Starting phenix.real_space_refine on Mon Jul 6 22:09:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ze0_74082/07_2026/9ze0_74082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ze0_74082/07_2026/9ze0_74082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ze0_74082/07_2026/9ze0_74082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ze0_74082/07_2026/9ze0_74082.map" model { file = "/net/cci-nas-00/data/ceres_data/9ze0_74082/07_2026/9ze0_74082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ze0_74082/07_2026/9ze0_74082.cif" } resolution = 3.43 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= 0.003 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 79 5.49 5 S 199 5.16 5 C 24018 2.51 5 N 6560 2.21 5 O 7397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38256 Number of models: 1 Model: "" Number of chains: 16 Chain: "2" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 781 Classifications: {'RNA': 37} Modifications used: {'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p': 8, 'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "B" Number of atoms: 5345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5345 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 37, 'TRANS': 627} Chain: "H" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "R" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 842 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 14, 'rna3p_pyr': 27} Link IDs: {'rna2p': 15, 'rna3p': 26} Chain: "C" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1451 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "A" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1262 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "B1" Number of atoms: 7142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7142 Classifications: {'peptide': 895} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 849} Chain breaks: 1 Chain: "B2" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1967 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 27, 'TRANS': 223} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B3" Number of atoms: 9396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1198, 9396 Classifications: {'peptide': 1198} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 59, 'TRANS': 1136} Chain breaks: 2 Chain: "B4" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1593 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "B5" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "A1" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1344 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 149} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A2" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1645 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "A3" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3270 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6216 SG CYS H 11 103.394 125.274 99.129 1.00 58.48 S ATOM 6479 SG CYS H 46 102.962 128.698 97.437 1.00 58.51 S ATOM 6502 SG CYS H 49 101.524 125.723 95.807 1.00 61.82 S ATOM 6773 SG CYS H 85 100.041 127.030 99.180 1.00 58.99 S ATOM 6303 SG CYS H 23 86.334 119.950 93.457 1.00 60.59 S ATOM 6327 SG CYS H 26 86.871 118.957 97.118 1.00 60.89 S ATOM 6574 SG CYS H 58 89.419 121.199 95.113 1.00 59.44 S ATOM 6595 SG CYS H 61 88.821 117.293 94.799 1.00 62.53 S ATOM 6354 SG CYS H 30 88.273 124.298 107.582 1.00 57.99 S ATOM 6375 SG CYS H 33 88.726 122.462 111.187 1.00 59.97 S ATOM 6670 SG CYS H 72 86.715 125.615 110.709 1.00 55.97 S ATOM 6694 SG CYS H 75 90.552 125.427 110.396 1.00 53.96 S Time building chain proxies: 6.76, per 1000 atoms: 0.18 Number of scatterers: 38256 At special positions: 0 Unit cell: (168.3, 217.8, 234.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 199 16.00 P 79 15.00 O 7397 8.00 N 6560 7.00 C 24018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 11 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 49 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 85 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 61 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 23 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 26 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 58 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 75 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 33 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 30 " Number of angles added : 18 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8608 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 40 sheets defined 48.3% alpha, 15.4% beta 7 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.625A pdb=" N LYS B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 6.106A pdb=" N VAL B 139 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 153 Processing helix chain 'B' and resid 165 through 181 Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 194 through 209 Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.548A pdb=" N ASN B 247 " --> pdb=" O ARG B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 281 removed outlier: 3.957A pdb=" N ARG B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 330 through 346 Processing helix chain 'B' and resid 358 through 377 removed outlier: 3.894A pdb=" N GLY B 377 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 399 through 402 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.191A pdb=" N THR B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 507 through 518 Processing helix chain 'B' and resid 532 through 546 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 568 through 578 Processing helix chain 'B' and resid 583 through 595 Processing helix chain 'B' and resid 606 through 617 removed outlier: 3.968A pdb=" N PHE B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 637 Processing helix chain 'B' and resid 640 through 647 Processing helix chain 'B' and resid 650 through 671 Processing helix chain 'B' and resid 683 through 697 removed outlier: 3.820A pdb=" N ILE B 687 " --> pdb=" O ARG B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 762 Processing helix chain 'B' and resid 774 through 788 Processing helix chain 'H' and resid 47 through 55 removed outlier: 4.127A pdb=" N TYR H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY H 52 " --> pdb=" O CYS H 49 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER H 53 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'H' and resid 93 through 103 Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 535 through 548 Processing helix chain 'C' and resid 552 through 566 Processing helix chain 'C' and resid 569 through 582 Processing helix chain 'C' and resid 587 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 611 through 621 removed outlier: 3.656A pdb=" N TYR C 615 " --> pdb=" O ASN C 611 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 616 " --> pdb=" O ALA C 612 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 621 " --> pdb=" O LYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 635 Processing helix chain 'C' and resid 639 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 685 through 701 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 745 through 755 Processing helix chain 'A' and resid 798 through 824 Processing helix chain 'B1' and resid 379 through 396 Processing helix chain 'B1' and resid 400 through 408 Processing helix chain 'B1' and resid 468 through 472 removed outlier: 3.938A pdb=" N ILEB1 472 " --> pdb=" O PROB1 469 " (cutoff:3.500A) Processing helix chain 'B1' and resid 488 through 507 removed outlier: 3.649A pdb=" N GLNB1 492 " --> pdb=" O SERB1 488 " (cutoff:3.500A) Processing helix chain 'B1' and resid 508 through 522 removed outlier: 3.629A pdb=" N ALAB1 514 " --> pdb=" O PROB1 510 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLNB1 518 " --> pdb=" O ALAB1 514 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRB1 520 " --> pdb=" O LEUB1 516 " (cutoff:3.500A) Processing helix chain 'B1' and resid 522 through 527 removed outlier: 3.567A pdb=" N GLYB1 527 " --> pdb=" O ALAB1 523 " (cutoff:3.500A) Processing helix chain 'B1' and resid 527 through 540 removed outlier: 4.017A pdb=" N GLNB1 534 " --> pdb=" O PROB1 530 " (cutoff:3.500A) Proline residue: B1 537 - end of helix Processing helix chain 'B1' and resid 545 through 563 removed outlier: 3.636A pdb=" N LYSB1 562 " --> pdb=" O ARGB1 558 " (cutoff:3.500A) Processing helix chain 'B1' and resid 570 through 579 removed outlier: 3.853A pdb=" N VALB1 577 " --> pdb=" O LYSB1 573 " (cutoff:3.500A) Processing helix chain 'B1' and resid 580 through 584 removed outlier: 3.512A pdb=" N ILEB1 583 " --> pdb=" O PROB1 580 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASPB1 584 " --> pdb=" O LEUB1 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 580 through 584' Processing helix chain 'B1' and resid 586 through 605 removed outlier: 3.919A pdb=" N ARGB1 590 " --> pdb=" O ASPB1 586 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALAB1 603 " --> pdb=" O ASNB1 599 " (cutoff:3.500A) Processing helix chain 'B1' and resid 606 through 614 Processing helix chain 'B1' and resid 615 through 619 removed outlier: 3.724A pdb=" N ASPB1 618 " --> pdb=" O PROB1 615 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASNB1 619 " --> pdb=" O ASPB1 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 615 through 619' Processing helix chain 'B1' and resid 621 through 640 removed outlier: 3.575A pdb=" N VALB1 634 " --> pdb=" O ARGB1 630 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VALB1 635 " --> pdb=" O ALAB1 631 " (cutoff:3.500A) Processing helix chain 'B1' and resid 641 through 643 No H-bonds generated for 'chain 'B1' and resid 641 through 643' Processing helix chain 'B1' and resid 644 through 654 Processing helix chain 'B1' and resid 657 through 675 removed outlier: 3.601A pdb=" N ARGB1 661 " --> pdb=" O SERB1 657 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VALB1 668 " --> pdb=" O GLYB1 664 " (cutoff:3.500A) Processing helix chain 'B1' and resid 676 through 680 removed outlier: 3.782A pdb=" N ILEB1 679 " --> pdb=" O GLYB1 676 " (cutoff:3.500A) Processing helix chain 'B1' and resid 682 through 692 removed outlier: 3.524A pdb=" N GLUB1 688 " --> pdb=" O ARGB1 684 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILEB1 689 " --> pdb=" O SERB1 685 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILEB1 690 " --> pdb=" O LEUB1 686 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HISB1 692 " --> pdb=" O GLUB1 688 " (cutoff:3.500A) Processing helix chain 'B1' and resid 693 through 695 No H-bonds generated for 'chain 'B1' and resid 693 through 695' Processing helix chain 'B1' and resid 698 through 716 removed outlier: 3.544A pdb=" N ALAB1 706 " --> pdb=" O ARGB1 702 " (cutoff:3.500A) Processing helix chain 'B1' and resid 721 through 723 No H-bonds generated for 'chain 'B1' and resid 721 through 723' Processing helix chain 'B1' and resid 724 through 736 removed outlier: 3.642A pdb=" N LEUB1 728 " --> pdb=" O PHEB1 724 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYSB1 729 " --> pdb=" O ASPB1 725 " (cutoff:3.500A) Proline residue: B1 730 - end of helix removed outlier: 3.577A pdb=" N LYSB1 733 " --> pdb=" O LYSB1 729 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARGB1 736 " --> pdb=" O TRPB1 732 " (cutoff:3.500A) Processing helix chain 'B1' and resid 740 through 754 removed outlier: 3.562A pdb=" N TYRB1 752 " --> pdb=" O LYSB1 748 " (cutoff:3.500A) Processing helix chain 'B1' and resid 758 through 777 removed outlier: 3.771A pdb=" N ASNB1 763 " --> pdb=" O ALAB1 759 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYRB1 764 " --> pdb=" O GLUB1 760 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLUB1 768 " --> pdb=" O TYRB1 764 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEUB1 771 " --> pdb=" O ARGB1 767 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILEB1 772 " --> pdb=" O GLUB1 768 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARGB1 775 " --> pdb=" O LEUB1 771 " (cutoff:3.500A) Processing helix chain 'B1' and resid 781 through 798 removed outlier: 3.646A pdb=" N LYSB1 793 " --> pdb=" O LEUB1 789 " (cutoff:3.500A) Processing helix chain 'B1' and resid 802 through 810 removed outlier: 4.087A pdb=" N ILEB1 806 " --> pdb=" O GLUB1 802 " (cutoff:3.500A) Processing helix chain 'B1' and resid 810 through 817 removed outlier: 3.943A pdb=" N LYSB1 816 " --> pdb=" O PROB1 812 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HISB1 817 " --> pdb=" O PROB1 813 " (cutoff:3.500A) Processing helix chain 'B1' and resid 820 through 825 Processing helix chain 'B1' and resid 826 through 845 removed outlier: 3.863A pdb=" N VALB1 834 " --> pdb=" O TYRB1 830 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYSB1 843 " --> pdb=" O GLUB1 839 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VALB1 844 " --> pdb=" O LEUB1 840 " (cutoff:3.500A) Processing helix chain 'B1' and resid 845 through 854 removed outlier: 3.540A pdb=" N ARGB1 852 " --> pdb=" O GLUB1 848 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILEB1 853 " --> pdb=" O ILEB1 849 " (cutoff:3.500A) Processing helix chain 'B1' and resid 855 through 859 Processing helix chain 'B1' and resid 861 through 880 removed outlier: 3.508A pdb=" N LYSB1 866 " --> pdb=" O GLUB1 862 " (cutoff:3.500A) Processing helix chain 'B1' and resid 885 through 903 removed outlier: 3.597A pdb=" N GLNB1 891 " --> pdb=" O LYSB1 887 " (cutoff:3.500A) Processing helix chain 'B1' and resid 908 through 922 removed outlier: 3.640A pdb=" N VALB1 917 " --> pdb=" O GLYB1 913 " (cutoff:3.500A) Processing helix chain 'B1' and resid 923 through 927 removed outlier: 3.928A pdb=" N LYSB1 926 " --> pdb=" O LYSB1 923 " (cutoff:3.500A) Proline residue: B1 927 - end of helix No H-bonds generated for 'chain 'B1' and resid 923 through 927' Processing helix chain 'B1' and resid 928 through 939 Processing helix chain 'B1' and resid 944 through 965 removed outlier: 3.701A pdb=" N ARGB1 948 " --> pdb=" O SERB1 944 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VALB1 960 " --> pdb=" O SERB1 956 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VALB1 961 " --> pdb=" O ARGB1 957 " (cutoff:3.500A) Processing helix chain 'B1' and resid 967 through 981 removed outlier: 3.878A pdb=" N METB1 971 " --> pdb=" O GLUB1 967 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HISB1 973 " --> pdb=" O LYSB1 969 " (cutoff:3.500A) Processing helix chain 'B1' and resid 986 through 1005 removed outlier: 3.546A pdb=" N SERB1 992 " --> pdb=" O GLUB1 988 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLYB11005 " --> pdb=" O VALB11001 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1012 through 1015 Processing helix chain 'B1' and resid 1016 through 1021 Processing helix chain 'B1' and resid 1022 through 1026 Processing helix chain 'B1' and resid 1028 through 1046 removed outlier: 3.738A pdb=" N ASNB11034 " --> pdb=" O LYSB11030 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1047 through 1050 removed outlier: 3.522A pdb=" N VALB11050 " --> pdb=" O ALAB11047 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1047 through 1050' Processing helix chain 'B1' and resid 1051 through 1065 removed outlier: 3.737A pdb=" N LEUB11063 " --> pdb=" O CYSB11059 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLUB11064 " --> pdb=" O PHEB11060 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEUB11065 " --> pdb=" O GLUB11061 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1066 through 1068 No H-bonds generated for 'chain 'B1' and resid 1066 through 1068' Processing helix chain 'B1' and resid 1070 through 1089 removed outlier: 3.530A pdb=" N ASNB11079 " --> pdb=" O ARGB11075 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEB11081 " --> pdb=" O THRB11077 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYB11082 " --> pdb=" O VALB11078 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1089 through 1100 removed outlier: 4.559A pdb=" N VALB11093 " --> pdb=" O GLYB11089 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASNB11100 " --> pdb=" O THRB11096 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1108 through 1123 Processing helix chain 'B1' and resid 1124 through 1127 Processing helix chain 'B1' and resid 1128 through 1136 removed outlier: 3.768A pdb=" N GLUB11135 " --> pdb=" O ALAB11131 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYRB11136 " --> pdb=" O LEUB11132 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1140 through 1159 removed outlier: 3.512A pdb=" N LEUB11148 " --> pdb=" O GLNB11144 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLUB11156 " --> pdb=" O SERB11152 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLYB11159 " --> pdb=" O PHEB11155 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1160 through 1164 removed outlier: 3.568A pdb=" N LYSB11163 " --> pdb=" O GLUB11160 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASPB11164 " --> pdb=" O METB11161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1160 through 1164' Processing helix chain 'B1' and resid 1165 through 1179 removed outlier: 3.549A pdb=" N VALB11169 " --> pdb=" O TYRB11165 " (cutoff:3.500A) Proline residue: B11171 - end of helix removed outlier: 3.576A pdb=" N ASPB11179 " --> pdb=" O ASPB11175 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1181 through 1199 removed outlier: 3.523A pdb=" N ALAB11190 " --> pdb=" O GLNB11186 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1204 through 1216 removed outlier: 4.108A pdb=" N LEUB11208 " --> pdb=" O CYSB11204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASNB11213 " --> pdb=" O ASNB11209 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYRB11214 " --> pdb=" O HISB11210 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1217 through 1221 removed outlier: 4.196A pdb=" N PHEB11220 " --> pdb=" O PROB11217 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1223 through 1242 removed outlier: 3.675A pdb=" N VALB11239 " --> pdb=" O GLUB11235 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1242 through 1251 removed outlier: 3.827A pdb=" N METB11246 " --> pdb=" O GLYB11242 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1258 through 1276 removed outlier: 3.646A pdb=" N VALB11264 " --> pdb=" O LYSB11260 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1278 through 1284 removed outlier: 3.680A pdb=" N ALAB11282 " --> pdb=" O ALAB11279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYRB11284 " --> pdb=" O ILEB11281 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1297 through 1302 removed outlier: 3.747A pdb=" N ASPB11301 " --> pdb=" O ARGB11297 " (cutoff:3.500A) Processing helix chain 'B2' and resid 452 through 459 removed outlier: 4.213A pdb=" N ASNB2 458 " --> pdb=" O LEUB2 454 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARGB2 459 " --> pdb=" O ARGB2 455 " (cutoff:3.500A) Processing helix chain 'B2' and resid 461 through 467 removed outlier: 3.587A pdb=" N GLNB2 467 " --> pdb=" O ALAB2 463 " (cutoff:3.500A) Processing helix chain 'B2' and resid 476 through 480 removed outlier: 3.997A pdb=" N VALB2 480 " --> pdb=" O METB2 477 " (cutoff:3.500A) Processing helix chain 'B2' and resid 484 through 493 Processing helix chain 'B2' and resid 501 through 505 removed outlier: 3.545A pdb=" N TRPB2 504 " --> pdb=" O PROB2 501 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYSB2 505 " --> pdb=" O ARGB2 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 501 through 505' Processing helix chain 'B2' and resid 525 through 530 Processing helix chain 'B2' and resid 532 through 548 Processing helix chain 'B2' and resid 551 through 561 removed outlier: 3.640A pdb=" N ARGB2 558 " --> pdb=" O ARGB2 554 " (cutoff:3.500A) Proline residue: B2 559 - end of helix Processing helix chain 'B2' and resid 568 through 578 removed outlier: 3.649A pdb=" N PHEB2 575 " --> pdb=" O LEUB2 571 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRPB2 578 " --> pdb=" O ALAB2 574 " (cutoff:3.500A) Processing helix chain 'B2' and resid 594 through 603 removed outlier: 3.695A pdb=" N GLUB2 598 " --> pdb=" O GLYB2 594 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARGB2 600 " --> pdb=" O GLUB2 596 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEUB2 601 " --> pdb=" O PHEB2 597 " (cutoff:3.500A) Processing helix chain 'B2' and resid 610 through 617 removed outlier: 4.032A pdb=" N ARGB2 614 " --> pdb=" O SERB2 610 " (cutoff:3.500A) Processing helix chain 'B2' and resid 622 through 628 removed outlier: 4.446A pdb=" N HISB2 626 " --> pdb=" O PROB2 623 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VALB2 628 " --> pdb=" O ALAB2 625 " (cutoff:3.500A) Processing helix chain 'B2' and resid 632 through 639 Processing helix chain 'B3' and resid 190 through 194 Processing helix chain 'B3' and resid 429 through 432 removed outlier: 3.761A pdb=" N ARGB3 432 " --> pdb=" O ARGB3 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 429 through 432' Processing helix chain 'B3' and resid 620 through 624 removed outlier: 4.031A pdb=" N CYSB3 624 " --> pdb=" O PROB3 621 " (cutoff:3.500A) Processing helix chain 'B3' and resid 808 through 827 removed outlier: 3.566A pdb=" N ALAB3 813 " --> pdb=" O GLUB3 809 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAB3 827 " --> pdb=" O METB3 823 " (cutoff:3.500A) Processing helix chain 'B3' and resid 832 through 845 Processing helix chain 'B3' and resid 848 through 853 Processing helix chain 'B3' and resid 1072 through 1077 removed outlier: 3.777A pdb=" N TRPB31077 " --> pdb=" O ASNB31073 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1134 through 1152 removed outlier: 3.587A pdb=" N HISB31138 " --> pdb=" O SERB31134 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASPB31139 " --> pdb=" O HISB31135 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SERB31150 " --> pdb=" O METB31146 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1159 through 1165 Processing helix chain 'B3' and resid 1176 through 1181 Processing helix chain 'B3' and resid 1186 through 1197 Processing helix chain 'B3' and resid 1200 through 1214 removed outlier: 3.555A pdb=" N ILEB31211 " --> pdb=" O LYSB31207 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGB31212 " --> pdb=" O LEUB31208 " (cutoff:3.500A) Processing helix chain 'B4' and resid 10 through 12 No H-bonds generated for 'chain 'B4' and resid 10 through 12' Processing helix chain 'B4' and resid 25 through 35 Processing helix chain 'B4' and resid 63 through 75 removed outlier: 3.529A pdb=" N LYSB4 72 " --> pdb=" O ASPB4 68 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N METB4 74 " --> pdb=" O ALAB4 70 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASNB4 75 " --> pdb=" O ILEB4 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 112 through 122 removed outlier: 3.757A pdb=" N ALAB4 122 " --> pdb=" O ASPB4 118 " (cutoff:3.500A) Processing helix chain 'B4' and resid 151 through 163 Processing helix chain 'B4' and resid 189 through 199 Processing helix chain 'B4' and resid 199 through 206 Processing helix chain 'B4' and resid 206 through 211 removed outlier: 3.626A pdb=" N LEUB4 210 " --> pdb=" O ARGB4 206 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHEB4 211 " --> pdb=" O PROB4 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B4' and resid 206 through 211' Processing helix chain 'B5' and resid 9 through 18 removed outlier: 3.563A pdb=" N LEUB5 14 " --> pdb=" O GLNB5 10 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYSB5 17 " --> pdb=" O HISB5 13 " (cutoff:3.500A) Processing helix chain 'B5' and resid 27 through 46 removed outlier: 3.518A pdb=" N ASNB5 34 " --> pdb=" O GLUB5 30 " (cutoff:3.500A) Processing helix chain 'B5' and resid 46 through 57 Processing helix chain 'B5' and resid 60 through 72 Processing helix chain 'B6' and resid 5 through 11 Processing helix chain 'B6' and resid 31 through 41 removed outlier: 3.769A pdb=" N LYSB6 41 " --> pdb=" O ASPB6 37 " (cutoff:3.500A) Processing helix chain 'B6' and resid 53 through 57 Processing helix chain 'B6' and resid 66 through 78 removed outlier: 3.697A pdb=" N SERB6 78 " --> pdb=" O CYSB6 74 " (cutoff:3.500A) Processing helix chain 'B6' and resid 93 through 98 Processing helix chain 'A1' and resid 161 through 189 removed outlier: 6.343A pdb=" N ARGA1 179 " --> pdb=" O ALAA1 175 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N GLNA1 180 " --> pdb=" O ARGA1 176 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEA1 181 " --> pdb=" O ASNA1 177 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUA1 182 " --> pdb=" O GLYA1 178 " (cutoff:3.500A) Processing helix chain 'A1' and resid 192 through 199 removed outlier: 3.513A pdb=" N PHEA1 195 " --> pdb=" O ASNA1 192 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHEA1 197 " --> pdb=" O GLNA1 194 " (cutoff:3.500A) Processing helix chain 'A1' and resid 204 through 220 Processing helix chain 'A1' and resid 224 through 233 Processing helix chain 'A1' and resid 237 through 244 removed outlier: 4.072A pdb=" N ASPA1 241 " --> pdb=" O ARGA1 237 " (cutoff:3.500A) Processing helix chain 'A1' and resid 244 through 273 removed outlier: 5.353A pdb=" N ALAA1 250 " --> pdb=" O ARGA1 246 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYSA1 251 " --> pdb=" O VALA1 247 " (cutoff:3.500A) Processing helix chain 'A1' and resid 300 through 318 removed outlier: 4.455A pdb=" N GLYA1 305 " --> pdb=" O PROA1 301 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALAA1 306 " --> pdb=" O GLUA1 302 " (cutoff:3.500A) Processing helix chain 'A2' and resid 20 through 36 Processing helix chain 'A2' and resid 65 through 74 removed outlier: 4.027A pdb=" N GLNA2 74 " --> pdb=" O LEUA2 70 " (cutoff:3.500A) Processing helix chain 'A2' and resid 75 through 92 Processing helix chain 'A3' and resid 3 through 28 Processing helix chain 'A3' and resid 32 through 63 Processing helix chain 'A3' and resid 66 through 76 Processing helix chain 'A3' and resid 79 through 98 Processing helix chain 'A3' and resid 105 through 119 removed outlier: 4.226A pdb=" N GLUA3 109 " --> pdb=" O PROA3 105 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHEA3 110 " --> pdb=" O META3 106 " (cutoff:3.500A) Processing helix chain 'A3' and resid 119 through 124 Processing helix chain 'A3' and resid 125 through 127 No H-bonds generated for 'chain 'A3' and resid 125 through 127' Processing helix chain 'A3' and resid 142 through 151 Processing helix chain 'A3' and resid 159 through 167 removed outlier: 3.620A pdb=" N SERA3 165 " --> pdb=" O ILEA3 161 " (cutoff:3.500A) Processing helix chain 'A3' and resid 169 through 173 Processing helix chain 'A3' and resid 174 through 178 Processing helix chain 'A3' and resid 179 through 201 Processing helix chain 'A3' and resid 205 through 224 Processing helix chain 'A3' and resid 317 through 334 Processing helix chain 'A3' and resid 334 through 350 Processing helix chain 'A3' and resid 393 through 400 removed outlier: 3.551A pdb=" N HISA3 400 " --> pdb=" O LEUA3 396 " (cutoff:3.500A) Processing helix chain 'A3' and resid 418 through 425 Processing helix chain 'A3' and resid 428 through 439 removed outlier: 3.533A pdb=" N LEUA3 438 " --> pdb=" O GLYA3 434 " (cutoff:3.500A) Processing helix chain 'A3' and resid 443 through 447 Processing helix chain 'A3' and resid 451 through 470 removed outlier: 3.522A pdb=" N SERA3 457 " --> pdb=" O GLUA3 453 " (cutoff:3.500A) Processing helix chain 'A3' and resid 472 through 477 removed outlier: 3.571A pdb=" N GLUA3 477 " --> pdb=" O PROA3 473 " (cutoff:3.500A) Processing helix chain 'A3' and resid 488 through 497 removed outlier: 4.195A pdb=" N ARGA3 497 " --> pdb=" O GLUA3 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.795A pdb=" N GLY B 218 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR B 237 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER B 220 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 188 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N MET B 236 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N CYS B 190 " --> pdb=" O MET B 236 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 187 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE B 258 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 189 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 383 through 388 removed outlier: 6.741A pdb=" N LEU B 352 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER B 420 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU B 354 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP B 351 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE B 437 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 353 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 434 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE B 482 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 436 " --> pdb=" O PHE B 482 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B 320 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG B 483 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE B 322 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 139 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR B 323 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ARG C 137 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 441 through 448 removed outlier: 3.585A pdb=" N LEU B 741 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 738 " --> pdb=" O ARG B 748 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN B 745 " --> pdb=" O VAL B 718 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.981A pdb=" N ALA H 18 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AA6, first strand: chain 'H' and resid 39 through 42 removed outlier: 6.376A pdb=" N TYR H 71 " --> pdb=" O CYS H 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 642 through 643 Processing sheet with id=AA8, first strand: chain 'B1' and resid 412 through 414 removed outlier: 3.633A pdb=" N GLNB6 47 " --> pdb=" O VALB6 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B3' and resid 1101 through 1107 removed outlier: 3.792A pdb=" N SERB31103 " --> pdb=" O THRB31120 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILEB31126 " --> pdb=" O LEUB3 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B3' and resid 16 through 20 removed outlier: 3.889A pdb=" N PHEB3 16 " --> pdb=" O SERB3 33 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEUB3 38 " --> pdb=" O THRB3 55 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THRB3 55 " --> pdb=" O LEUB3 38 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEUB3 40 " --> pdb=" O LEUB3 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B3' and resid 62 through 68 removed outlier: 3.526A pdb=" N VALB3 80 " --> pdb=" O VALB3 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VALB3 88 " --> pdb=" O VALB3 80 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SERB3 82 " --> pdb=" O ARGB3 86 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ARGB3 86 " --> pdb=" O SERB3 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILEB3 87 " --> pdb=" O GLNB3 104 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLNB3 104 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILEB3 89 " --> pdb=" O ILEB3 102 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METB3 98 " --> pdb=" O GLNB3 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B3' and resid 120 through 123 Processing sheet with id=AB4, first strand: chain 'B3' and resid 120 through 123 Processing sheet with id=AB5, first strand: chain 'B3' and resid 166 through 173 removed outlier: 5.941A pdb=" N VALB3 167 " --> pdb=" O METB3 187 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N METB3 187 " --> pdb=" O VALB3 167 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HISB3 169 " --> pdb=" O LEUB3 185 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N METB3 181 " --> pdb=" O VALB3 173 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEUB3 208 " --> pdb=" O SERB3 225 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SERB3 225 " --> pdb=" O LEUB3 208 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHEB3 210 " --> pdb=" O LYSB3 223 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HISB3 219 " --> pdb=" O ASPB3 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B3' and resid 232 through 238 removed outlier: 3.858A pdb=" N PHEB3 234 " --> pdb=" O CYSB3 251 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLYB3 247 " --> pdb=" O VALB3 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VALB3 248 " --> pdb=" O LYSB3 259 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYRB3 255 " --> pdb=" O SERB3 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B3' and resid 273 through 274 removed outlier: 5.953A pdb=" N ARGB3 273 " --> pdb=" O PHEB3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B3' and resid 287 through 294 removed outlier: 6.777A pdb=" N GLNB3 304 " --> pdb=" O VALB3 288 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SERB3 290 " --> pdb=" O LEUB3 302 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEUB3 302 " --> pdb=" O SERB3 290 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THRB3 292 " --> pdb=" O PHEB3 300 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHEB3 300 " --> pdb=" O THRB3 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHEB3 299 " --> pdb=" O LEUB3 315 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEUB3 315 " --> pdb=" O PHEB3 299 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASPB3 309 " --> pdb=" O THRB3 305 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILEB3 310 " --> pdb=" O PHEB3 330 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLUB3 324 " --> pdb=" O GLUB3 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B3' and resid 336 through 342 removed outlier: 7.370A pdb=" N ALAB3 350 " --> pdb=" O ALAB3 337 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N METB3 339 " --> pdb=" O PHEB3 348 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHEB3 348 " --> pdb=" O METB3 339 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VALB3 341 " --> pdb=" O PHEB3 346 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHEB3 346 " --> pdb=" O VALB3 341 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUB3 358 " --> pdb=" O ASPB3 399 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASPB3 399 " --> pdb=" O LEUB3 358 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLNB3 360 " --> pdb=" O LEUB3 397 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEUB3 397 " --> pdb=" O GLNB3 360 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 407 through 413 removed outlier: 3.641A pdb=" N PHEB3 409 " --> pdb=" O ALAB3 426 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 445 through 451 removed outlier: 5.263A pdb=" N GLUB3 446 " --> pdb=" O ALAB3 766 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALAB3 766 " --> pdb=" O GLUB3 446 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALAB3 448 " --> pdb=" O ILEB3 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 458 through 462 removed outlier: 4.241A pdb=" N VALB3 484 " --> pdb=" O VALB3 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B3' and resid 507 through 510 removed outlier: 3.860A pdb=" N HISB3 526 " --> pdb=" O ASNB3 534 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASNB3 534 " --> pdb=" O HISB3 526 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B3' and resid 544 through 548 removed outlier: 3.618A pdb=" N ASNB3 575 " --> pdb=" O GLUB3 567 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B3' and resid 587 through 592 removed outlier: 4.023A pdb=" N CYSB3 589 " --> pdb=" O GLYB3 608 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THRB3 613 " --> pdb=" O LEUB3 609 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VALB3 614 " --> pdb=" O METB3 630 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N METB3 630 " --> pdb=" O VALB3 614 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILEB3 616 " --> pdb=" O LEUB3 628 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SERB3 618 " --> pdb=" O GLNB3 626 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLNB3 626 " --> pdb=" O SERB3 618 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B3' and resid 637 through 643 removed outlier: 4.198A pdb=" N SERB3 639 " --> pdb=" O GLYB3 668 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 700 through 706 removed outlier: 3.639A pdb=" N LYSB3 700 " --> pdb=" O METB3 715 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 784 through 790 removed outlier: 3.750A pdb=" N THRB3 784 " --> pdb=" O THRB3 802 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILEB3 800 " --> pdb=" O ARGB3 786 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHEB3 788 " --> pdb=" O ILEB3 798 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILEB3 798 " --> pdb=" O PHEB3 788 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N SERB3 864 " --> pdb=" O GLNB3 881 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLNB3 881 " --> pdb=" O SERB3 864 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILEB3 866 " --> pdb=" O LEUB3 879 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEUB3 879 " --> pdb=" O ILEB3 866 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VALB3 868 " --> pdb=" O LEUB3 877 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 886 through 894 removed outlier: 5.806A pdb=" N ALAB3 888 " --> pdb=" O ALAB3 910 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALAB3 910 " --> pdb=" O ALAB3 888 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SERB3 890 " --> pdb=" O GLYB3 908 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLYB3 923 " --> pdb=" O PROB3 944 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VALB3 925 " --> pdb=" O LYSB3 942 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYSB3 942 " --> pdb=" O VALB3 925 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THRB3 927 " --> pdb=" O LEUB3 940 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 951 through 955 removed outlier: 4.172A pdb=" N ALAB3 951 " --> pdb=" O GLYB3 962 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEUB3 967 " --> pdb=" O GLUB3 982 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLUB3 982 " --> pdb=" O LEUB3 967 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VALB3 969 " --> pdb=" O LYSB3 980 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLYB3 973 " --> pdb=" O LYSB3 976 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYSB3 976 " --> pdb=" O GLYB3 973 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 990 through 995 removed outlier: 3.818A pdb=" N GLYB3 992 " --> pdb=" O SERB31003 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHEB31009 " --> pdb=" O ASPB31026 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASPB31026 " --> pdb=" O PHEB31009 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TRPB31011 " --> pdb=" O PHEB31024 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLNB31087 " --> pdb=" O PHEB31024 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B3' and resid 1033 through 1038 removed outlier: 7.072A pdb=" N ALAB31047 " --> pdb=" O THRB31034 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALAB31036 " --> pdb=" O ALAB31045 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALAB31045 " --> pdb=" O ALAB31036 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEUB31038 " --> pdb=" O THRB31043 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THRB31043 " --> pdb=" O LEUB31038 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASNB31052 " --> pdb=" O ASPB31048 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILEB31053 " --> pdb=" O ASNB31094 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASNB31094 " --> pdb=" O ILEB31053 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VALB31055 " --> pdb=" O ILEB31092 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B4' and resid 39 through 43 removed outlier: 3.707A pdb=" N ASNB4 41 " --> pdb=" O GLUB4 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALB4 59 " --> pdb=" O VALB4 15 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILEB4 77 " --> pdb=" O ILEB4 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B4' and resid 131 through 134 removed outlier: 7.347A pdb=" N LYSB4 131 " --> pdb=" O TYRB4 144 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYRB4 144 " --> pdb=" O LYSB4 131 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N METB4 133 " --> pdb=" O LYSB4 142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALAB4 145 " --> pdb=" O ILEB4 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B6' and resid 81 through 82 Processing sheet with id=AD8, first strand: chain 'A1' and resid 279 through 284 removed outlier: 6.246A pdb=" N VALA1 280 " --> pdb=" O ALAA2 180 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LYSA2 182 " --> pdb=" O VALA1 280 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N VALA1 282 " --> pdb=" O LYSA2 182 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N THRA1 284 " --> pdb=" O PROA2 184 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A2' and resid 46 through 47 removed outlier: 3.587A pdb=" N THRA2 61 " --> pdb=" O CYSA2 56 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.744A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HISA2 211 " --> pdb=" O ASPA2 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.744A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A3' and resid 406 through 408 Processing sheet with id=AE4, first strand: chain 'A3' and resid 479 through 480 1745 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10707 1.33 - 1.45: 6647 1.45 - 1.57: 21377 1.57 - 1.69: 156 1.69 - 1.81: 318 Bond restraints: 39205 Sorted by residual: bond pdb=" N ILEB11303 " pdb=" CA ILEB11303 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.32e-02 5.74e+03 8.54e+00 bond pdb=" N ASPB4 21 " pdb=" CA ASPB4 21 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.13e+00 bond pdb=" N VALB4 24 " pdb=" CA VALB4 24 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.35e-02 5.49e+03 7.57e+00 bond pdb=" N GLUB2 710 " pdb=" CA GLUB2 710 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 6.97e+00 bond pdb=" N GLUB4 22 " pdb=" CA GLUB4 22 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.66e+00 ... (remaining 39200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 52992 2.49 - 4.98: 350 4.98 - 7.47: 17 7.47 - 9.96: 5 9.96 - 12.45: 1 Bond angle restraints: 53365 Sorted by residual: angle pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sigma weight residual 117.70 123.55 -5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" C ILEB2 566 " pdb=" N ASPB2 567 " pdb=" CA ASPB2 567 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" C ASPB3 263 " pdb=" N GLNB3 264 " pdb=" CA GLNB3 264 " ideal model delta sigma weight residual 121.61 116.73 4.88 1.39e+00 5.18e-01 1.23e+01 angle pdb=" N PROB2 713 " pdb=" CA PROB2 713 " pdb=" CB PROB2 713 " ideal model delta sigma weight residual 103.00 99.21 3.79 1.10e+00 8.26e-01 1.19e+01 angle pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C6 U R 12 " ideal model delta sigma weight residual 121.20 116.39 4.81 1.40e+00 5.10e-01 1.18e+01 ... (remaining 53360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 23115 35.77 - 71.53: 845 71.53 - 107.30: 40 107.30 - 143.06: 3 143.06 - 178.83: 6 Dihedral angle restraints: 24009 sinusoidal: 10664 harmonic: 13345 Sorted by residual: dihedral pdb=" O4' U R 12 " pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sinusoidal sigma weight residual 200.00 69.36 130.64 1 1.50e+01 4.44e-03 7.05e+01 dihedral pdb=" O4' U R 9 " pdb=" C1' U R 9 " pdb=" N1 U R 9 " pdb=" C2 U R 9 " ideal model delta sinusoidal sigma weight residual -128.00 50.23 -178.23 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 8 " pdb=" C1' U R 8 " pdb=" N1 U R 8 " pdb=" C2 U R 8 " ideal model delta sinusoidal sigma weight residual -128.00 44.13 -172.13 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 24006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 5848 0.114 - 0.228: 67 0.228 - 0.341: 0 0.341 - 0.455: 1 0.455 - 0.569: 1 Chirality restraints: 5917 Sorted by residual: chirality pdb=" P U R -18 " pdb=" OP1 U R -18 " pdb=" OP2 U R -18 " pdb=" O5' U R -18 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" P U R -17 " pdb=" OP1 U R -17 " pdb=" OP2 U R -17 " pdb=" O5' U R -17 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CB THRB3 204 " pdb=" CA THRB3 204 " pdb=" OG1 THRB3 204 " pdb=" CG2 THRB3 204 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 5914 not shown) Planarity restraints: 6673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRB1 508 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PROB1 509 " -0.086 5.00e-02 4.00e+02 pdb=" CA PROB1 509 " 0.026 5.00e-02 4.00e+02 pdb=" CD PROB1 509 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEA3 392 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PROA3 393 " 0.085 5.00e-02 4.00e+02 pdb=" CA PROA3 393 " -0.025 5.00e-02 4.00e+02 pdb=" CD PROA3 393 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U R 2 " 0.027 2.00e-02 2.50e+03 1.30e-02 3.80e+00 pdb=" N1 U R 2 " -0.025 2.00e-02 2.50e+03 pdb=" C2 U R 2 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U R 2 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U R 2 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U R 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U R 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U R 2 " -0.007 2.00e-02 2.50e+03 ... (remaining 6670 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 10522 2.81 - 3.33: 34762 3.33 - 3.86: 60997 3.86 - 4.38: 70284 4.38 - 4.90: 119990 Nonbonded interactions: 296555 Sorted by model distance: nonbonded pdb=" N2 G 2 33 " pdb=" O2 U R 1 " model vdw 2.291 2.496 nonbonded pdb=" O6 G 2 33 " pdb=" O4 U R 1 " model vdw 2.346 2.432 nonbonded pdb=" O CYSB11123 " pdb=" CA SERB11124 " model vdw 2.429 2.776 nonbonded pdb=" N1 G 2 33 " pdb=" N3 U R 1 " model vdw 2.458 2.560 nonbonded pdb=" O5' G 2 31 " pdb=" O4' G 2 31 " model vdw 2.481 2.432 ... (remaining 296550 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 38.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 39217 Z= 0.142 Angle : 0.511 13.550 53383 Z= 0.278 Chirality : 0.041 0.569 5917 Planarity : 0.004 0.050 6673 Dihedral : 17.102 178.829 15401 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.10 % Allowed : 18.44 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 4527 helix: 1.03 (0.12), residues: 1919 sheet: 0.58 (0.20), residues: 692 loop : -0.35 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGB1 702 TYR 0.017 0.001 TYRB1 830 PHE 0.018 0.001 PHE C 120 TRP 0.019 0.001 TRPA3 387 HIS 0.005 0.001 HISB11028 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (39205) covalent geometry : angle 0.50024 / 0.28 (53365) hydrogen bonds : bond 0.22908 / 18.59 ( 1740) hydrogen bonds : angle 6.74025 / 5.54 ( 4974) metal coordination : bond 0.00511 / 0.34 ( 12) metal coordination : angle 5.71357 / 10.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 620 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.6695 (t0) cc_final: 0.6272 (p0) REVERT: B 496 ASP cc_start: 0.6273 (m-30) cc_final: 0.6067 (p0) REVERT: B 537 MET cc_start: 0.2728 (mtt) cc_final: 0.1465 (ptt) REVERT: B 655 MET cc_start: 0.3549 (mmm) cc_final: 0.2975 (ptt) REVERT: B 668 MET cc_start: 0.1496 (mtp) cc_final: 0.1210 (mtp) REVERT: C 560 MET cc_start: 0.4081 (mmm) cc_final: 0.2984 (mtt) REVERT: A 799 TYR cc_start: 0.7216 (t80) cc_final: 0.6648 (t80) REVERT: B1 592 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7801 (tm-30) REVERT: B1 656 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7388 (tmtt) REVERT: B1 690 ILE cc_start: 0.9060 (mm) cc_final: 0.8851 (mm) REVERT: B1 704 ILE cc_start: 0.8836 (tp) cc_final: 0.8567 (tp) REVERT: B1 908 SER cc_start: 0.8662 (m) cc_final: 0.8397 (t) REVERT: B1 949 GLN cc_start: 0.8270 (tt0) cc_final: 0.8036 (tt0) REVERT: B1 970 LEU cc_start: 0.8218 (tp) cc_final: 0.7724 (tp) REVERT: B1 979 TYR cc_start: 0.8596 (t80) cc_final: 0.8359 (t80) REVERT: B3 447 MET cc_start: 0.6260 (mmm) cc_final: 0.5696 (mmp) REVERT: B3 645 MET cc_start: 0.4855 (ppp) cc_final: 0.3826 (tpp) REVERT: B4 1 MET cc_start: 0.6741 (tmm) cc_final: 0.6524 (ttp) REVERT: B4 53 HIS cc_start: 0.6485 (OUTLIER) cc_final: 0.6170 (p-80) REVERT: B4 101 ASN cc_start: 0.4051 (m-40) cc_final: 0.3738 (t0) REVERT: B4 117 TYR cc_start: 0.6562 (t80) cc_final: 0.6314 (t80) REVERT: B4 148 ASN cc_start: 0.3350 (t0) cc_final: 0.3116 (m110) REVERT: B6 101 MET cc_start: 0.3661 (ptp) cc_final: 0.2145 (ppp) REVERT: A2 31 ARG cc_start: 0.2786 (mpt180) cc_final: 0.1570 (mtt-85) REVERT: A2 45 TYR cc_start: 0.8120 (m-80) cc_final: 0.7899 (m-10) REVERT: A3 106 MET cc_start: 0.0410 (mtp) cc_final: -0.0951 (tpt) REVERT: A3 463 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8258 (ttpt) outliers start: 4 outliers final: 1 residues processed: 624 average time/residue: 0.2365 time to fit residues: 234.8802 Evaluate side-chains 354 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B4 residue 53 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 570 GLN B 717 GLN B 720 GLN B 737 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 459 GLN B1 738 HIS B1 903 GLN B1 931 GLN ** B11256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 666 HIS B3 138 GLN A2 167 GLN ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 98 HIS A3 425 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.209878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131900 restraints weight = 71242.782| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 5.77 r_work: 0.3266 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39217 Z= 0.163 Angle : 0.633 15.438 53383 Z= 0.325 Chirality : 0.043 0.293 5917 Planarity : 0.005 0.064 6673 Dihedral : 13.009 179.871 6226 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.90 % Allowed : 18.61 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.13), residues: 4527 helix: 1.43 (0.12), residues: 1959 sheet: 0.62 (0.20), residues: 703 loop : -0.32 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGA2 164 TYR 0.028 0.001 TYRB1 623 PHE 0.023 0.001 PHE C 562 TRP 0.037 0.002 TRPA3 387 HIS 0.017 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (39205) covalent geometry : angle 0.62306 / 0.32 (53365) hydrogen bonds : bond 0.06308 / 5.16 ( 1740) hydrogen bonds : angle 5.00219 / 4.17 ( 4974) metal coordination : bond 0.00393 / 0.25 ( 12) metal coordination : angle 5.96271 / 10.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 362 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.7929 (t0) cc_final: 0.7456 (p0) REVERT: B 537 MET cc_start: 0.3144 (mtt) cc_final: 0.1934 (ptt) REVERT: B 655 MET cc_start: 0.3758 (mmm) cc_final: 0.3164 (ptt) REVERT: B 668 MET cc_start: 0.0974 (mtp) cc_final: 0.0737 (mtp) REVERT: H 103 LYS cc_start: 0.6957 (tppt) cc_final: 0.6742 (ttmt) REVERT: A 807 MET cc_start: 0.6980 (tpt) cc_final: 0.6754 (tpt) REVERT: B1 540 MET cc_start: 0.8002 (tpt) cc_final: 0.7553 (tpt) REVERT: B1 592 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7397 (tm-30) REVERT: B1 632 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B1 656 LYS cc_start: 0.8346 (mmtm) cc_final: 0.7576 (tmtt) REVERT: B1 690 ILE cc_start: 0.9007 (mm) cc_final: 0.8713 (mt) REVERT: B1 818 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B1 870 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8935 (mt-10) REVERT: B1 907 ASP cc_start: 0.7193 (t0) cc_final: 0.6783 (m-30) REVERT: B1 1019 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7397 (tpt170) REVERT: B1 1057 ARG cc_start: 0.8285 (mtp85) cc_final: 0.8049 (ptp-170) REVERT: B3 29 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: B3 114 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8207 (ttm170) REVERT: B3 447 MET cc_start: 0.5637 (mmm) cc_final: 0.4896 (mmp) REVERT: B3 645 MET cc_start: 0.4915 (ppp) cc_final: 0.4112 (tpp) REVERT: B3 706 MET cc_start: 0.8918 (tpp) cc_final: 0.8297 (tmm) REVERT: B3 802 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7393 (p) REVERT: B3 814 GLN cc_start: 0.8618 (tt0) cc_final: 0.8361 (tp-100) REVERT: B3 1074 LYS cc_start: 0.8813 (tppt) cc_final: 0.7968 (tttm) REVERT: B4 1 MET cc_start: 0.6206 (tmm) cc_final: 0.5996 (ttp) REVERT: B4 53 HIS cc_start: 0.6292 (OUTLIER) cc_final: 0.5753 (p-80) REVERT: B4 117 TYR cc_start: 0.6841 (t80) cc_final: 0.6614 (t80) REVERT: B4 167 LEU cc_start: 0.5495 (mt) cc_final: 0.5294 (mm) REVERT: B6 101 MET cc_start: 0.4663 (ptp) cc_final: 0.3164 (ppp) REVERT: A1 186 MET cc_start: 0.1989 (mtm) cc_final: 0.1253 (tmm) REVERT: A2 45 TYR cc_start: 0.8754 (m-80) cc_final: 0.8433 (m-10) REVERT: A3 106 MET cc_start: -0.1418 (mtp) cc_final: -0.2590 (tpt) outliers start: 115 outliers final: 46 residues processed: 455 average time/residue: 0.2187 time to fit residues: 162.0881 Evaluate side-chains 363 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain B1 residue 480 VAL Chi-restraints excluded: chain B1 residue 559 ILE Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 887 LYS Chi-restraints excluded: chain B1 residue 917 VAL Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 931 GLN Chi-restraints excluded: chain B1 residue 976 VAL Chi-restraints excluded: chain B1 residue 1008 LYS Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 566 ILE Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 650 ILE Chi-restraints excluded: chain B3 residue 10 ARG Chi-restraints excluded: chain B3 residue 29 GLU Chi-restraints excluded: chain B3 residue 50 VAL Chi-restraints excluded: chain B3 residue 114 ARG Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 138 GLN Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 802 THR Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B6 residue 28 TYR Chi-restraints excluded: chain A3 residue 425 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 77 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 50.0000 chunk 355 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 426 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 GLN B1 903 GLN B1 941 ASN B11007 HIS B11256 HIS B3 776 GLN ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.207269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128036 restraints weight = 71113.650| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.74 r_work: 0.3244 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 39217 Z= 0.230 Angle : 0.664 16.268 53383 Z= 0.337 Chirality : 0.044 0.221 5917 Planarity : 0.005 0.063 6673 Dihedral : 13.006 179.093 6225 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.63 % Allowed : 19.09 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4527 helix: 1.48 (0.12), residues: 1956 sheet: 0.53 (0.20), residues: 684 loop : -0.46 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 265 TYR 0.041 0.002 TYRA3 416 PHE 0.036 0.002 PHE A 808 TRP 0.055 0.002 TRPA3 387 HIS 0.015 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (39205) covalent geometry : angle 0.65024 / 0.34 (53365) hydrogen bonds : bond 0.05693 / 4.59 ( 1740) hydrogen bonds : angle 4.81466 / 4.03 ( 4974) metal coordination : bond 0.00565 / 0.37 ( 12) metal coordination : angle 7.24685 / 13.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 315 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.7963 (t0) cc_final: 0.7508 (p0) REVERT: B 537 MET cc_start: 0.2673 (mtt) cc_final: 0.1464 (ptt) REVERT: B 655 MET cc_start: 0.3855 (mmm) cc_final: 0.3213 (ptt) REVERT: C 560 MET cc_start: 0.4152 (mtt) cc_final: 0.3096 (mmm) REVERT: C 623 LEU cc_start: 0.0075 (OUTLIER) cc_final: -0.0181 (mm) REVERT: A 807 MET cc_start: 0.7272 (tpt) cc_final: 0.6947 (tpt) REVERT: B1 540 MET cc_start: 0.7796 (tpt) cc_final: 0.7058 (tpt) REVERT: B1 592 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B1 610 ILE cc_start: 0.8740 (mm) cc_final: 0.8372 (pt) REVERT: B1 632 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B1 656 LYS cc_start: 0.8380 (mmtm) cc_final: 0.7575 (tmtt) REVERT: B1 690 ILE cc_start: 0.9022 (mm) cc_final: 0.8785 (mt) REVERT: B1 809 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: B1 818 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7463 (t80) REVERT: B1 870 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8906 (mt-10) REVERT: B1 892 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7554 (tt) REVERT: B1 903 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: B1 907 ASP cc_start: 0.7335 (t0) cc_final: 0.6785 (m-30) REVERT: B1 941 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: B1 1015 ASP cc_start: 0.7873 (m-30) cc_final: 0.7548 (m-30) REVERT: B2 579 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7846 (tp40) REVERT: B3 29 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: B3 114 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8334 (ttm170) REVERT: B3 213 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8278 (tp) REVERT: B3 423 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B3 447 MET cc_start: 0.5384 (mmm) cc_final: 0.4721 (mmp) REVERT: B3 715 MET cc_start: 0.6741 (mmp) cc_final: 0.5857 (mmt) REVERT: B3 755 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7701 (m) REVERT: B4 53 HIS cc_start: 0.6451 (OUTLIER) cc_final: 0.5930 (p-80) REVERT: B6 4 GLN cc_start: 0.4573 (OUTLIER) cc_final: 0.3849 (tp-100) REVERT: B6 101 MET cc_start: 0.4511 (ptp) cc_final: 0.2877 (ppp) REVERT: A2 45 TYR cc_start: 0.8656 (m-80) cc_final: 0.8315 (m-10) REVERT: A2 171 MET cc_start: 0.7648 (tpp) cc_final: 0.6939 (tpp) REVERT: A3 106 MET cc_start: -0.1328 (mtp) cc_final: -0.2559 (tpt) REVERT: A3 424 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7818 (ttm170) outliers start: 144 outliers final: 80 residues processed: 432 average time/residue: 0.2016 time to fit residues: 145.8061 Evaluate side-chains 385 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 288 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 378 MET Chi-restraints excluded: chain B1 residue 480 VAL Chi-restraints excluded: chain B1 residue 559 ILE Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 645 LEU Chi-restraints excluded: chain B1 residue 657 SER Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 798 THR Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 892 LEU Chi-restraints excluded: chain B1 residue 894 ASP Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 940 LEU Chi-restraints excluded: chain B1 residue 941 ASN Chi-restraints excluded: chain B1 residue 976 VAL Chi-restraints excluded: chain B1 residue 1008 LYS Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1119 VAL Chi-restraints excluded: chain B1 residue 1160 GLU Chi-restraints excluded: chain B1 residue 1277 GLN Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 566 ILE Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 579 GLN Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 599 THR Chi-restraints excluded: chain B2 residue 650 ILE Chi-restraints excluded: chain B3 residue 10 ARG Chi-restraints excluded: chain B3 residue 29 GLU Chi-restraints excluded: chain B3 residue 114 ARG Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 191 GLU Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 219 HIS Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 423 LEU Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 776 GLN Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1028 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1148 LEU Chi-restraints excluded: chain B3 residue 1198 ASP Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 25 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B4 residue 176 TYR Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 28 TYR Chi-restraints excluded: chain A1 residue 269 VAL Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A3 residue 424 ARG Chi-restraints excluded: chain A3 residue 443 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 353 optimal weight: 0.0970 chunk 282 optimal weight: 10.0000 chunk 342 optimal weight: 0.5980 chunk 394 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 328 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 672 GLN B1 903 GLN B1 941 ASN B3 138 GLN B3 709 GLN B3 804 HIS ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.209197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131890 restraints weight = 71330.638| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 5.85 r_work: 0.3285 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39217 Z= 0.118 Angle : 0.578 15.233 53383 Z= 0.291 Chirality : 0.041 0.211 5917 Planarity : 0.004 0.055 6673 Dihedral : 12.928 179.214 6225 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.90 % Allowed : 20.63 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4527 helix: 1.64 (0.12), residues: 1954 sheet: 0.58 (0.20), residues: 697 loop : -0.39 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGB4 170 TYR 0.019 0.001 TYRB4 117 PHE 0.039 0.001 PHE A 808 TRP 0.047 0.002 TRPB1 732 HIS 0.010 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (39205) covalent geometry : angle 0.56852 / 0.29 (53365) hydrogen bonds : bond 0.04359 / 3.49 ( 1740) hydrogen bonds : angle 4.51023 / 3.81 ( 4974) metal coordination : bond 0.00395 / 0.26 ( 12) metal coordination : angle 5.79280 / 10.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 327 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.7881 (t0) cc_final: 0.7460 (p0) REVERT: B 537 MET cc_start: 0.2700 (mtt) cc_final: 0.1506 (ptt) REVERT: B 655 MET cc_start: 0.3886 (mmm) cc_final: 0.3265 (ptt) REVERT: B 670 ARG cc_start: 0.0312 (OUTLIER) cc_final: 0.0067 (ptm160) REVERT: C 119 GLU cc_start: 0.6557 (mp0) cc_final: 0.6222 (mp0) REVERT: C 560 MET cc_start: 0.3912 (mtt) cc_final: 0.2809 (mmm) REVERT: C 623 LEU cc_start: 0.0304 (OUTLIER) cc_final: 0.0015 (mm) REVERT: C 660 TRP cc_start: 0.6314 (m100) cc_final: 0.6051 (m100) REVERT: A 816 MET cc_start: 0.4523 (mmm) cc_final: 0.3758 (ttp) REVERT: B1 540 MET cc_start: 0.7702 (tpt) cc_final: 0.7308 (tpt) REVERT: B1 592 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B1 632 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B1 656 LYS cc_start: 0.8324 (mmtm) cc_final: 0.7624 (tmtt) REVERT: B1 690 ILE cc_start: 0.8953 (mm) cc_final: 0.8747 (mt) REVERT: B1 809 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: B1 818 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B1 870 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8927 (mt-10) REVERT: B1 907 ASP cc_start: 0.7480 (t0) cc_final: 0.6408 (m-30) REVERT: B1 1015 ASP cc_start: 0.7788 (m-30) cc_final: 0.7431 (m-30) REVERT: B1 1178 MET cc_start: 0.7898 (mtt) cc_final: 0.7594 (mtp) REVERT: B3 213 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8447 (tp) REVERT: B3 706 MET cc_start: 0.8760 (tpp) cc_final: 0.8089 (tmm) REVERT: B3 715 MET cc_start: 0.6737 (mmp) cc_final: 0.4896 (mmt) REVERT: B3 723 TYR cc_start: 0.7585 (p90) cc_final: 0.7219 (p90) REVERT: B3 755 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (m) REVERT: B3 762 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B3 814 GLN cc_start: 0.8563 (tt0) cc_final: 0.8294 (tp-100) REVERT: B4 53 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.6084 (p-80) REVERT: B6 4 GLN cc_start: 0.4651 (OUTLIER) cc_final: 0.3984 (tp-100) REVERT: B6 101 MET cc_start: 0.4467 (ptp) cc_final: 0.2829 (ppp) REVERT: A1 186 MET cc_start: 0.2380 (mtm) cc_final: 0.1590 (tmm) REVERT: A2 45 TYR cc_start: 0.8626 (m-80) cc_final: 0.8293 (m-10) REVERT: A2 171 MET cc_start: 0.7715 (tpp) cc_final: 0.7245 (tpp) REVERT: A3 106 MET cc_start: -0.1145 (mtp) cc_final: -0.2374 (tpt) outliers start: 115 outliers final: 58 residues processed: 414 average time/residue: 0.2273 time to fit residues: 157.5790 Evaluate side-chains 367 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 298 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 378 MET Chi-restraints excluded: chain B1 residue 543 THR Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 769 VAL Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 1008 LYS Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 462 VAL Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 540 LEU Chi-restraints excluded: chain B2 residue 566 ILE Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 10 ARG Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 713 LEU Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 797 LEU Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B4 residue 176 TYR Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 28 TYR Chi-restraints excluded: chain A1 residue 249 TRP Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A2 residue 118 LYS Chi-restraints excluded: chain A3 residue 443 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 407 optimal weight: 2.9990 chunk 450 optimal weight: 3.9990 chunk 419 optimal weight: 50.0000 chunk 154 optimal weight: 0.7980 chunk 402 optimal weight: 5.9990 chunk 361 optimal weight: 8.9990 chunk 444 optimal weight: 20.0000 chunk 345 optimal weight: 2.9990 chunk 268 optimal weight: 0.4980 chunk 340 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 672 GLN B1 903 GLN ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 209 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 = 0.4641 r_free = 0.4641 target = 0.207025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128102 restraints weight = 70562.849| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 5.38 r_work: 0.3221 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 39217 Z= 0.191 Angle : 0.617 15.783 53383 Z= 0.310 Chirality : 0.043 0.210 5917 Planarity : 0.004 0.053 6673 Dihedral : 12.915 178.911 6225 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.86 % Allowed : 19.57 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4527 helix: 1.60 (0.12), residues: 1943 sheet: 0.51 (0.20), residues: 694 loop : -0.48 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGB4 170 TYR 0.022 0.002 TYRB3 189 PHE 0.029 0.002 PHE A 808 TRP 0.057 0.002 TRPB1 732 HIS 0.009 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (39205) covalent geometry : angle 0.60435 / 0.31 (53365) hydrogen bonds : bond 0.04735 / 3.76 ( 1740) hydrogen bonds : angle 4.51360 / 3.81 ( 4974) metal coordination : bond 0.00514 / 0.34 ( 12) metal coordination : angle 6.74491 / 12.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 310 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.7891 (t0) cc_final: 0.7482 (p0) REVERT: B 537 MET cc_start: 0.2476 (mtt) cc_final: 0.1284 (ptt) REVERT: B 655 MET cc_start: 0.3971 (mmm) cc_final: 0.3260 (ptt) REVERT: C 623 LEU cc_start: 0.0420 (OUTLIER) cc_final: 0.0159 (mm) REVERT: B1 540 MET cc_start: 0.7719 (tpt) cc_final: 0.7355 (tpt) REVERT: B1 592 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B1 632 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8150 (t80) REVERT: B1 656 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7594 (tmtt) REVERT: B1 690 ILE cc_start: 0.9005 (mm) cc_final: 0.8779 (mt) REVERT: B1 809 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: B1 818 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B1 823 MET cc_start: 0.6655 (tpt) cc_final: 0.6405 (tpt) REVERT: B1 870 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8937 (mt-10) REVERT: B1 903 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: B1 907 ASP cc_start: 0.7292 (t0) cc_final: 0.7052 (m-30) REVERT: B1 937 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8507 (mt) REVERT: B1 1015 ASP cc_start: 0.7916 (m-30) cc_final: 0.7013 (t0) REVERT: B3 213 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (tp) REVERT: B3 715 MET cc_start: 0.7120 (mmp) cc_final: 0.6371 (mmt) REVERT: B3 723 TYR cc_start: 0.7677 (p90) cc_final: 0.7411 (p90) REVERT: B3 762 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8323 (pp) REVERT: B3 881 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: B3 1110 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8421 (tp) REVERT: B4 53 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.6169 (p-80) REVERT: B6 4 GLN cc_start: 0.4679 (OUTLIER) cc_final: 0.4010 (tp40) REVERT: B6 8 ARG cc_start: 0.3188 (OUTLIER) cc_final: 0.2893 (ttp-110) REVERT: B6 101 MET cc_start: 0.4719 (ptp) cc_final: 0.3076 (ppp) REVERT: A2 45 TYR cc_start: 0.8652 (m-80) cc_final: 0.8331 (m-10) REVERT: A3 26 MET cc_start: -0.1441 (mmt) cc_final: -0.2451 (ptt) REVERT: A3 106 MET cc_start: -0.1202 (mtp) cc_final: -0.2483 (tpt) outliers start: 153 outliers final: 99 residues processed: 439 average time/residue: 0.2261 time to fit residues: 167.6730 Evaluate side-chains 408 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 295 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 378 MET Chi-restraints excluded: chain B1 residue 480 VAL Chi-restraints excluded: chain B1 residue 543 THR Chi-restraints excluded: chain B1 residue 559 ILE Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 645 LEU Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 798 THR Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 937 LEU Chi-restraints excluded: chain B1 residue 940 LEU Chi-restraints excluded: chain B1 residue 955 ILE Chi-restraints excluded: chain B1 residue 1008 LYS Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B1 residue 1058 ILE Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1119 VAL Chi-restraints excluded: chain B1 residue 1294 THR Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 462 VAL Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 540 LEU Chi-restraints excluded: chain B2 residue 566 ILE Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 599 THR Chi-restraints excluded: chain B2 residue 650 ILE Chi-restraints excluded: chain B2 residue 657 ILE Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 10 ARG Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 191 GLU Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 219 HIS Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 631 GLN Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 761 THR Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 821 GLU Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 881 GLN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1018 GLU Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1033 VAL Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1110 ILE Chi-restraints excluded: chain B3 residue 1148 LEU Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 79 LEU Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 8 ARG Chi-restraints excluded: chain B6 residue 21 LEU Chi-restraints excluded: chain B6 residue 28 TYR Chi-restraints excluded: chain A1 residue 248 GLU Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A2 residue 47 MET Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 29 optimal weight: 7.9990 chunk 254 optimal weight: 0.0270 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 331 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 370 optimal weight: 0.0060 chunk 100 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 672 GLN ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 891 GLN B1 903 GLN B3 709 GLN ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 149 HIS ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.209256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131906 restraints weight = 71389.513| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 5.51 r_work: 0.3293 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39217 Z= 0.108 Angle : 0.563 13.722 53383 Z= 0.282 Chirality : 0.041 0.203 5917 Planarity : 0.004 0.054 6673 Dihedral : 12.841 179.225 6225 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.72 % Allowed : 21.24 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4527 helix: 1.77 (0.12), residues: 1940 sheet: 0.60 (0.20), residues: 689 loop : -0.40 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGB4 170 TYR 0.020 0.001 TYRB4 117 PHE 0.030 0.001 PHE A 808 TRP 0.061 0.002 TRPB1 732 HIS 0.008 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (39205) covalent geometry : angle 0.55408 / 0.28 (53365) hydrogen bonds : bond 0.03842 / 3.03 ( 1740) hydrogen bonds : angle 4.30884 / 3.67 ( 4974) metal coordination : bond 0.00399 / 0.26 ( 12) metal coordination : angle 5.51772 / 10.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 322 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.3942 (mpp) cc_final: 0.3404 (mmm) REVERT: B 448 ASN cc_start: 0.7883 (t0) cc_final: 0.7497 (p0) REVERT: B 537 MET cc_start: 0.2440 (mtt) cc_final: 0.1319 (ptt) REVERT: B 655 MET cc_start: 0.3992 (mmm) cc_final: 0.3294 (ptt) REVERT: C 119 GLU cc_start: 0.6606 (mp0) cc_final: 0.6311 (mp0) REVERT: C 623 LEU cc_start: 0.0300 (OUTLIER) cc_final: 0.0074 (mm) REVERT: A 816 MET cc_start: 0.4454 (mmm) cc_final: 0.3728 (ttp) REVERT: B1 540 MET cc_start: 0.7666 (tpt) cc_final: 0.7293 (tpt) REVERT: B1 592 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B1 632 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8227 (t80) REVERT: B1 656 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7633 (tmtt) REVERT: B1 809 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: B1 818 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B1 870 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: B1 876 MET cc_start: 0.8996 (mmm) cc_final: 0.8431 (mmm) REVERT: B1 907 ASP cc_start: 0.7578 (t0) cc_final: 0.6692 (m-30) REVERT: B1 937 LEU cc_start: 0.8920 (tp) cc_final: 0.8515 (mt) REVERT: B1 1015 ASP cc_start: 0.7960 (m-30) cc_final: 0.7052 (t0) REVERT: B3 631 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: B3 715 MET cc_start: 0.7045 (mmp) cc_final: 0.6253 (mmt) REVERT: B3 723 TYR cc_start: 0.7602 (p90) cc_final: 0.7274 (p90) REVERT: B3 762 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B3 769 LYS cc_start: 0.7460 (ptmm) cc_final: 0.6674 (ptpp) REVERT: B3 814 GLN cc_start: 0.8599 (tt0) cc_final: 0.8345 (tp-100) REVERT: B4 53 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6191 (p-80) REVERT: B6 4 GLN cc_start: 0.4365 (OUTLIER) cc_final: 0.3890 (tp40) REVERT: B6 7 LYS cc_start: 0.1061 (OUTLIER) cc_final: 0.0541 (tppt) REVERT: B6 101 MET cc_start: 0.4732 (ptp) cc_final: 0.3092 (ppp) REVERT: A2 45 TYR cc_start: 0.8643 (m-80) cc_final: 0.8351 (m-10) REVERT: A2 171 MET cc_start: 0.7355 (tpp) cc_final: 0.6525 (tpp) REVERT: A3 26 MET cc_start: -0.1366 (mmt) cc_final: -0.2364 (ptt) REVERT: A3 106 MET cc_start: -0.0931 (mtp) cc_final: -0.2251 (tpt) REVERT: A3 382 ASN cc_start: 0.8012 (t0) cc_final: 0.7801 (t0) outliers start: 108 outliers final: 75 residues processed: 414 average time/residue: 0.2357 time to fit residues: 162.3818 Evaluate side-chains 385 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 300 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 543 THR Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 892 LEU Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 955 ILE Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 540 LEU Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 191 GLU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 367 ASP Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 630 MET Chi-restraints excluded: chain B3 residue 631 GLN Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 713 LEU Chi-restraints excluded: chain B3 residue 761 THR Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 797 LEU Chi-restraints excluded: chain B3 residue 821 GLU Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 974 LYS Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1033 VAL Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 73 ILE Chi-restraints excluded: chain B4 residue 79 LEU Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 7 LYS Chi-restraints excluded: chain B6 residue 13 LEU Chi-restraints excluded: chain B6 residue 21 LEU Chi-restraints excluded: chain A1 residue 249 TRP Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A2 residue 179 ILE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 293 optimal weight: 9.9990 chunk 84 optimal weight: 0.0060 chunk 67 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 167 GLN ** A2 209 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 = 0.4657 r_free = 0.4657 target = 0.208536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130732 restraints weight = 71050.775| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 4.92 r_work: 0.3264 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39217 Z= 0.132 Angle : 0.571 14.159 53383 Z= 0.285 Chirality : 0.041 0.202 5917 Planarity : 0.004 0.054 6673 Dihedral : 12.795 179.195 6225 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.03 % Allowed : 21.03 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4527 helix: 1.77 (0.12), residues: 1945 sheet: 0.55 (0.20), residues: 692 loop : -0.38 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGB3 463 TYR 0.018 0.001 TYRB4 117 PHE 0.029 0.001 PHE A 808 TRP 0.062 0.002 TRPB1 732 HIS 0.010 0.001 HISB4 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (39205) covalent geometry : angle 0.56076 / 0.28 (53365) hydrogen bonds : bond 0.03948 / 3.11 ( 1740) hydrogen bonds : angle 4.30151 / 3.67 ( 4974) metal coordination : bond 0.00423 / 0.28 ( 12) metal coordination : angle 5.79489 / 11.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 309 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.7881 (t0) cc_final: 0.7500 (p0) REVERT: B 498 THR cc_start: 0.3173 (OUTLIER) cc_final: 0.2956 (t) REVERT: B 537 MET cc_start: 0.2446 (mtt) cc_final: 0.2056 (mmt) REVERT: B 655 MET cc_start: 0.4036 (mmm) cc_final: 0.3304 (ptt) REVERT: A 816 MET cc_start: 0.4446 (mmm) cc_final: 0.3764 (ttp) REVERT: B1 540 MET cc_start: 0.7697 (tpt) cc_final: 0.7336 (tpt) REVERT: B1 592 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B1 632 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8262 (t80) REVERT: B1 656 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7635 (tmtt) REVERT: B1 809 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B1 818 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B1 870 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8848 (mt-10) REVERT: B1 876 MET cc_start: 0.9035 (mmm) cc_final: 0.8452 (mmm) REVERT: B1 907 ASP cc_start: 0.7450 (t0) cc_final: 0.6909 (m-30) REVERT: B1 937 LEU cc_start: 0.8986 (tp) cc_final: 0.8533 (mt) REVERT: B3 631 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: B3 715 MET cc_start: 0.7090 (mmp) cc_final: 0.6213 (mmt) REVERT: B3 762 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B3 769 LYS cc_start: 0.7503 (ptmm) cc_final: 0.6672 (ptpp) REVERT: B3 814 GLN cc_start: 0.8588 (tt0) cc_final: 0.8367 (tp-100) REVERT: B4 49 VAL cc_start: 0.6334 (t) cc_final: 0.6074 (t) REVERT: B4 53 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6316 (p-80) REVERT: B6 4 GLN cc_start: 0.4358 (OUTLIER) cc_final: 0.3826 (tp40) REVERT: B6 101 MET cc_start: 0.4581 (ptp) cc_final: 0.2904 (ppp) REVERT: A2 45 TYR cc_start: 0.8561 (m-80) cc_final: 0.8284 (m-10) REVERT: A2 171 MET cc_start: 0.7417 (tpp) cc_final: 0.6749 (tpp) REVERT: A3 19 MET cc_start: 0.0617 (tpt) cc_final: -0.0299 (mtt) REVERT: A3 26 MET cc_start: -0.1532 (mmt) cc_final: -0.2491 (ptt) REVERT: A3 106 MET cc_start: -0.1191 (mtp) cc_final: -0.2458 (tpt) outliers start: 120 outliers final: 86 residues processed: 409 average time/residue: 0.2295 time to fit residues: 157.2355 Evaluate side-chains 393 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 298 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 543 THR Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 892 LEU Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 940 LEU Chi-restraints excluded: chain B1 residue 955 ILE Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B1 residue 1152 SER Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 540 LEU Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 657 ILE Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 10 ARG Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 191 GLU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 630 MET Chi-restraints excluded: chain B3 residue 631 GLN Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 713 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 761 THR Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 797 LEU Chi-restraints excluded: chain B3 residue 821 GLU Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 974 LYS Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1033 VAL Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 79 LEU Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B4 residue 187 HIS Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 13 LEU Chi-restraints excluded: chain B6 residue 21 LEU Chi-restraints excluded: chain A1 residue 249 TRP Chi-restraints excluded: chain A3 residue 410 ILE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 56 optimal weight: 8.9990 chunk 324 optimal weight: 0.8980 chunk 155 optimal weight: 0.0870 chunk 148 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 404 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B11002 ASN ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130495 restraints weight = 71123.875| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.43 r_work: 0.3275 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39217 Z= 0.119 Angle : 0.566 13.821 53383 Z= 0.283 Chirality : 0.041 0.199 5917 Planarity : 0.004 0.054 6673 Dihedral : 12.749 179.465 6225 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.03 % Allowed : 20.98 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4527 helix: 1.79 (0.12), residues: 1948 sheet: 0.51 (0.20), residues: 700 loop : -0.36 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGB4 170 TYR 0.025 0.001 TYRB3 723 PHE 0.032 0.001 PHE A 808 TRP 0.066 0.002 TRPB1 732 HIS 0.008 0.001 HISB4 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (39205) covalent geometry : angle 0.55688 / 0.28 (53365) hydrogen bonds : bond 0.03770 / 2.96 ( 1740) hydrogen bonds : angle 4.25657 / 3.66 ( 4974) metal coordination : bond 0.00403 / 0.27 ( 12) metal coordination : angle 5.57580 / 10.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 317 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 448 ASN cc_start: 0.7861 (t0) cc_final: 0.7481 (p0) REVERT: B 498 THR cc_start: 0.3184 (OUTLIER) cc_final: 0.2964 (t) REVERT: B 537 MET cc_start: 0.2448 (mtt) cc_final: 0.2063 (mmt) REVERT: B 655 MET cc_start: 0.4036 (mmm) cc_final: 0.3287 (ptt) REVERT: C 119 GLU cc_start: 0.6727 (mp0) cc_final: 0.6481 (mp0) REVERT: A 816 MET cc_start: 0.4338 (mmm) cc_final: 0.3536 (ttp) REVERT: B1 540 MET cc_start: 0.7678 (tpt) cc_final: 0.7314 (tpt) REVERT: B1 632 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8331 (t80) REVERT: B1 644 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7904 (pp) REVERT: B1 656 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7625 (tmtt) REVERT: B1 809 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: B1 818 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B1 823 MET cc_start: 0.6545 (tpt) cc_final: 0.6260 (tpt) REVERT: B1 870 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8837 (mt-10) REVERT: B1 876 MET cc_start: 0.9046 (mmm) cc_final: 0.8473 (mmm) REVERT: B1 903 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8043 (tm130) REVERT: B1 937 LEU cc_start: 0.8942 (tp) cc_final: 0.8433 (mt) REVERT: B3 61 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8147 (p) REVERT: B3 631 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: B3 715 MET cc_start: 0.7116 (mmp) cc_final: 0.6465 (mmt) REVERT: B3 762 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (pp) REVERT: B3 769 LYS cc_start: 0.7446 (ptmm) cc_final: 0.6637 (ptpp) REVERT: B3 814 GLN cc_start: 0.8563 (tt0) cc_final: 0.8342 (tp-100) REVERT: B3 821 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: B3 881 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: B3 1110 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (tp) REVERT: B4 53 HIS cc_start: 0.6773 (OUTLIER) cc_final: 0.6316 (p-80) REVERT: B6 4 GLN cc_start: 0.4489 (OUTLIER) cc_final: 0.4145 (tp40) REVERT: B6 7 LYS cc_start: 0.1155 (OUTLIER) cc_final: 0.0593 (tppt) REVERT: B6 8 ARG cc_start: 0.3177 (OUTLIER) cc_final: 0.2950 (mtm110) REVERT: B6 101 MET cc_start: 0.4519 (ptp) cc_final: 0.2825 (ppp) REVERT: A1 186 MET cc_start: 0.2141 (mtm) cc_final: 0.1203 (tmm) REVERT: A2 45 TYR cc_start: 0.8595 (m-80) cc_final: 0.8337 (m-10) REVERT: A2 171 MET cc_start: 0.7392 (tpp) cc_final: 0.7110 (tpp) REVERT: A3 19 MET cc_start: 0.0667 (tpt) cc_final: -0.0307 (mtt) REVERT: A3 26 MET cc_start: -0.1733 (mmt) cc_final: -0.2675 (ptt) REVERT: A3 106 MET cc_start: -0.1298 (mtp) cc_final: -0.2553 (tpt) outliers start: 120 outliers final: 85 residues processed: 418 average time/residue: 0.2203 time to fit residues: 153.6639 Evaluate side-chains 402 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 300 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 644 LEU Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 955 ILE Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B1 residue 1152 SER Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 462 VAL Chi-restraints excluded: chain B2 residue 486 LYS Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 540 LEU Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 650 ILE Chi-restraints excluded: chain B2 residue 657 ILE Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 61 VAL Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 191 GLU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 367 ASP Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 630 MET Chi-restraints excluded: chain B3 residue 631 GLN Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 761 THR Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 797 LEU Chi-restraints excluded: chain B3 residue 821 GLU Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 881 GLN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1033 VAL Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1110 ILE Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 79 LEU Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B4 residue 187 HIS Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 7 LYS Chi-restraints excluded: chain B6 residue 8 ARG Chi-restraints excluded: chain B6 residue 13 LEU Chi-restraints excluded: chain A1 residue 248 GLU Chi-restraints excluded: chain A1 residue 249 TRP Chi-restraints excluded: chain A3 residue 410 ILE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 346 optimal weight: 1.9990 chunk 409 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 290 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 376 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 341 GLN C 130 ASN C 672 GLN A 672 HIS B2 483 GLN B2 579 GLN B31052 ASN ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.207774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129904 restraints weight = 71444.633| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 5.15 r_work: 0.3263 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39217 Z= 0.158 Angle : 0.595 14.785 53383 Z= 0.297 Chirality : 0.042 0.199 5917 Planarity : 0.004 0.053 6673 Dihedral : 12.736 179.193 6225 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.08 % Allowed : 20.96 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4527 helix: 1.75 (0.12), residues: 1940 sheet: 0.45 (0.20), residues: 696 loop : -0.43 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB3 463 TYR 0.019 0.001 TYRB4 117 PHE 0.035 0.001 PHEB1 647 TRP 0.070 0.002 TRPB1 732 HIS 0.007 0.001 HISB4 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (39205) covalent geometry : angle 0.58457 / 0.30 (53365) hydrogen bonds : bond 0.04105 / 3.23 ( 1740) hydrogen bonds : angle 4.29369 / 3.68 ( 4974) metal coordination : bond 0.00429 / 0.29 ( 12) metal coordination : angle 6.14860 / 11.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 309 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.3954 (mpp) cc_final: 0.3287 (mmm) REVERT: B 448 ASN cc_start: 0.7739 (t0) cc_final: 0.7388 (p0) REVERT: B 537 MET cc_start: 0.2401 (mtt) cc_final: 0.1998 (mmt) REVERT: B 655 MET cc_start: 0.4071 (mmm) cc_final: 0.3276 (ptt) REVERT: C 119 GLU cc_start: 0.6702 (mp0) cc_final: 0.6414 (mp0) REVERT: A 807 MET cc_start: 0.7217 (tpt) cc_final: 0.6530 (tpt) REVERT: B1 632 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8221 (t80) REVERT: B1 656 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7610 (tmtt) REVERT: B1 765 TYR cc_start: 0.7350 (m-80) cc_final: 0.7095 (m-80) REVERT: B1 809 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: B1 818 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7288 (t80) REVERT: B1 823 MET cc_start: 0.6501 (tpt) cc_final: 0.6235 (tpt) REVERT: B1 870 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8853 (mt-10) REVERT: B1 903 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: B1 937 LEU cc_start: 0.8924 (tp) cc_final: 0.8421 (mt) REVERT: B1 1015 ASP cc_start: 0.7977 (m-30) cc_final: 0.7194 (t0) REVERT: B2 579 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7795 (tp-100) REVERT: B2 604 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6212 (mmmm) REVERT: B2 614 ARG cc_start: 0.7098 (mtt90) cc_final: 0.6839 (mtt90) REVERT: B3 40 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8646 (tt) REVERT: B3 61 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8150 (p) REVERT: B3 631 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: B3 640 LEU cc_start: 0.8159 (mp) cc_final: 0.7827 (tt) REVERT: B3 713 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7693 (mp) REVERT: B3 715 MET cc_start: 0.7119 (mmp) cc_final: 0.6188 (mmt) REVERT: B3 762 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (pp) REVERT: B3 769 LYS cc_start: 0.7365 (ptmm) cc_final: 0.6435 (ptpp) REVERT: B3 881 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: B3 1110 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8470 (tp) REVERT: B4 53 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6345 (p-80) REVERT: B6 4 GLN cc_start: 0.4337 (OUTLIER) cc_final: 0.3929 (tp40) REVERT: B6 7 LYS cc_start: 0.1117 (OUTLIER) cc_final: 0.0541 (tppt) REVERT: B6 101 MET cc_start: 0.4449 (ptp) cc_final: 0.2667 (ppp) REVERT: A1 186 MET cc_start: 0.1863 (mtm) cc_final: 0.0932 (tmm) REVERT: A2 31 ARG cc_start: 0.4048 (mmt180) cc_final: 0.3096 (mmt-90) REVERT: A2 45 TYR cc_start: 0.8562 (m-80) cc_final: 0.8305 (m-10) REVERT: A2 171 MET cc_start: 0.7487 (tpp) cc_final: 0.7226 (tpp) REVERT: A3 19 MET cc_start: 0.0604 (tpt) cc_final: -0.0420 (mtt) REVERT: A3 26 MET cc_start: -0.1832 (mmt) cc_final: -0.2818 (ptt) REVERT: A3 106 MET cc_start: -0.1346 (mtp) cc_final: -0.2607 (tpt) outliers start: 122 outliers final: 89 residues processed: 412 average time/residue: 0.2171 time to fit residues: 150.6439 Evaluate side-chains 407 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 301 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 543 THR Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 940 LEU Chi-restraints excluded: chain B1 residue 955 ILE Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1119 VAL Chi-restraints excluded: chain B1 residue 1152 SER Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 462 VAL Chi-restraints excluded: chain B2 residue 483 GLN Chi-restraints excluded: chain B2 residue 486 LYS Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 579 GLN Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 604 LYS Chi-restraints excluded: chain B2 residue 650 ILE Chi-restraints excluded: chain B2 residue 657 ILE Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 40 LEU Chi-restraints excluded: chain B3 residue 61 VAL Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 228 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 367 ASP Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 630 MET Chi-restraints excluded: chain B3 residue 631 GLN Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 713 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 761 THR Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 821 GLU Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 881 GLN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1018 GLU Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1033 VAL Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1110 ILE Chi-restraints excluded: chain B3 residue 1129 LEU Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 79 LEU Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 7 LYS Chi-restraints excluded: chain A1 residue 248 GLU Chi-restraints excluded: chain A3 residue 410 ILE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 214 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 315 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 891 GLN B2 483 GLN ** B3 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 209 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 = 0.4630 r_free = 0.4630 target = 0.206141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126469 restraints weight = 70318.510| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.44 r_work: 0.3261 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 39217 Z= 0.238 Angle : 0.665 16.553 53383 Z= 0.333 Chirality : 0.044 0.233 5917 Planarity : 0.005 0.052 6673 Dihedral : 12.788 178.603 6225 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.72 % Allowed : 21.34 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4527 helix: 1.58 (0.12), residues: 1950 sheet: 0.39 (0.20), residues: 698 loop : -0.52 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGB11262 TYR 0.029 0.002 TYRB3 189 PHE 0.027 0.002 PHEB1 647 TRP 0.068 0.002 TRPB1 732 HIS 0.013 0.001 HISB1 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (39205) covalent geometry : angle 0.65221 / 0.33 (53365) hydrogen bonds : bond 0.04675 / 3.70 ( 1740) hydrogen bonds : angle 4.43227 / 3.79 ( 4974) metal coordination : bond 0.00572 / 0.38 ( 12) metal coordination : angle 7.02351 / 13.35 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9054 Ramachandran restraints generated. 4527 Oldfield, 0 Emsley, 4527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 293 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.3992 (mpp) cc_final: 0.3249 (mmm) REVERT: B 240 MET cc_start: 0.0343 (mmt) cc_final: 0.0135 (tpp) REVERT: B 448 ASN cc_start: 0.7689 (t0) cc_final: 0.7338 (p0) REVERT: B 498 THR cc_start: 0.3177 (OUTLIER) cc_final: 0.2955 (t) REVERT: B 537 MET cc_start: 0.2419 (mtt) cc_final: 0.2050 (mmt) REVERT: B 655 MET cc_start: 0.4165 (mmm) cc_final: 0.3343 (ptt) REVERT: C 119 GLU cc_start: 0.6748 (mp0) cc_final: 0.6479 (mp0) REVERT: A 807 MET cc_start: 0.7031 (tpt) cc_final: 0.6443 (tpt) REVERT: A 816 MET cc_start: 0.4436 (mmm) cc_final: 0.3759 (ttp) REVERT: B1 632 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8535 (t80) REVERT: B1 656 LYS cc_start: 0.8322 (mmtm) cc_final: 0.7632 (tmtt) REVERT: B1 809 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: B1 818 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7182 (t80) REVERT: B1 870 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8848 (mt-10) REVERT: B1 909 VAL cc_start: 0.8014 (t) cc_final: 0.7666 (t) REVERT: B1 937 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8469 (mt) REVERT: B1 1015 ASP cc_start: 0.7954 (m-30) cc_final: 0.7700 (m-30) REVERT: B3 640 LEU cc_start: 0.8221 (mp) cc_final: 0.7903 (tt) REVERT: B3 715 MET cc_start: 0.7156 (mmp) cc_final: 0.6384 (mmt) REVERT: B3 762 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8265 (pp) REVERT: B3 838 MET cc_start: 0.8583 (ptt) cc_final: 0.8130 (ppp) REVERT: B3 881 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: B3 1110 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8497 (tp) REVERT: B4 53 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.6375 (p-80) REVERT: B6 4 GLN cc_start: 0.4117 (OUTLIER) cc_final: 0.3908 (tm-30) REVERT: B6 13 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5747 (pp) REVERT: B6 101 MET cc_start: 0.4417 (ptp) cc_final: 0.2591 (ppp) REVERT: A1 186 MET cc_start: 0.1679 (mtm) cc_final: 0.0739 (tmm) REVERT: A2 45 TYR cc_start: 0.8581 (m-80) cc_final: 0.8320 (m-10) REVERT: A2 168 TYR cc_start: 0.7231 (m-80) cc_final: 0.7010 (m-80) REVERT: A3 19 MET cc_start: 0.0602 (tpt) cc_final: -0.0591 (mtt) REVERT: A3 106 MET cc_start: -0.1411 (mtp) cc_final: -0.2810 (tpt) outliers start: 108 outliers final: 90 residues processed: 386 average time/residue: 0.2260 time to fit residues: 147.6915 Evaluate side-chains 390 residues out of total 3988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 288 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B1 residue 543 THR Chi-restraints excluded: chain B1 residue 573 LYS Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 632 PHE Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 637 SER Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 809 GLU Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 891 GLN Chi-restraints excluded: chain B1 residue 923 LYS Chi-restraints excluded: chain B1 residue 937 LEU Chi-restraints excluded: chain B1 residue 940 LEU Chi-restraints excluded: chain B1 residue 955 ILE Chi-restraints excluded: chain B1 residue 1021 THR Chi-restraints excluded: chain B1 residue 1049 TYR Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1119 VAL Chi-restraints excluded: chain B1 residue 1152 SER Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 462 VAL Chi-restraints excluded: chain B2 residue 486 LYS Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 586 ILE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 650 ILE Chi-restraints excluded: chain B2 residue 657 ILE Chi-restraints excluded: chain B2 residue 706 THR Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 181 MET Chi-restraints excluded: chain B3 residue 228 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 285 MET Chi-restraints excluded: chain B3 residue 367 ASP Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 462 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 487 ILE Chi-restraints excluded: chain B3 residue 503 THR Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 559 THR Chi-restraints excluded: chain B3 residue 630 MET Chi-restraints excluded: chain B3 residue 631 GLN Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 713 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 761 THR Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 821 GLU Chi-restraints excluded: chain B3 residue 844 ASN Chi-restraints excluded: chain B3 residue 881 GLN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 946 GLU Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1018 GLU Chi-restraints excluded: chain B3 residue 1019 ASN Chi-restraints excluded: chain B3 residue 1033 VAL Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1110 ILE Chi-restraints excluded: chain B3 residue 1129 LEU Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B4 residue 79 LEU Chi-restraints excluded: chain B4 residue 141 SER Chi-restraints excluded: chain B5 residue 7 ILE Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 13 LEU Chi-restraints excluded: chain B6 residue 21 LEU Chi-restraints excluded: chain A1 residue 248 GLU Chi-restraints excluded: chain A3 residue 410 ILE Chi-restraints excluded: chain A3 residue 443 THR Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 192 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 150 optimal weight: 0.0770 chunk 193 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 332 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 672 GLN B1 903 GLN B3 28 GLN B4 208 HIS ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.208624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131608 restraints weight = 70719.602| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 5.57 r_work: 0.3263 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39217 Z= 0.115 Angle : 0.592 14.946 53383 Z= 0.294 Chirality : 0.041 0.199 5917 Planarity : 0.004 0.051 6673 Dihedral : 12.742 179.589 6225 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.50 % Allowed : 21.64 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.13), residues: 4527 helix: 1.69 (0.12), residues: 1949 sheet: 0.41 (0.20), residues: 696 loop : -0.39 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB3 463 TYR 0.020 0.001 TYRB4 117 PHE 0.031 0.001 PHE A 808 TRP 0.076 0.002 TRPB1 732 HIS 0.012 0.001 HISB1 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (39205) covalent geometry : angle 0.58187 / 0.29 (53365) hydrogen bonds : bond 0.03811 / 2.99 ( 1740) hydrogen bonds : angle 4.24560 / 3.66 ( 4974) metal coordination : bond 0.00435 / 0.29 ( 12) metal coordination : angle 5.84144 / 10.97 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14019.34 seconds wall clock time: 239 minutes 24.61 seconds (14364.61 seconds total)