Starting phenix.real_space_refine on Sun Aug 24 23:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9caz_45410/08_2025/9caz_45410.cif Found real_map, /net/cci-nas-00/data/ceres_data/9caz_45410/08_2025/9caz_45410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9caz_45410/08_2025/9caz_45410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9caz_45410/08_2025/9caz_45410.map" model { file = "/net/cci-nas-00/data/ceres_data/9caz_45410/08_2025/9caz_45410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9caz_45410/08_2025/9caz_45410.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 126 5.16 5 C 15240 2.51 5 N 3931 2.21 5 O 4448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23745 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5848 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 27, 'TRANS': 710} Chain breaks: 2 Chain: "B" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5953 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 723} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5922 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5868 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 713} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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: "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: 5.97, per 1000 atoms: 0.25 Number of scatterers: 23745 At special positions: 0 Unit cell: (119.78, 159, 186.56, 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 126 16.00 O 4448 8.00 N 3931 7.00 C 15240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " 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 NAG-ASN " NAG A1001 " - " ASN A 546 " " NAG A1002 " - " ASN A 275 " " NAG A1003 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 546 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 751 " " NAG D1002 " - " ASN D 546 " " NAG D1003 " - " ASN D 275 " " NAG D1004 " - " ASN D 412 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 35 sheets defined 47.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.863A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.916A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.791A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.590A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 246 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.469A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.470A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 560 through 582 Processing helix chain 'A' and resid 632 through 665 removed outlier: 3.934A pdb=" N GLU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.960A pdb=" N ALA A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 696 removed outlier: 3.843A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 723 through 730 removed outlier: 3.661A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 774 through 789 Processing helix chain 'A' and resid 789 through 802 removed outlier: 3.655A pdb=" N ARG A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 802 " --> pdb=" O TRP A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 834 removed outlier: 3.976A pdb=" N VAL A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.572A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.845A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.559A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 337 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.625A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 556 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 634 through 662 Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.647A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 701 through 712 removed outlier: 4.076A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 739 through 747 Processing helix chain 'B' and resid 772 through 788 removed outlier: 3.589A pdb=" N ASP B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.792A pdb=" N MET B 793 " --> pdb=" O GLY B 789 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 843 removed outlier: 4.215A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.615A pdb=" N ARG C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 113 through 125 removed outlier: 4.078A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.374A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.507A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.600A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 454 through 457 removed outlier: 3.735A pdb=" N ASP C 457 " --> pdb=" O TYR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.746A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.655A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 560 through 584 Processing helix chain 'C' and resid 631 through 665 removed outlier: 4.367A pdb=" N GLU C 662 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.589A pdb=" N THR C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 720 through 731 removed outlier: 5.177A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 731 " --> pdb=" O ARG C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 773 through 789 removed outlier: 3.606A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 4.043A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 804 Processing helix chain 'C' and resid 822 through 834 removed outlier: 3.917A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 178 through 183 removed outlier: 4.222A pdb=" N LEU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 183' Processing helix chain 'D' and resid 185 through 195 Proline residue: D 192 - end of helix Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.829A pdb=" N GLY D 273 " --> pdb=" O ARG D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 317 through 337 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.638A pdb=" N ARG D 458 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 560 through 580 Processing helix chain 'D' and resid 634 through 665 Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.720A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.826A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.766A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 801 removed outlier: 3.700A pdb=" N MET D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY D 801 " --> pdb=" O LYS D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 841 removed outlier: 4.438A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU D 841 " --> pdb=" O VAL D 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 8.268A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ARG A 384 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N SER A 148 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 394 removed outlier: 3.534A pdb=" N TRP A 405 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 403 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.741A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 736 through 738 Processing sheet with id=AA7, first strand: chain 'B' and resid 75 through 83 removed outlier: 3.636A pdb=" N GLY B 40 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 83 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 105 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 41 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.834A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 395 Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.684A pdb=" N ASP B 406 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 433 through 437 removed outlier: 3.870A pdb=" N GLU B 479 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 437 " --> pdb=" O ARG B 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB5, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 683 removed outlier: 7.369A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 74 through 83 removed outlier: 5.912A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'C' and resid 202 through 203 removed outlier: 5.940A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AC2, first strand: chain 'C' and resid 433 through 437 removed outlier: 6.019A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC4, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 684 removed outlier: 6.356A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.099A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 102 through 103 removed outlier: 3.822A pdb=" N VAL D 103 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D 343 " --> pdb=" O VAL D 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 130 through 131 removed outlier: 5.927A pdb=" N VAL D 147 " --> pdb=" O GLN D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.846A pdb=" N TYR D 176 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 225 through 226 Processing sheet with id=AD2, first strand: chain 'D' and resid 368 through 370 removed outlier: 8.835A pdb=" N THR D 376 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR D 385 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN D 378 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU D 383 " --> pdb=" O ASN D 378 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 392 through 395 Processing sheet with id=AD4, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD5, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AD6, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AD7, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.632A pdb=" N LEU D 536 " --> pdb=" O LYS D 762 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS D 762 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 681 through 682 removed outlier: 7.109A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2901 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: 4.65 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7563 1.34 - 1.46: 5632 1.46 - 1.58: 10847 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 24262 Sorted by residual: bond pdb=" C1 NAG D1003 " pdb=" O5 NAG D1003 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" N TYR D 254 " pdb=" CA TYR D 254 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.38e-02 5.25e+03 2.30e+00 bond pdb=" C1 NAG A1003 " pdb=" O5 NAG A1003 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 24257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 32008 1.58 - 3.16: 667 3.16 - 4.75: 118 4.75 - 6.33: 41 6.33 - 7.91: 11 Bond angle restraints: 32845 Sorted by residual: angle pdb=" N ILE D 820 " pdb=" CA ILE D 820 " pdb=" C ILE D 820 " ideal model delta sigma weight residual 113.71 109.70 4.01 9.50e-01 1.11e+00 1.78e+01 angle pdb=" C PHE B 708 " pdb=" N MET B 709 " pdb=" CA MET B 709 " ideal model delta sigma weight residual 121.58 113.67 7.91 1.95e+00 2.63e-01 1.65e+01 angle pdb=" C TYR D 254 " pdb=" CA TYR D 254 " pdb=" CB TYR D 254 " ideal model delta sigma weight residual 112.05 106.91 5.14 1.52e+00 4.33e-01 1.14e+01 angle pdb=" CA MET A 323 " pdb=" CB MET A 323 " pdb=" CG MET A 323 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.64e+00 angle pdb=" CA MET D 737 " pdb=" CB MET D 737 " pdb=" CG MET D 737 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.64e+00 ... (remaining 32840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 12953 17.54 - 35.08: 1339 35.08 - 52.61: 257 52.61 - 70.15: 30 70.15 - 87.69: 24 Dihedral angle restraints: 14603 sinusoidal: 5982 harmonic: 8621 Sorted by residual: dihedral pdb=" CA MET A 737 " pdb=" C MET A 737 " pdb=" N GLU A 738 " pdb=" CA GLU A 738 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA MET D 50 " pdb=" C MET D 50 " pdb=" N GLY D 51 " pdb=" CA GLY D 51 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TRP A 353 " pdb=" C TRP A 353 " pdb=" N ARG A 354 " pdb=" CA ARG A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 14600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3413 0.076 - 0.153: 306 0.153 - 0.229: 2 0.229 - 0.306: 1 0.306 - 0.382: 2 Chirality restraints: 3724 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 275 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C1 NAG A1003 " pdb=" ND2 ASN A 412 " pdb=" C2 NAG A1003 " pdb=" O5 NAG A1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3721 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 275 " 0.003 2.00e-02 2.50e+03 1.55e-02 2.99e+00 pdb=" CG ASN D 275 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 275 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 275 " -0.010 2.00e-02 2.50e+03 pdb=" C1 NAG D1003 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 804 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 805 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 805 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 805 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 772 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO D 773 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 773 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 773 " -0.022 5.00e-02 4.00e+02 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2182 2.74 - 3.28: 26073 3.28 - 3.82: 41700 3.82 - 4.36: 47165 4.36 - 4.90: 78456 Nonbonded interactions: 195576 Sorted by model distance: nonbonded pdb=" OE1 GLU D 440 " pdb=" OH TYR D 488 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR B 317 " pdb=" OD1 ASP B 319 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR C 488 " pdb=" O PRO C 516 " model vdw 2.217 3.040 nonbonded pdb=" OG SER C 670 " pdb=" OD1 ASP C 672 " model vdw 2.234 3.040 nonbonded pdb=" O LYS A 190 " pdb=" OG SER A 193 " model vdw 2.234 3.040 ... (remaining 195571 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 33 through 580 or resid 633 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB )) or resid 665 through 681 or \ (resid 682 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 3 through 814 or (resid 815 and (name N or name CA or name C or name O or name C \ B )) or resid 816 through 834 or resid 1002 through 1003)) selection = (chain 'B' and (resid 33 through 429 or resid 433 through 580 or resid 633 throu \ gh 681 or (resid 682 and (name N or name CA or name C or name O or name CB )) or \ resid 683 through 814 or (resid 815 and (name N or name CA or name C or name O \ or name CB )) or resid 816 through 834 or resid 1001 through 1002)) selection = (chain 'C' and (resid 33 through 428 or resid 434 through 580 or resid 633 throu \ gh 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) or \ resid 665 through 834 or resid 1001 through 1002)) selection = (chain 'D' and (resid 33 through 681 or (resid 682 and (name N or name CA or nam \ e C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N o \ r name CA or name C or name O or name CB )) or resid 816 through 834 or resid 10 \ 03 through 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.110 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.003 0.049 24277 Z= 0.129 Angle : 0.603 9.840 32886 Z= 0.301 Chirality : 0.043 0.382 3724 Planarity : 0.003 0.040 4138 Dihedral : 14.508 87.687 9047 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2954 helix: 1.47 (0.15), residues: 1216 sheet: -2.44 (0.28), residues: 344 loop : -1.83 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.025 0.001 TYR C 651 PHE 0.026 0.001 PHE A 642 TRP 0.025 0.001 TRP A 353 HIS 0.011 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00276 (24262) covalent geometry : angle 0.59247 (32845) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.74052 ( 8) hydrogen bonds : bond 0.16587 ( 1003) hydrogen bonds : angle 6.36881 ( 2901) link_NAG-ASN : bond 0.00717 ( 11) link_NAG-ASN : angle 3.59573 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6649 (m-80) cc_final: 0.6276 (m-80) REVERT: A 323 MET cc_start: 0.8018 (mmp) cc_final: 0.7548 (tpp) REVERT: B 544 LYS cc_start: 0.8660 (ptmm) cc_final: 0.8382 (tmtt) REVERT: B 565 MET cc_start: 0.8827 (mpp) cc_final: 0.8625 (mpp) REVERT: C 218 MET cc_start: 0.8697 (tmm) cc_final: 0.8407 (tmm) REVERT: C 276 MET cc_start: 0.7685 (tmm) cc_final: 0.7463 (tmm) REVERT: C 649 SER cc_start: 0.9244 (m) cc_final: 0.8745 (p) REVERT: D 541 LEU cc_start: 0.8642 (tt) cc_final: 0.8189 (tt) REVERT: D 655 LEU cc_start: 0.9439 (tp) cc_final: 0.9222 (tp) REVERT: D 659 LEU cc_start: 0.9587 (mm) cc_final: 0.9050 (mp) REVERT: D 735 PHE cc_start: 0.7951 (t80) cc_final: 0.7518 (t80) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1448 time to fit residues: 72.1884 Evaluate side-chains 227 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 336 GLN D 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.121818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.091572 restraints weight = 73742.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090509 restraints weight = 43270.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.091444 restraints weight = 33548.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.091557 restraints weight = 25740.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.091864 restraints weight = 26145.164| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24277 Z= 0.208 Angle : 0.661 9.985 32886 Z= 0.336 Chirality : 0.045 0.388 3724 Planarity : 0.004 0.042 4138 Dihedral : 5.264 53.790 3444 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.09 % Allowed : 11.21 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.16), residues: 2954 helix: 1.36 (0.15), residues: 1229 sheet: -2.91 (0.28), residues: 310 loop : -1.85 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.032 0.001 TYR C 651 PHE 0.031 0.002 PHE A 693 TRP 0.021 0.002 TRP A 353 HIS 0.012 0.002 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00457 (24262) covalent geometry : angle 0.65193 (32845) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.87943 ( 8) hydrogen bonds : bond 0.04257 ( 1003) hydrogen bonds : angle 5.21148 ( 2901) link_NAG-ASN : bond 0.00715 ( 11) link_NAG-ASN : angle 3.48439 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8150 (mmp) cc_final: 0.7720 (tpp) REVERT: A 664 MET cc_start: 0.8497 (ptp) cc_final: 0.8045 (ptp) REVERT: B 544 LYS cc_start: 0.8886 (ptmm) cc_final: 0.8537 (tmtt) REVERT: B 752 LEU cc_start: 0.9160 (mm) cc_final: 0.8907 (tp) REVERT: C 276 MET cc_start: 0.7940 (tmm) cc_final: 0.7597 (tmm) REVERT: C 651 TYR cc_start: 0.8129 (t80) cc_final: 0.7775 (t80) REVERT: C 694 PHE cc_start: 0.7850 (m-80) cc_final: 0.7427 (m-80) REVERT: D 534 MET cc_start: 0.3014 (mmm) cc_final: 0.2766 (mmt) REVERT: D 659 LEU cc_start: 0.9600 (mm) cc_final: 0.9373 (mt) outliers start: 28 outliers final: 19 residues processed: 255 average time/residue: 0.1399 time to fit residues: 61.8458 Evaluate side-chains 244 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 87 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 292 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN ** C 137 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 = 0.4229 r_free = 0.4229 target = 0.121707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.093759 restraints weight = 73731.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090485 restraints weight = 48505.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091700 restraints weight = 39240.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.092153 restraints weight = 30923.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092530 restraints weight = 27975.620| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24277 Z= 0.191 Angle : 0.647 10.332 32886 Z= 0.326 Chirality : 0.044 0.409 3724 Planarity : 0.004 0.044 4138 Dihedral : 5.128 54.020 3444 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.47 % Allowed : 14.24 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.16), residues: 2954 helix: 1.26 (0.15), residues: 1237 sheet: -2.75 (0.29), residues: 315 loop : -1.90 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.031 0.001 TYR C 651 PHE 0.025 0.001 PHE D 735 TRP 0.019 0.001 TRP A 353 HIS 0.009 0.002 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00418 (24262) covalent geometry : angle 0.63758 (32845) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.88859 ( 8) hydrogen bonds : bond 0.03900 ( 1003) hydrogen bonds : angle 4.97367 ( 2901) link_NAG-ASN : bond 0.00719 ( 11) link_NAG-ASN : angle 3.46911 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.8625 (ptp) cc_final: 0.8402 (ptp) REVERT: B 565 MET cc_start: 0.8960 (mpp) cc_final: 0.8751 (mmm) REVERT: B 705 MET cc_start: 0.8500 (tpp) cc_final: 0.8234 (tpp) REVERT: B 752 LEU cc_start: 0.9196 (mm) cc_final: 0.8931 (tt) REVERT: C 649 SER cc_start: 0.9270 (m) cc_final: 0.8793 (p) REVERT: C 651 TYR cc_start: 0.8298 (t80) cc_final: 0.7976 (t80) REVERT: C 694 PHE cc_start: 0.7875 (m-80) cc_final: 0.7478 (m-80) outliers start: 38 outliers final: 30 residues processed: 268 average time/residue: 0.1402 time to fit residues: 64.6746 Evaluate side-chains 257 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 737 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 270 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 241 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.120472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.092568 restraints weight = 74456.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.089429 restraints weight = 52103.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.090707 restraints weight = 43672.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090995 restraints weight = 33185.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.091224 restraints weight = 31016.757| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24277 Z= 0.224 Angle : 0.680 11.577 32886 Z= 0.341 Chirality : 0.045 0.422 3724 Planarity : 0.004 0.044 4138 Dihedral : 5.257 54.661 3444 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.75 % Allowed : 16.83 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.15), residues: 2954 helix: 1.16 (0.15), residues: 1244 sheet: -2.87 (0.29), residues: 307 loop : -2.02 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 202 TYR 0.025 0.001 TYR C 651 PHE 0.031 0.002 PHE A 153 TRP 0.018 0.002 TRP A 353 HIS 0.011 0.002 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00489 (24262) covalent geometry : angle 0.67125 (32845) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.01494 ( 8) hydrogen bonds : bond 0.03827 ( 1003) hydrogen bonds : angle 4.96819 ( 2901) link_NAG-ASN : bond 0.00728 ( 11) link_NAG-ASN : angle 3.54785 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.4649 (OUTLIER) cc_final: 0.3745 (ppp) REVERT: A 501 MET cc_start: 0.2980 (mmm) cc_final: 0.2776 (mmm) REVERT: A 512 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5008 (pp) REVERT: A 660 THR cc_start: 0.9408 (p) cc_final: 0.9120 (p) REVERT: A 664 MET cc_start: 0.8583 (ptp) cc_final: 0.8313 (ptp) REVERT: B 129 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7327 (t-170) REVERT: B 269 TYR cc_start: 0.9348 (OUTLIER) cc_final: 0.8994 (m-80) REVERT: B 705 MET cc_start: 0.8522 (tpp) cc_final: 0.8188 (tpp) REVERT: C 340 MET cc_start: 0.6968 (tpt) cc_final: 0.6107 (tmm) REVERT: C 649 SER cc_start: 0.9306 (m) cc_final: 0.8866 (p) REVERT: C 651 TYR cc_start: 0.8289 (t80) cc_final: 0.7928 (t80) REVERT: D 654 ASN cc_start: 0.8642 (t0) cc_final: 0.8438 (t0) outliers start: 71 outliers final: 40 residues processed: 286 average time/residue: 0.1310 time to fit residues: 65.1214 Evaluate side-chains 277 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 129 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Chi-restraints excluded: chain D residue 737 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 223 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 175 optimal weight: 0.0470 chunk 195 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 184 optimal weight: 0.0070 chunk 39 optimal weight: 10.0000 chunk 282 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 overall best weight: 2.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 225 HIS ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN D 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.121939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.091462 restraints weight = 72761.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.090560 restraints weight = 43163.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091308 restraints weight = 32762.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092066 restraints weight = 25915.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092176 restraints weight = 25483.276| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24277 Z= 0.147 Angle : 0.645 13.144 32886 Z= 0.315 Chirality : 0.044 0.419 3724 Planarity : 0.004 0.044 4138 Dihedral : 5.045 53.533 3444 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.53 % Rotamer: Outliers : 1.82 % Allowed : 19.24 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.16), residues: 2954 helix: 1.23 (0.15), residues: 1248 sheet: -2.96 (0.28), residues: 319 loop : -1.92 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.018 0.001 TYR C 651 PHE 0.020 0.001 PHE D 735 TRP 0.015 0.001 TRP A 353 HIS 0.008 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00328 (24262) covalent geometry : angle 0.63565 (32845) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.92990 ( 8) hydrogen bonds : bond 0.03556 ( 1003) hydrogen bonds : angle 4.76899 ( 2901) link_NAG-ASN : bond 0.00694 ( 11) link_NAG-ASN : angle 3.43597 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.2930 (mmm) cc_final: 0.2525 (mmm) REVERT: A 512 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5082 (pp) REVERT: A 664 MET cc_start: 0.8550 (ptp) cc_final: 0.8254 (ptm) REVERT: B 269 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: C 340 MET cc_start: 0.6676 (tpt) cc_final: 0.5919 (tmm) REVERT: C 548 THR cc_start: 0.7046 (OUTLIER) cc_final: 0.6705 (p) REVERT: C 649 SER cc_start: 0.9255 (m) cc_final: 0.8816 (p) REVERT: C 651 TYR cc_start: 0.8176 (t80) cc_final: 0.7830 (t80) REVERT: C 655 LEU cc_start: 0.9461 (pp) cc_final: 0.9194 (pp) REVERT: C 752 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8614 (mm) REVERT: D 50 MET cc_start: 0.8567 (tmm) cc_final: 0.8276 (tmm) REVERT: D 319 ASP cc_start: 0.8700 (p0) cc_final: 0.8454 (p0) REVERT: D 654 ASN cc_start: 0.8680 (t0) cc_final: 0.8409 (t0) REVERT: D 677 GLN cc_start: 0.6539 (tm-30) cc_final: 0.5893 (mt0) outliers start: 47 outliers final: 28 residues processed: 289 average time/residue: 0.1350 time to fit residues: 67.8010 Evaluate side-chains 272 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.122181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.094747 restraints weight = 73767.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090659 restraints weight = 49651.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.091575 restraints weight = 42808.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092072 restraints weight = 33370.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.092400 restraints weight = 30453.625| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24277 Z= 0.146 Angle : 0.652 13.193 32886 Z= 0.317 Chirality : 0.044 0.409 3724 Planarity : 0.004 0.047 4138 Dihedral : 4.969 53.275 3444 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 2.13 % Allowed : 20.33 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.16), residues: 2954 helix: 1.25 (0.15), residues: 1247 sheet: -2.94 (0.28), residues: 309 loop : -1.97 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.015 0.001 TYR D 462 PHE 0.028 0.001 PHE A 42 TRP 0.013 0.001 TRP A 353 HIS 0.008 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00325 (24262) covalent geometry : angle 0.64329 (32845) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.88181 ( 8) hydrogen bonds : bond 0.03460 ( 1003) hydrogen bonds : angle 4.69469 ( 2901) link_NAG-ASN : bond 0.00683 ( 11) link_NAG-ASN : angle 3.39230 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: A 501 MET cc_start: 0.2839 (mmm) cc_final: 0.2631 (mmm) REVERT: A 512 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5214 (pp) REVERT: B 269 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: B 691 MET cc_start: 0.8411 (ppp) cc_final: 0.8195 (ppp) REVERT: B 705 MET cc_start: 0.8822 (tpt) cc_final: 0.8318 (tpp) REVERT: C 149 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9054 (mm) REVERT: C 340 MET cc_start: 0.7108 (tpt) cc_final: 0.6064 (tmm) REVERT: C 548 THR cc_start: 0.7254 (OUTLIER) cc_final: 0.6967 (p) REVERT: C 649 SER cc_start: 0.9236 (m) cc_final: 0.8803 (p) REVERT: C 651 TYR cc_start: 0.8328 (t80) cc_final: 0.7915 (t80) REVERT: C 655 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9124 (pp) REVERT: C 752 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8626 (mm) REVERT: D 319 ASP cc_start: 0.8723 (p0) cc_final: 0.8462 (p0) REVERT: D 328 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8207 (m170) outliers start: 55 outliers final: 34 residues processed: 285 average time/residue: 0.1356 time to fit residues: 67.6128 Evaluate side-chains 278 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 328 HIS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 268 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 205 optimal weight: 0.0030 chunk 52 optimal weight: 20.0000 chunk 225 optimal weight: 0.4980 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 654 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 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 = 0.4255 r_free = 0.4255 target = 0.123303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.095277 restraints weight = 72542.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.094829 restraints weight = 43555.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.095526 restraints weight = 32199.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.095691 restraints weight = 24642.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.096241 restraints weight = 24345.194| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24277 Z= 0.123 Angle : 0.651 14.077 32886 Z= 0.312 Chirality : 0.044 0.403 3724 Planarity : 0.003 0.045 4138 Dihedral : 4.850 53.367 3444 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 1.67 % Allowed : 21.72 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.16), residues: 2954 helix: 1.29 (0.15), residues: 1246 sheet: -2.75 (0.28), residues: 320 loop : -1.93 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 503 TYR 0.015 0.001 TYR D 462 PHE 0.032 0.001 PHE A 693 TRP 0.012 0.001 TRP A 353 HIS 0.016 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00275 (24262) covalent geometry : angle 0.64305 (32845) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.83319 ( 8) hydrogen bonds : bond 0.03379 ( 1003) hydrogen bonds : angle 4.61116 ( 2901) link_NAG-ASN : bond 0.00693 ( 11) link_NAG-ASN : angle 3.34800 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8247 (mm) cc_final: 0.7983 (mt) REVERT: A 512 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5038 (pp) REVERT: A 664 MET cc_start: 0.8515 (ptp) cc_final: 0.8150 (ptp) REVERT: B 691 MET cc_start: 0.8238 (ppp) cc_final: 0.7999 (ppp) REVERT: B 705 MET cc_start: 0.8708 (tpt) cc_final: 0.8213 (tpp) REVERT: C 276 MET cc_start: 0.7924 (tmm) cc_final: 0.7683 (tmm) REVERT: C 340 MET cc_start: 0.6777 (tpt) cc_final: 0.5881 (tmm) REVERT: C 548 THR cc_start: 0.6984 (OUTLIER) cc_final: 0.6644 (p) REVERT: C 649 SER cc_start: 0.9235 (m) cc_final: 0.8936 (p) REVERT: C 651 TYR cc_start: 0.8187 (t80) cc_final: 0.7807 (t80) REVERT: C 655 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9136 (pp) REVERT: C 743 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9164 (pm20) REVERT: C 752 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8563 (mm) REVERT: D 319 ASP cc_start: 0.8734 (p0) cc_final: 0.8491 (p0) REVERT: D 677 GLN cc_start: 0.6256 (tm-30) cc_final: 0.5854 (mt0) outliers start: 43 outliers final: 29 residues processed: 281 average time/residue: 0.1383 time to fit residues: 67.3344 Evaluate side-chains 270 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 58 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 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 = 0.4226 r_free = 0.4226 target = 0.121416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.090720 restraints weight = 73106.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.089573 restraints weight = 43188.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.090557 restraints weight = 33392.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090575 restraints weight = 26255.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.090821 restraints weight = 26759.500| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24277 Z= 0.183 Angle : 0.692 13.670 32886 Z= 0.335 Chirality : 0.044 0.403 3724 Planarity : 0.004 0.045 4138 Dihedral : 4.983 53.492 3444 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 2.17 % Allowed : 21.80 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.16), residues: 2954 helix: 1.28 (0.15), residues: 1237 sheet: -2.87 (0.28), residues: 314 loop : -1.93 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.016 0.001 TYR D 462 PHE 0.030 0.001 PHE D 735 TRP 0.013 0.001 TRP A 498 HIS 0.009 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00406 (24262) covalent geometry : angle 0.68395 (32845) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.88167 ( 8) hydrogen bonds : bond 0.03491 ( 1003) hydrogen bonds : angle 4.71557 ( 2901) link_NAG-ASN : bond 0.00692 ( 11) link_NAG-ASN : angle 3.38605 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7893 (tp) cc_final: 0.7183 (tp) REVERT: A 218 MET cc_start: 0.8583 (tmm) cc_final: 0.8278 (tmm) REVERT: A 247 MET cc_start: 0.5143 (OUTLIER) cc_final: 0.4323 (ppp) REVERT: A 501 MET cc_start: 0.2459 (mmm) cc_final: 0.2169 (mmm) REVERT: A 512 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5054 (pp) REVERT: A 664 MET cc_start: 0.8582 (ptp) cc_final: 0.8257 (ptp) REVERT: A 696 LYS cc_start: 0.7973 (pttm) cc_final: 0.7652 (tptp) REVERT: B 129 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.6973 (t-170) REVERT: B 691 MET cc_start: 0.8315 (ppp) cc_final: 0.8029 (ppp) REVERT: B 705 MET cc_start: 0.8779 (tpt) cc_final: 0.8288 (tpp) REVERT: C 340 MET cc_start: 0.6985 (tpt) cc_final: 0.5952 (tmm) REVERT: C 362 LEU cc_start: 0.8838 (mp) cc_final: 0.8160 (tp) REVERT: C 548 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6906 (p) REVERT: C 649 SER cc_start: 0.9335 (m) cc_final: 0.8927 (p) REVERT: C 651 TYR cc_start: 0.8271 (t80) cc_final: 0.7844 (t80) REVERT: C 655 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9038 (pp) REVERT: C 752 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8353 (mm) REVERT: D 50 MET cc_start: 0.8728 (tmm) cc_final: 0.7927 (tmm) REVERT: D 54 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: D 319 ASP cc_start: 0.8755 (p0) cc_final: 0.8536 (p0) outliers start: 56 outliers final: 39 residues processed: 274 average time/residue: 0.1412 time to fit residues: 67.1653 Evaluate side-chains 276 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 129 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 232 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 286 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 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 = 0.4238 r_free = 0.4238 target = 0.122156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.091510 restraints weight = 73066.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.090067 restraints weight = 42183.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.091301 restraints weight = 32772.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091326 restraints weight = 25250.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091609 restraints weight = 25238.511| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24277 Z= 0.161 Angle : 0.694 14.502 32886 Z= 0.333 Chirality : 0.045 0.410 3724 Planarity : 0.004 0.045 4138 Dihedral : 4.968 53.592 3444 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 2.09 % Allowed : 22.27 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.16), residues: 2954 helix: 1.25 (0.15), residues: 1242 sheet: -2.79 (0.29), residues: 306 loop : -1.94 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.017 0.001 TYR D 462 PHE 0.015 0.001 PHE D 555 TRP 0.014 0.001 TRP A 498 HIS 0.009 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00359 (24262) covalent geometry : angle 0.68586 (32845) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.88838 ( 8) hydrogen bonds : bond 0.03458 ( 1003) hydrogen bonds : angle 4.71052 ( 2901) link_NAG-ASN : bond 0.00658 ( 11) link_NAG-ASN : angle 3.42945 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 1.007 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 218 MET cc_start: 0.8547 (tmm) cc_final: 0.8261 (tmm) REVERT: A 501 MET cc_start: 0.2672 (mmm) cc_final: 0.2349 (mmm) REVERT: A 512 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5183 (pp) REVERT: B 269 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.8589 (m-80) REVERT: B 691 MET cc_start: 0.8324 (ppp) cc_final: 0.8026 (ppp) REVERT: B 705 MET cc_start: 0.8780 (tpt) cc_final: 0.8277 (tpp) REVERT: C 340 MET cc_start: 0.6930 (tpt) cc_final: 0.5910 (tmm) REVERT: C 362 LEU cc_start: 0.8746 (mp) cc_final: 0.8154 (tp) REVERT: C 541 LEU cc_start: 0.8937 (tp) cc_final: 0.8580 (tp) REVERT: C 548 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6767 (p) REVERT: C 649 SER cc_start: 0.9340 (m) cc_final: 0.8911 (p) REVERT: C 651 TYR cc_start: 0.8332 (t80) cc_final: 0.7855 (t80) REVERT: C 655 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9020 (pp) REVERT: C 752 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8342 (mm) outliers start: 54 outliers final: 39 residues processed: 278 average time/residue: 0.1414 time to fit residues: 68.3363 Evaluate side-chains 279 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 5 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 111 optimal weight: 0.0470 chunk 179 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 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 = 0.4224 r_free = 0.4224 target = 0.121399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.091288 restraints weight = 74179.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.090213 restraints weight = 44250.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.091228 restraints weight = 33183.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091294 restraints weight = 25719.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091632 restraints weight = 25960.891| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24277 Z= 0.181 Angle : 0.728 14.981 32886 Z= 0.348 Chirality : 0.045 0.409 3724 Planarity : 0.004 0.045 4138 Dihedral : 5.052 53.450 3444 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 1.94 % Allowed : 22.50 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.16), residues: 2954 helix: 1.23 (0.15), residues: 1237 sheet: -2.80 (0.29), residues: 301 loop : -1.98 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.017 0.001 TYR C 764 PHE 0.017 0.001 PHE D 555 TRP 0.015 0.001 TRP A 498 HIS 0.010 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00403 (24262) covalent geometry : angle 0.71987 (32845) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.91247 ( 8) hydrogen bonds : bond 0.03515 ( 1003) hydrogen bonds : angle 4.77902 ( 2901) link_NAG-ASN : bond 0.00658 ( 11) link_NAG-ASN : angle 3.44900 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8521 (tmm) cc_final: 0.8222 (tmm) REVERT: A 247 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4345 (ppp) REVERT: A 501 MET cc_start: 0.2672 (mmm) cc_final: 0.2368 (mmm) REVERT: A 512 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5138 (pp) REVERT: A 696 LYS cc_start: 0.8252 (pttm) cc_final: 0.7997 (tptp) REVERT: B 129 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.6990 (t-170) REVERT: B 691 MET cc_start: 0.8303 (ppp) cc_final: 0.8013 (ppp) REVERT: B 705 MET cc_start: 0.8659 (tpt) cc_final: 0.8170 (tpp) REVERT: B 714 GLN cc_start: 0.8000 (pm20) cc_final: 0.6973 (tm-30) REVERT: C 323 MET cc_start: 0.8787 (tpt) cc_final: 0.8425 (tpp) REVERT: C 340 MET cc_start: 0.6896 (tpt) cc_final: 0.5871 (tmm) REVERT: C 362 LEU cc_start: 0.8756 (mp) cc_final: 0.8137 (tp) REVERT: C 541 LEU cc_start: 0.8937 (tp) cc_final: 0.8612 (tp) REVERT: C 548 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6802 (p) REVERT: C 649 SER cc_start: 0.9346 (m) cc_final: 0.8915 (p) REVERT: C 651 TYR cc_start: 0.8257 (t80) cc_final: 0.7767 (t80) REVERT: C 655 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9016 (pp) REVERT: C 752 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8311 (mm) REVERT: D 50 MET cc_start: 0.8871 (tmm) cc_final: 0.8510 (tmm) REVERT: D 55 LEU cc_start: 0.9436 (mt) cc_final: 0.8978 (mt) outliers start: 50 outliers final: 42 residues processed: 271 average time/residue: 0.1381 time to fit residues: 64.9622 Evaluate side-chains 283 residues out of total 2582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain B residue 129 HIS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 725 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 760 ASP Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 650 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 130 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 289 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 151 optimal weight: 0.1980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS D 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.121439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.093232 restraints weight = 73022.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090692 restraints weight = 50371.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.091814 restraints weight = 39161.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.092421 restraints weight = 31137.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092831 restraints weight = 27417.781| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24277 Z= 0.183 Angle : 0.719 14.525 32886 Z= 0.348 Chirality : 0.045 0.415 3724 Planarity : 0.004 0.044 4138 Dihedral : 5.082 53.537 3444 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 2.13 % Allowed : 22.54 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.16), residues: 2954 helix: 1.20 (0.15), residues: 1236 sheet: -2.77 (0.30), residues: 285 loop : -1.98 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.020 0.001 TYR D 269 PHE 0.017 0.001 PHE D 555 TRP 0.020 0.001 TRP B 564 HIS 0.010 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00405 (24262) covalent geometry : angle 0.71120 (32845) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.92038 ( 8) hydrogen bonds : bond 0.03519 ( 1003) hydrogen bonds : angle 4.80271 ( 2901) link_NAG-ASN : bond 0.00665 ( 11) link_NAG-ASN : angle 3.46607 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.82 seconds wall clock time: 72 minutes 5.51 seconds (4325.51 seconds total)