb=" CB THR D 35 " ideal model delta sigma weight residual 115.89 109.47 6.42 1.32e+00 5.74e-01 2.36e+01 angle pdb=" CA ASP E 106 " pdb=" C ASP E 106 " pdb=" N GLY E 107 " ideal model delta sigma weight residual 119.98 116.51 3.47 8.50e-01 1.38e+00 1.67e+01 angle pdb=" C SER A 225 " pdb=" N VAL A 226 " pdb=" CA VAL A 226 " ideal model delta sigma weight residual 120.49 125.04 -4.55 1.38e+00 5.25e-01 1.09e+01 angle pdb=" N ASP E 106 " pdb=" CA ASP E 106 " pdb=" C ASP E 106 " ideal model delta sigma weight residual 108.67 113.92 -5.25 1.67e+00 3.59e-01 9.88e+00 ... (remaining 43034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 18520 24.83 - 49.65: 515 49.65 - 74.48: 38 74.48 - 99.31: 11 99.31 - 124.14: 1 Dihedral angle restraints: 19085 sinusoidal: 7652 harmonic: 11433 Sorted by residual: dihedral pdb=" C2 NAG D 904 " pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " pdb=" C5 NAG D 904 " ideal model delta sinusoidal sigma weight residual -62.96 61.18 -124.14 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CA THR D 35 " pdb=" C THR D 35 " pdb=" N ARG D 36 " pdb=" CA ARG D 36 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C1 NAG D 904 " pdb=" C5 NAG D 904 " pdb=" O5 NAG D 904 " pdb=" C6 NAG D 904 " ideal model delta sinusoidal sigma weight residual 171.16 -92.60 -96.24 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 19082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3441 0.035 - 0.070: 1005 0.070 - 0.105: 362 0.105 - 0.141: 107 0.141 - 0.176: 5 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" C1 NAG D 904 " pdb=" ND2 ASN D 203 " pdb=" C2 NAG D 904 " pdb=" O5 NAG D 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 4917 not shown) Planarity restraints: 5446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 159 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO G 160 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 160 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 160 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 516 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 56 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 57 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " 0.019 5.00e-02 4.00e+02 ... (remaining 5443 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2273 2.74 - 3.28: 32263 3.28 - 3.82: 52424 3.82 - 4.36: 58976 4.36 - 4.90: 102123 Nonbonded interactions: 248059 Sorted by model distance: nonbonded pdb=" OG1 THR D 486 " pdb=" O GLN D 686 " model vdw 2.200 3.040 nonbonded pdb=" O VAL A 339 " pdb=" OG SER A 349 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR C 531 " pdb=" OD1 ASP C 731 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR D 205 " pdb=" O7 NAG D 904 " model vdw 2.253 3.040 nonbonded pdb=" NH1 ARG F 108 " pdb=" O ASP F 170 " model vdw 2.264 3.120 ... (remaining 248054 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 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 211 or (resid 212 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 395 or \ (resid 396 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 7 through 545 or resid 547 through 580 or resid 599 through 625 or resid 627 thr \ ough 796 or resid 813 through 837 or resid 900)) selection = (chain 'C' and (resid 34 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 58 or (resid 59 throu \ gh 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throu \ gh 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 through 193 or (resid 194 and (name N or name CA or name C or name O or \ name CB )) or resid 195 through 292 or (resid 293 and (name N or name CA or name \ C or name O or name CB )) or resid 294 through 535 or (resid 536 and (name N or \ name CA or name C or name O or name CB )) or resid 537 through 654 or resid 660 \ through 665 or (resid 666 and (name N or name CA or name C or name O or name CB \ )) or resid 667 through 796 or resid 813 through 837 or resid 900)) } ncs_group { reference = (chain 'B' and (resid 25 through 294 or (resid 295 and (name N or name CA or nam \ e C or name O or name CB )) or resid 296 through 488 or (resid 489 and (name N o \ r name CA or name C or name O or name CB )) or resid 490 through 553 or resid 55 \ 5 through 601 or resid 604 through 617 or resid 627 through 844 or resid 901 thr \ ough 902)) selection = (chain 'D' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 34 or (resid 35 and (name N or name CA or name C or name \ O or name CB )) or resid 36 through 83 or (resid 84 and (name N or name CA or na \ me C or name O or name CB )) or resid 85 through 326 or (resid 327 and (name N o \ r name CA or name C or name O or name CB )) or resid 328 through 414 or (resid 4 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 416 or (res \ id 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thr \ ough 657 or (resid 658 through 663 and (name N or name CA or name C or name O or \ name CB )) or resid 664 through 844 or resid 901 through 902)) } ncs_group { reference = (chain 'E' and (resid 1 through 138 or resid 145 through 225)) selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 6.220 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: 1.310 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 69.870 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 0.072 31742 Z= 0.112 Angle : 0.489 9.315 43129 Z= 0.259 Chirality : 0.040 0.176 4920 Planarity : 0.003 0.040 5433 Dihedral : 10.593 124.137 11659 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.12 % Rotamer: Outliers : 4.73 % Allowed : 8.21 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3896 helix: 2.17 (0.15), residues: 1253 sheet: 0.59 (0.20), residues: 774 loop : -0.71 (0.16), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 110 HIS 0.004 0.000 HIS A 119 PHE 0.011 0.001 PHE A 310 TYR 0.008 0.001 TYR G 105 ARG 0.002 0.000 ARG C 386 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 13) link_NAG-ASN : angle 1.35280 ( 39) link_BETA1-4 : bond 0.01497 ( 5) link_BETA1-4 : angle 4.65857 ( 15) hydrogen bonds : bond 0.17767 ( 1244) hydrogen bonds : angle 6.75271 ( 3588) SS BOND : bond 0.00162 ( 18) SS BOND : angle 0.61986 ( 36) covalent geometry : bond 0.00203 (31706) covalent geometry : angle 0.47917 (43039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 337 time to evaluate : 3.278 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: A 40 LEU cc_start: 0.7696 (mm) cc_final: 0.7438 (mm) REVERT: A 323 GLN cc_start: 0.8077 (mt0) cc_final: 0.7560 (tm-30) REVERT: A 408 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 512 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8814 (pp) REVERT: A 561 MET cc_start: 0.1486 (pmm) cc_final: 0.0156 (mmt) REVERT: A 564 MET cc_start: 0.5825 (tmm) cc_final: 0.5348 (tmm) REVERT: A 677 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 379 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8735 (mt) REVERT: B 785 MET cc_start: 0.9017 (mmt) cc_final: 0.8348 (mpp) REVERT: B 834 GLU cc_start: 0.3618 (OUTLIER) cc_final: 0.2550 (tp30) REVERT: C 69 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8200 (t) REVERT: C 561 MET cc_start: 0.2411 (pmm) cc_final: 0.1640 (pmm) REVERT: C 761 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: D 209 MET cc_start: 0.8079 (tpp) cc_final: 0.7621 (tpp) REVERT: D 315 TRP cc_start: 0.6983 (OUTLIER) cc_final: 0.6070 (t60) REVERT: D 548 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.4991 (tmt170) REVERT: D 695 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7859 (tpp80) REVERT: E 128 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6356 (ptpt) REVERT: G 155 ASP cc_start: 0.8059 (m-30) cc_final: 0.7854 (m-30) REVERT: G 217 LYS cc_start: 0.8841 (mttt) cc_final: 0.8417 (tppt) outliers start: 159 outliers final: 34 residues processed: 476 average time/residue: 0.4614 time to fit residues: 337.8706 Evaluate side-chains 249 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 761 TYR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain E residue 128 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 306 optimal weight: 8.9990 chunk 118 optimal weight: 0.5980 chunk 186 optimal weight: 4.9990 chunk 228 optimal weight: 40.0000 chunk 355 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 146 GLN A 193 ASN A 216 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN B 134 HIS C 35 ASN C 146 GLN C 154 GLN ** C 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN C 693 ASN D 86 GLN D 477 HIS ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 55 GLN H 124 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.065472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.050729 restraints weight = 195953.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.050089 restraints weight = 150840.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.050355 restraints weight = 124832.307| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31742 Z= 0.218 Angle : 0.657 14.336 43129 Z= 0.333 Chirality : 0.045 0.234 4920 Planarity : 0.004 0.058 5433 Dihedral : 7.193 115.806 4677 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 3.75 % Allowed : 11.01 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3896 helix: 1.61 (0.15), residues: 1278 sheet: 0.23 (0.20), residues: 784 loop : -0.83 (0.16), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 55 HIS 0.011 0.001 HIS D 477 PHE 0.022 0.002 PHE D 533 TYR 0.024 0.002 TYR D 703 ARG 0.008 0.001 ARG G 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 13) link_NAG-ASN : angle 2.22612 ( 39) link_BETA1-4 : bond 0.01409 ( 5) link_BETA1-4 : angle 4.12118 ( 15) hydrogen bonds : bond 0.03737 ( 1244) hydrogen bonds : angle 5.16846 ( 3588) SS BOND : bond 0.00500 ( 18) SS BOND : angle 1.37332 ( 36) covalent geometry : bond 0.00486 (31706) covalent geometry : angle 0.64890 (43039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 220 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.1728 (pmm) cc_final: 0.0425 (mmt) REVERT: A 564 MET cc_start: 0.5281 (tmm) cc_final: 0.4953 (tmm) REVERT: A 677 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8033 (p) REVERT: B 74 MET cc_start: 0.8702 (tmm) cc_final: 0.8231 (tmm) REVERT: B 834 GLU cc_start: 0.4245 (OUTLIER) cc_final: 0.2311 (tp30) REVERT: C 69 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8570 (t) REVERT: C 74 MET cc_start: 0.7965 (pmm) cc_final: 0.7696 (pmm) REVERT: C 133 MET cc_start: 0.8559 (mpt) cc_final: 0.8113 (mpt) REVERT: C 170 PHE cc_start: 0.7633 (m-80) cc_final: 0.7229 (m-10) REVERT: C 561 MET cc_start: 0.1675 (OUTLIER) cc_final: -0.0369 (mmm) REVERT: C 761 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: D 315 TRP cc_start: 0.7592 (OUTLIER) cc_final: 0.6625 (t60) REVERT: D 354 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7982 (mpt) REVERT: D 512 MET cc_start: 0.8611 (tpp) cc_final: 0.8343 (ttm) REVERT: D 548 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.4746 (tmt170) REVERT: D 695 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7887 (tpp80) REVERT: D 818 MET cc_start: -0.2234 (mmm) cc_final: -0.3265 (mtm) REVERT: E 128 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7015 (ptpt) REVERT: F 116 PHE cc_start: 0.6700 (m-80) cc_final: 0.6293 (m-10) outliers start: 126 outliers final: 64 residues processed: 335 average time/residue: 0.4179 time to fit residues: 225.4958 Evaluate side-chains 264 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 761 TYR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 221 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 172 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 348 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 278 optimal weight: 0.3980 chunk 316 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 218 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.065406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.048565 restraints weight = 195168.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.049005 restraints weight = 127028.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.049950 restraints weight = 96265.615| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31742 Z= 0.132 Angle : 0.574 12.532 43129 Z= 0.287 Chirality : 0.043 0.220 4920 Planarity : 0.004 0.050 5433 Dihedral : 6.834 115.287 4655 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.49 % Favored : 94.30 % Rotamer: Outliers : 3.30 % Allowed : 11.96 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3896 helix: 1.63 (0.15), residues: 1276 sheet: 0.13 (0.19), residues: 805 loop : -0.88 (0.16), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 55 HIS 0.009 0.001 HIS F 189 PHE 0.027 0.001 PHE C 183 TYR 0.040 0.001 TYR D 703 ARG 0.006 0.000 ARG A 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 13) link_NAG-ASN : angle 2.02694 ( 39) link_BETA1-4 : bond 0.01593 ( 5) link_BETA1-4 : angle 4.25373 ( 15) hydrogen bonds : bond 0.03299 ( 1244) hydrogen bonds : angle 4.89098 ( 3588) SS BOND : bond 0.00265 ( 18) SS BOND : angle 1.41353 ( 36) covalent geometry : bond 0.00292 (31706) covalent geometry : angle 0.56479 (43039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 199 time to evaluate : 3.396 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: A 200 MET cc_start: 0.7334 (mmt) cc_final: 0.6786 (mmt) REVERT: A 408 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 561 MET cc_start: 0.1714 (pmm) cc_final: 0.0582 (mmt) REVERT: A 564 MET cc_start: 0.4913 (tmm) cc_final: 0.4526 (tmm) REVERT: A 669 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7922 (mmtm) REVERT: A 677 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8038 (p) REVERT: B 74 MET cc_start: 0.8933 (tmm) cc_final: 0.8398 (tmm) REVERT: B 379 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8921 (mt) REVERT: B 785 MET cc_start: 0.8778 (tpp) cc_final: 0.8469 (mpp) REVERT: B 818 MET cc_start: -0.1377 (tpp) cc_final: -0.1903 (mpp) REVERT: B 834 GLU cc_start: 0.4105 (OUTLIER) cc_final: 0.2516 (tp30) REVERT: C 69 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8565 (t) REVERT: C 74 MET cc_start: 0.8081 (pmm) cc_final: 0.7800 (pmm) REVERT: C 419 VAL cc_start: 0.7229 (OUTLIER) cc_final: 0.7008 (p) REVERT: C 630 MET cc_start: 0.2123 (ptm) cc_final: 0.1882 (ppp) REVERT: D 470 MET cc_start: 0.8646 (mtm) cc_final: 0.7927 (ptp) REVERT: D 472 PHE cc_start: 0.7336 (m-10) cc_final: 0.6811 (m-10) REVERT: D 548 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.4783 (tmt170) REVERT: D 695 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7937 (tpp80) REVERT: D 818 MET cc_start: -0.1838 (mmm) cc_final: -0.2887 (mtm) REVERT: E 128 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7831 (pttm) outliers start: 111 outliers final: 66 residues processed: 297 average time/residue: 0.4000 time to fit residues: 195.3572 Evaluate side-chains 264 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 188 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 161 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 362 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 222 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 71 optimal weight: 0.2980 overall best weight: 3.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.063346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045615 restraints weight = 195629.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046671 restraints weight = 124306.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.047771 restraints weight = 83634.909| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 31742 Z= 0.257 Angle : 0.691 15.654 43129 Z= 0.348 Chirality : 0.046 0.255 4920 Planarity : 0.005 0.070 5433 Dihedral : 7.074 118.185 4647 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 3.84 % Allowed : 12.53 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3896 helix: 1.26 (0.14), residues: 1269 sheet: -0.14 (0.19), residues: 798 loop : -1.06 (0.16), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 198 HIS 0.009 0.001 HIS C 119 PHE 0.034 0.002 PHE C 183 TYR 0.041 0.002 TYR C 230 ARG 0.013 0.001 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 13) link_NAG-ASN : angle 2.50321 ( 39) link_BETA1-4 : bond 0.01350 ( 5) link_BETA1-4 : angle 4.48777 ( 15) hydrogen bonds : bond 0.03736 ( 1244) hydrogen bonds : angle 5.02047 ( 3588) SS BOND : bond 0.00298 ( 18) SS BOND : angle 1.32697 ( 36) covalent geometry : bond 0.00573 (31706) covalent geometry : angle 0.68109 (43039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 183 time to evaluate : 3.258 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: A 561 MET cc_start: 0.1805 (pmm) cc_final: 0.0630 (mmt) REVERT: A 677 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8100 (p) REVERT: B 379 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8845 (mt) REVERT: B 818 MET cc_start: -0.1322 (tpp) cc_final: -0.1863 (mpp) REVERT: B 834 GLU cc_start: 0.4322 (OUTLIER) cc_final: 0.2788 (tp30) REVERT: C 74 MET cc_start: 0.8033 (pmm) cc_final: 0.7726 (pmm) REVERT: C 256 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9279 (mt) REVERT: C 439 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7999 (t80) REVERT: C 630 MET cc_start: 0.2232 (ptm) cc_final: 0.1996 (ppp) REVERT: C 765 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.8810 (mp) REVERT: D 115 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.6641 (tpp80) REVERT: D 470 MET cc_start: 0.8677 (mtm) cc_final: 0.8235 (ptp) REVERT: D 472 PHE cc_start: 0.7737 (m-10) cc_final: 0.7472 (m-10) REVERT: D 548 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.4609 (tmt170) REVERT: D 657 LEU cc_start: 0.2245 (OUTLIER) cc_final: 0.1621 (pp) REVERT: D 695 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8031 (tpp80) REVERT: E 46 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7978 (tm-30) REVERT: E 128 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7955 (pttm) outliers start: 129 outliers final: 78 residues processed: 303 average time/residue: 0.3843 time to fit residues: 194.0595 Evaluate side-chains 264 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 175 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 43 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 323 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 322 optimal weight: 0.0040 chunk 21 optimal weight: 0.9990 chunk 321 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.064811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.047251 restraints weight = 194220.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.048292 restraints weight = 122488.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048144 restraints weight = 85023.769| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31742 Z= 0.110 Angle : 0.589 12.617 43129 Z= 0.293 Chirality : 0.043 0.260 4920 Planarity : 0.004 0.052 5433 Dihedral : 6.688 113.602 4645 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.03 % Favored : 93.76 % Rotamer: Outliers : 2.95 % Allowed : 13.39 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3896 helix: 1.42 (0.15), residues: 1274 sheet: 0.03 (0.20), residues: 763 loop : -1.03 (0.16), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 198 HIS 0.006 0.001 HIS C 119 PHE 0.027 0.001 PHE C 183 TYR 0.021 0.001 TYR C 230 ARG 0.006 0.000 ARG D 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 13) link_NAG-ASN : angle 2.43709 ( 39) link_BETA1-4 : bond 0.01437 ( 5) link_BETA1-4 : angle 4.43960 ( 15) hydrogen bonds : bond 0.03065 ( 1244) hydrogen bonds : angle 4.74775 ( 3588) SS BOND : bond 0.00188 ( 18) SS BOND : angle 1.17524 ( 36) covalent geometry : bond 0.00239 (31706) covalent geometry : angle 0.57791 (43039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 188 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 MET cc_start: 0.1887 (pmm) cc_final: 0.0820 (mmt) REVERT: A 677 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 823 MET cc_start: 0.5974 (ppp) cc_final: 0.5709 (ptp) REVERT: B 147 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: B 379 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8909 (mt) REVERT: B 614 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7757 (pp) REVERT: B 818 MET cc_start: -0.1311 (tpp) cc_final: -0.1854 (mpp) REVERT: B 834 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.2910 (tp30) REVERT: C 74 MET cc_start: 0.8171 (pmm) cc_final: 0.7875 (pmm) REVERT: C 439 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7748 (t80) REVERT: C 478 TYR cc_start: 0.6465 (t80) cc_final: 0.6204 (t80) REVERT: D 115 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6545 (tpp80) REVERT: D 470 MET cc_start: 0.8752 (mtm) cc_final: 0.8354 (ptp) REVERT: D 472 PHE cc_start: 0.7642 (m-10) cc_final: 0.7269 (m-10) REVERT: D 548 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.4755 (tmt170) REVERT: D 669 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.7492 (t70) REVERT: D 695 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8000 (tpp80) REVERT: E 46 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 128 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7800 (pttm) outliers start: 99 outliers final: 60 residues processed: 280 average time/residue: 0.4267 time to fit residues: 198.3900 Evaluate side-chains 247 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 297 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 164 optimal weight: 0.0870 chunk 272 optimal weight: 0.9990 chunk 383 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.064709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.047068 restraints weight = 194934.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.048186 restraints weight = 120785.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049394 restraints weight = 79582.533| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31742 Z= 0.118 Angle : 0.575 11.101 43129 Z= 0.286 Chirality : 0.043 0.278 4920 Planarity : 0.004 0.132 5433 Dihedral : 6.430 112.715 4638 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 3.01 % Allowed : 13.78 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3896 helix: 1.47 (0.15), residues: 1278 sheet: -0.02 (0.19), residues: 792 loop : -1.03 (0.16), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 198 HIS 0.006 0.001 HIS C 119 PHE 0.025 0.001 PHE C 183 TYR 0.021 0.001 TYR C 230 ARG 0.023 0.000 ARG D 673 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 13) link_NAG-ASN : angle 2.30267 ( 39) link_BETA1-4 : bond 0.01449 ( 5) link_BETA1-4 : angle 4.43613 ( 15) hydrogen bonds : bond 0.02960 ( 1244) hydrogen bonds : angle 4.65980 ( 3588) SS BOND : bond 0.00168 ( 18) SS BOND : angle 1.08627 ( 36) covalent geometry : bond 0.00261 (31706) covalent geometry : angle 0.56441 (43039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 187 time to evaluate : 3.434 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: A 507 MET cc_start: 0.8676 (ttm) cc_final: 0.8256 (ttm) REVERT: A 561 MET cc_start: 0.1826 (pmm) cc_final: 0.0835 (mmt) REVERT: A 677 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8118 (p) REVERT: A 701 MET cc_start: 0.7909 (mmt) cc_final: 0.7385 (mmt) REVERT: A 788 MET cc_start: 0.9217 (mpp) cc_final: 0.8989 (mmt) REVERT: A 823 MET cc_start: 0.6033 (ppp) cc_final: 0.5795 (ptp) REVERT: B 147 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: B 379 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8903 (mt) REVERT: B 785 MET cc_start: 0.8855 (mmm) cc_final: 0.8454 (mpp) REVERT: B 818 MET cc_start: -0.1348 (tpp) cc_final: -0.1871 (mpp) REVERT: B 834 GLU cc_start: 0.4414 (OUTLIER) cc_final: 0.2906 (tp30) REVERT: C 331 MET cc_start: 0.3303 (ptm) cc_final: 0.3089 (ptm) REVERT: C 439 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7777 (t80) REVERT: C 478 TYR cc_start: 0.6423 (t80) cc_final: 0.6204 (t80) REVERT: D 115 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6686 (tpp80) REVERT: D 470 MET cc_start: 0.8700 (mtm) cc_final: 0.8354 (ptp) REVERT: D 472 PHE cc_start: 0.7686 (m-10) cc_final: 0.7268 (m-10) REVERT: D 548 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.4705 (tmt170) REVERT: D 669 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8134 (t70) REVERT: D 695 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7990 (tpp80) REVERT: E 46 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 128 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7879 (pttm) outliers start: 101 outliers final: 71 residues processed: 276 average time/residue: 0.3906 time to fit residues: 179.2469 Evaluate side-chains 261 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 180 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 343 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 147 optimal weight: 0.0070 chunk 316 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.064072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046490 restraints weight = 195071.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047509 restraints weight = 122932.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048790 restraints weight = 82895.973| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31742 Z= 0.169 Angle : 0.604 10.177 43129 Z= 0.302 Chirality : 0.043 0.276 4920 Planarity : 0.004 0.072 5433 Dihedral : 6.485 113.710 4638 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.42 % Favored : 93.38 % Rotamer: Outliers : 3.09 % Allowed : 14.04 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3896 helix: 1.43 (0.15), residues: 1277 sheet: -0.13 (0.19), residues: 799 loop : -1.02 (0.16), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 198 HIS 0.007 0.001 HIS C 119 PHE 0.026 0.001 PHE C 183 TYR 0.024 0.001 TYR C 230 ARG 0.013 0.000 ARG D 673 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 13) link_NAG-ASN : angle 2.37802 ( 39) link_BETA1-4 : bond 0.01518 ( 5) link_BETA1-4 : angle 4.48844 ( 15) hydrogen bonds : bond 0.03092 ( 1244) hydrogen bonds : angle 4.67295 ( 3588) SS BOND : bond 0.00371 ( 18) SS BOND : angle 1.13136 ( 36) covalent geometry : bond 0.00381 (31706) covalent geometry : angle 0.59335 (43039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 181 time to evaluate : 3.364 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: A 561 MET cc_start: 0.1933 (pmm) cc_final: 0.0952 (mmt) REVERT: A 677 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8138 (p) REVERT: A 701 MET cc_start: 0.7859 (mmt) cc_final: 0.7355 (mmt) REVERT: A 788 MET cc_start: 0.9358 (mpp) cc_final: 0.8888 (mmt) REVERT: A 823 MET cc_start: 0.6166 (ppp) cc_final: 0.5944 (ptp) REVERT: B 147 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: B 379 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8880 (mt) REVERT: B 614 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7412 (tt) REVERT: B 818 MET cc_start: -0.1273 (tpp) cc_final: -0.1796 (mpp) REVERT: B 834 GLU cc_start: 0.4600 (OUTLIER) cc_final: 0.2996 (tp30) REVERT: C 439 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7770 (t80) REVERT: C 478 TYR cc_start: 0.6491 (t80) cc_final: 0.6248 (t80) REVERT: D 470 MET cc_start: 0.8694 (mtm) cc_final: 0.8395 (ptp) REVERT: D 472 PHE cc_start: 0.7671 (m-10) cc_final: 0.7286 (m-10) REVERT: D 548 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.4643 (tmt170) REVERT: D 657 LEU cc_start: 0.2736 (OUTLIER) cc_final: 0.2173 (pp) REVERT: D 669 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7289 (t70) REVERT: D 695 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8018 (tpp80) REVERT: D 706 MET cc_start: 0.8440 (mmp) cc_final: 0.8005 (tpp) REVERT: E 46 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8145 (tm-30) REVERT: E 128 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7966 (pttm) outliers start: 104 outliers final: 77 residues processed: 278 average time/residue: 0.3934 time to fit residues: 183.2208 Evaluate side-chains 266 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 178 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 248 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 308 optimal weight: 0.7980 chunk 167 optimal weight: 0.0470 chunk 117 optimal weight: 9.9990 chunk 245 optimal weight: 0.0170 chunk 358 optimal weight: 5.9990 overall best weight: 1.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.064490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047001 restraints weight = 195140.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.048035 restraints weight = 123684.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048135 restraints weight = 84197.474| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31742 Z= 0.122 Angle : 0.588 10.821 43129 Z= 0.292 Chirality : 0.043 0.279 4920 Planarity : 0.004 0.050 5433 Dihedral : 6.417 112.367 4638 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 3.21 % Allowed : 14.19 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3896 helix: 1.45 (0.15), residues: 1273 sheet: -0.00 (0.20), residues: 779 loop : -1.02 (0.16), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 198 HIS 0.006 0.001 HIS C 119 PHE 0.023 0.001 PHE C 183 TYR 0.019 0.001 TYR C 230 ARG 0.008 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 13) link_NAG-ASN : angle 2.30671 ( 39) link_BETA1-4 : bond 0.01433 ( 5) link_BETA1-4 : angle 4.47616 ( 15) hydrogen bonds : bond 0.02920 ( 1244) hydrogen bonds : angle 4.58928 ( 3588) SS BOND : bond 0.00325 ( 18) SS BOND : angle 1.08692 ( 36) covalent geometry : bond 0.00273 (31706) covalent geometry : angle 0.57802 (43039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 182 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 TRP cc_start: 0.5913 (OUTLIER) cc_final: 0.5494 (t-100) REVERT: A 473 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.4131 (m-80) REVERT: A 561 MET cc_start: 0.1949 (pmm) cc_final: 0.1033 (mmt) REVERT: A 677 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 701 MET cc_start: 0.8017 (mmt) cc_final: 0.7461 (mmt) REVERT: A 788 MET cc_start: 0.9352 (mpp) cc_final: 0.8965 (mmt) REVERT: A 823 MET cc_start: 0.6296 (ppp) cc_final: 0.6072 (ptp) REVERT: B 147 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: B 614 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7400 (tt) REVERT: B 818 MET cc_start: -0.1309 (tpp) cc_final: -0.1806 (mpp) REVERT: B 834 GLU cc_start: 0.4692 (OUTLIER) cc_final: 0.2999 (tp30) REVERT: C 439 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7739 (t80) REVERT: D 115 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6531 (tpp80) REVERT: D 354 MET cc_start: 0.8231 (tpp) cc_final: 0.7537 (mpp) REVERT: D 470 MET cc_start: 0.8735 (mtm) cc_final: 0.8418 (ptp) REVERT: D 472 PHE cc_start: 0.7724 (m-10) cc_final: 0.7281 (m-10) REVERT: D 548 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.4714 (tmt170) REVERT: D 657 LEU cc_start: 0.2847 (OUTLIER) cc_final: 0.2312 (pp) REVERT: D 669 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.7483 (t70) REVERT: D 695 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8028 (tpp80) REVERT: D 706 MET cc_start: 0.8560 (mmp) cc_final: 0.8140 (tpp) REVERT: E 46 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 128 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7913 (pttm) REVERT: G 221 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6795 (tpp-160) outliers start: 108 outliers final: 74 residues processed: 281 average time/residue: 0.4093 time to fit residues: 189.6023 Evaluate side-chains 264 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 176 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 221 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 3 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 320 optimal weight: 30.0000 chunk 268 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 376 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.063220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.045588 restraints weight = 194260.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046408 restraints weight = 125410.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.047613 restraints weight = 86979.086| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31742 Z= 0.235 Angle : 0.673 11.765 43129 Z= 0.336 Chirality : 0.045 0.277 4920 Planarity : 0.004 0.056 5433 Dihedral : 6.710 115.554 4638 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.44 % Favored : 92.38 % Rotamer: Outliers : 2.98 % Allowed : 14.61 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3896 helix: 1.26 (0.15), residues: 1276 sheet: -0.26 (0.19), residues: 798 loop : -1.08 (0.16), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 198 HIS 0.009 0.001 HIS C 119 PHE 0.044 0.002 PHE A 183 TYR 0.037 0.002 TYR A 230 ARG 0.007 0.001 ARG A 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 13) link_NAG-ASN : angle 2.57769 ( 39) link_BETA1-4 : bond 0.01447 ( 5) link_BETA1-4 : angle 4.60134 ( 15) hydrogen bonds : bond 0.03371 ( 1244) hydrogen bonds : angle 4.79079 ( 3588) SS BOND : bond 0.00267 ( 18) SS BOND : angle 1.18672 ( 36) covalent geometry : bond 0.00533 (31706) covalent geometry : angle 0.66327 (43039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 170 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.4420 (m-80) REVERT: A 507 MET cc_start: 0.8647 (ttm) cc_final: 0.8221 (ttm) REVERT: A 561 MET cc_start: 0.2591 (pmm) cc_final: 0.1567 (mmt) REVERT: A 677 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 701 MET cc_start: 0.7880 (mmt) cc_final: 0.7422 (mmt) REVERT: A 788 MET cc_start: 0.9289 (mpp) cc_final: 0.8923 (mmt) REVERT: A 823 MET cc_start: 0.6290 (ppp) cc_final: 0.6048 (ptp) REVERT: B 74 MET cc_start: 0.9323 (tpp) cc_final: 0.8766 (tpp) REVERT: B 614 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7355 (tt) REVERT: B 818 MET cc_start: -0.1213 (tpp) cc_final: -0.1723 (mpp) REVERT: B 834 GLU cc_start: 0.4675 (OUTLIER) cc_final: 0.2986 (tp30) REVERT: C 198 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7696 (p90) REVERT: C 439 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7951 (t80) REVERT: D 115 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.6691 (tpp80) REVERT: D 354 MET cc_start: 0.8413 (tpp) cc_final: 0.7723 (mpp) REVERT: D 470 MET cc_start: 0.8703 (mtm) cc_final: 0.8383 (ptp) REVERT: D 548 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.4657 (tmt170) REVERT: D 657 LEU cc_start: 0.2904 (OUTLIER) cc_final: 0.2380 (pp) REVERT: D 669 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7489 (t70) REVERT: D 695 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8027 (tpp80) REVERT: E 128 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8014 (pttm) REVERT: G 221 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6802 (tpp-160) outliers start: 100 outliers final: 79 residues processed: 262 average time/residue: 0.3916 time to fit residues: 170.3993 Evaluate side-chains 255 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 163 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 221 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 289 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 chunk 315 optimal weight: 0.1980 chunk 146 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 25 optimal weight: 0.0000 chunk 202 optimal weight: 0.1980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN B 162 HIS B 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.064782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047423 restraints weight = 193631.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048462 restraints weight = 121884.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.048739 restraints weight = 82196.381| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31742 Z= 0.105 Angle : 0.609 12.488 43129 Z= 0.300 Chirality : 0.044 0.329 4920 Planarity : 0.004 0.053 5433 Dihedral : 6.407 110.174 4638 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.93 % Favored : 93.87 % Rotamer: Outliers : 2.65 % Allowed : 15.00 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3896 helix: 1.40 (0.15), residues: 1275 sheet: -0.13 (0.20), residues: 778 loop : -1.01 (0.16), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 198 HIS 0.006 0.001 HIS C 119 PHE 0.022 0.001 PHE C 183 TYR 0.030 0.001 TYR C 478 ARG 0.006 0.000 ARG F 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 13) link_NAG-ASN : angle 2.32253 ( 39) link_BETA1-4 : bond 0.01566 ( 5) link_BETA1-4 : angle 4.55241 ( 15) hydrogen bonds : bond 0.02870 ( 1244) hydrogen bonds : angle 4.57462 ( 3588) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.02533 ( 36) covalent geometry : bond 0.00230 (31706) covalent geometry : angle 0.59907 (43039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 178 time to evaluate : 3.353 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: A 200 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.4219 (mmp) REVERT: A 392 ARG cc_start: 0.7277 (ppt170) cc_final: 0.7033 (pmt-80) REVERT: A 473 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4174 (m-80) REVERT: A 561 MET cc_start: 0.2332 (pmm) cc_final: 0.1321 (mmt) REVERT: A 677 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 701 MET cc_start: 0.8002 (mmt) cc_final: 0.7297 (mmt) REVERT: A 788 MET cc_start: 0.9306 (mpp) cc_final: 0.9039 (mmt) REVERT: B 74 MET cc_start: 0.9246 (tpp) cc_final: 0.8740 (tpp) REVERT: B 502 MET cc_start: 0.8087 (mmt) cc_final: 0.7792 (tpt) REVERT: B 614 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7444 (tt) REVERT: B 818 MET cc_start: -0.1231 (tpp) cc_final: -0.1743 (mpp) REVERT: B 834 GLU cc_start: 0.4707 (OUTLIER) cc_final: 0.3016 (tp30) REVERT: C 198 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7741 (p90) REVERT: C 439 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 817 MET cc_start: 0.3107 (tpt) cc_final: 0.2605 (tpt) REVERT: D 115 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.6615 (tpp80) REVERT: D 470 MET cc_start: 0.8807 (mtm) cc_final: 0.8528 (ptp) REVERT: D 548 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.4769 (tmt170) REVERT: D 657 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2548 (pp) REVERT: D 669 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.7612 (t70) REVERT: D 695 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8019 (tpp80) REVERT: E 46 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7691 (tm-30) REVERT: E 128 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7877 (pttm) REVERT: G 221 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6895 (tpp-160) outliers start: 89 outliers final: 65 residues processed: 256 average time/residue: 0.4179 time to fit residues: 180.1084 Evaluate side-chains 253 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 174 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 606 TRP Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 CYS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 390 TRP Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 79 CYS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 548 ARG Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 695 ARG Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 221 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 234 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 283 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 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** D 28 ASN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.064616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.047399 restraints weight = 193604.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048429 restraints weight = 124011.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048455 restraints weight = 87911.460| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 31742 Z= 0.178 Angle : 0.719 59.040 43129 Z= 0.381 Chirality : 0.046 0.581 4920 Planarity : 0.004 0.053 5433 Dihedral : 6.403 110.144 4638 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.03 % Favored : 93.74 % Rotamer: Outliers : 2.47 % Allowed : 15.20 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3896 helix: 1.37 (0.15), residues: 1276 sheet: -0.12 (0.20), residues: 778 loop : -1.03 (0.16), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 198 HIS 0.005 0.001 HIS C 119 PHE 0.020 0.001 PHE C 183 TYR 0.032 0.001 TYR E 108 ARG 0.006 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 13) link_NAG-ASN : angle 2.34043 ( 39) link_BETA1-4 : bond 0.01398 ( 5) link_BETA1-4 : angle 4.60452 ( 15) hydrogen bonds : bond 0.02873 ( 1244) hydrogen bonds : angle 4.56609 ( 3588) SS BOND : bond 0.00241 ( 18) SS BOND : angle 1.05357 ( 36) covalent geometry : bond 0.00408 (31706) covalent geometry : angle 0.71004 (43039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10114.94 seconds wall clock time: 178 minutes 20.73 seconds (10700.73 seconds total)