Starting phenix.real_space_refine on Sun Aug 9 23:14:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ze3_74090/08_2026/9ze3_74090.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ze3_74090/08_2026/9ze3_74090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ze3_74090/08_2026/9ze3_74090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ze3_74090/08_2026/9ze3_74090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ze3_74090/08_2026/9ze3_74090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ze3_74090/08_2026/9ze3_74090.map" } resolution = 3.93 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= 0.046 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 81 5.49 5 S 198 5.16 5 C 23843 2.51 5 N 6514 2.21 5 O 7348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37987 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1113 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 2 Chain: "B" Number of atoms: 5409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5409 Classifications: {'peptide': 672} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 634} Chain: "C" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1234 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "2" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 781 Classifications: {'RNA': 29, 'RNAv2': 8} 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: "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: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 882 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 16, 'rna3p_pyr': 27} Link IDs: {'rna2p': 17, 'rna3p': 26} 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: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1960 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 26, '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 8627 SG CYS H 11 102.827 127.179 94.814 1.00 50.95 S ATOM 8890 SG CYS H 46 102.134 130.514 93.130 1.00 54.41 S ATOM 8913 SG CYS H 49 100.849 127.341 91.544 1.00 58.09 S ATOM 9184 SG CYS H 85 99.269 128.887 94.671 1.00 50.08 S ATOM 8714 SG CYS H 23 85.889 119.886 89.512 1.00 61.73 S ATOM 8738 SG CYS H 26 86.788 119.788 93.182 1.00 62.55 S ATOM 8985 SG CYS H 58 89.011 121.730 90.634 1.00 59.79 S ATOM 9006 SG CYS H 61 88.771 117.850 90.792 1.00 60.23 S ATOM 8765 SG CYS H 30 87.598 125.230 103.463 1.00 45.64 S ATOM 8786 SG CYS H 33 87.947 123.554 107.041 1.00 47.77 S ATOM 9081 SG CYS H 72 85.684 126.520 106.309 1.00 43.36 S ATOM 9105 SG CYS H 75 89.658 126.721 106.383 1.00 43.67 S Time building chain proxies: 7.76, per 1000 atoms: 0.20 Number of scatterers: 37987 At special positions: 0 Unit cell: (187, 218.9, 231, 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 198 16.00 P 81 15.00 O 7348 8.00 N 6514 7.00 C 23843 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 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 49 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 85 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 11 " 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 75 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 30 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 33 " Number of angles added : 18 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8538 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 39 sheets defined 47.9% alpha, 14.8% beta 7 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... 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 removed outlier: 3.916A pdb=" N GLU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 754 Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.613A pdb=" N LYS B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 6.093A 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: 3.657A 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: 3.945A 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 376 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: 4.136A 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 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' 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 517 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 618 removed outlier: 4.001A 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: 3.839A 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 795 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: 3.530A pdb=" N TYR C 615 " --> pdb=" O ASN C 611 " (cutoff:3.500A) removed outlier: 3.729A 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 'H' and resid 47 through 55 removed outlier: 3.973A pdb=" N TYR H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY H 52 " --> pdb=" O CYS H 49 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N SER H 53 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.899A pdb=" N ARG H 82 " --> pdb=" O GLU H 79 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP H 83 " --> pdb=" O LYS H 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 79 through 83' Processing helix chain 'H' and resid 93 through 103 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: 3.754A pdb=" N ILEB1 472 " --> pdb=" O PROB1 469 " (cutoff:3.500A) Processing helix chain 'B1' and resid 475 through 479 Processing helix chain 'B1' and resid 488 through 507 Processing helix chain 'B1' and resid 508 through 520 removed outlier: 3.645A pdb=" N GLNB1 518 " --> pdb=" O ALAB1 514 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THRB1 520 " --> pdb=" O LEUB1 516 " (cutoff:3.500A) Processing helix chain 'B1' and resid 522 through 527 removed outlier: 3.765A pdb=" N GLYB1 527 " --> pdb=" O ALAB1 523 " (cutoff:3.500A) Processing helix chain 'B1' and resid 527 through 540 removed outlier: 4.004A 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: 3.541A pdb=" N LYSB1 562 " --> pdb=" O ARGB1 558 " (cutoff:3.500A) Processing helix chain 'B1' and resid 567 through 569 No H-bonds generated for 'chain 'B1' and resid 567 through 569' Processing helix chain 'B1' and resid 570 through 579 removed outlier: 3.694A pdb=" N VALB1 577 " --> pdb=" O LYSB1 573 " (cutoff:3.500A) Processing helix chain 'B1' and resid 580 through 582 No H-bonds generated for 'chain 'B1' and resid 580 through 582' Processing helix chain 'B1' and resid 586 through 605 removed outlier: 3.613A pdb=" N ARGB1 590 " --> pdb=" O ASPB1 586 " (cutoff:3.500A) Processing helix chain 'B1' and resid 606 through 614 Processing helix chain 'B1' and resid 615 through 619 removed outlier: 3.902A pdb=" N ASPB1 618 " --> pdb=" O PROB1 615 " (cutoff:3.500A) Processing helix chain 'B1' and resid 621 through 640 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: 3.806A pdb=" N ARGB1 661 " --> pdb=" O SERB1 657 " (cutoff:3.500A) Processing helix chain 'B1' and resid 682 through 692 removed outlier: 3.865A pdb=" N ILEB1 689 " --> pdb=" O SERB1 685 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILEB1 690 " --> pdb=" O LEUB1 686 " (cutoff:3.500A) removed outlier: 4.294A 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 Processing helix chain 'B1' and resid 724 through 736 removed outlier: 3.866A pdb=" N LEUB1 728 " --> pdb=" O PHEB1 724 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYSB1 729 " --> pdb=" O ASPB1 725 " (cutoff:3.500A) Proline residue: B1 730 - end of helix removed outlier: 3.503A pdb=" N LYSB1 733 " --> pdb=" O LYSB1 729 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARGB1 736 " --> pdb=" O TRPB1 732 " (cutoff:3.500A) Processing helix chain 'B1' and resid 740 through 754 Processing helix chain 'B1' and resid 758 through 776 removed outlier: 3.708A pdb=" N ASNB1 763 " --> pdb=" O ALAB1 759 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYRB1 764 " --> pdb=" O GLUB1 760 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLUB1 768 " --> pdb=" O TYRB1 764 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEUB1 771 " --> pdb=" O ARGB1 767 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILEB1 772 " --> pdb=" O GLUB1 768 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARGB1 775 " --> pdb=" O LEUB1 771 " (cutoff:3.500A) Processing helix chain 'B1' and resid 777 through 779 No H-bonds generated for 'chain 'B1' and resid 777 through 779' Processing helix chain 'B1' and resid 781 through 798 removed outlier: 3.532A pdb=" N THRB1 798 " --> pdb=" O GLNB1 794 " (cutoff:3.500A) Processing helix chain 'B1' and resid 802 through 810 removed outlier: 3.987A pdb=" N ILEB1 806 " --> pdb=" O GLUB1 802 " (cutoff:3.500A) Processing helix chain 'B1' and resid 810 through 818 removed outlier: 3.797A pdb=" N LYSB1 816 " --> pdb=" O PROB1 812 " (cutoff:3.500A) removed outlier: 3.507A 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: 3.913A pdb=" N ASNB1 842 " --> pdb=" O VALB1 838 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYSB1 843 " --> pdb=" O GLUB1 839 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VALB1 844 " --> pdb=" O LEUB1 840 " (cutoff:3.500A) Processing helix chain 'B1' and resid 845 through 854 removed outlier: 3.546A pdb=" N ILEB1 849 " --> pdb=" O GLYB1 845 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARGB1 852 " --> pdb=" O GLUB1 848 " (cutoff:3.500A) removed outlier: 3.568A 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 Processing helix chain 'B1' and resid 885 through 903 Processing helix chain 'B1' and resid 908 through 922 Processing helix chain 'B1' and resid 923 through 927 removed outlier: 3.636A 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: 3.636A pdb=" N ARGB1 948 " --> pdb=" O SERB1 944 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VALB1 960 " --> pdb=" O SERB1 956 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VALB1 961 " --> pdb=" O ARGB1 957 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYSB1 963 " --> pdb=" O ALAB1 959 " (cutoff:3.500A) Processing helix chain 'B1' and resid 967 through 981 removed outlier: 3.811A pdb=" N METB1 971 " --> pdb=" O GLUB1 967 " (cutoff:3.500A) Processing helix chain 'B1' and resid 986 through 1005 Processing helix chain 'B1' and resid 1016 through 1024 Proline residue: B11022 - end of helix Processing helix chain 'B1' and resid 1028 through 1046 Processing helix chain 'B1' and resid 1047 through 1050 removed outlier: 3.575A 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 1066 removed outlier: 3.864A pdb=" N LEUB11063 " --> pdb=" O CYSB11059 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLUB11064 " --> pdb=" O PHEB11060 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEUB11065 " --> pdb=" O GLUB11061 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1070 through 1089 removed outlier: 3.624A pdb=" N ASNB11079 " --> pdb=" O ARGB11075 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLYB11082 " --> pdb=" O VALB11078 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1090 through 1100 removed outlier: 3.673A pdb=" N ASNB11099 " --> pdb=" O ALAB11095 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASNB11100 " --> pdb=" O THRB11096 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1108 through 1123 removed outlier: 3.689A pdb=" N THRB11112 " --> pdb=" O ASNB11108 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1124 through 1127 Processing helix chain 'B1' and resid 1128 through 1135 removed outlier: 3.621A pdb=" N GLUB11135 " --> pdb=" O ALAB11131 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1136 through 1138 No H-bonds generated for 'chain 'B1' and resid 1136 through 1138' Processing helix chain 'B1' and resid 1140 through 1159 removed outlier: 3.736A pdb=" N GLYB11159 " --> pdb=" O PHEB11155 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1160 through 1164 removed outlier: 3.526A pdb=" N LYSB11163 " --> pdb=" O GLUB11160 " (cutoff:3.500A) removed outlier: 3.864A 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 1177 Proline residue: B11171 - end of helix Processing helix chain 'B1' and resid 1181 through 1199 removed outlier: 4.035A pdb=" N ARGB11185 " --> pdb=" O ASPB11181 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALAB11190 " --> pdb=" O GLNB11186 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1204 through 1216 removed outlier: 4.241A pdb=" N LEUB11208 " --> pdb=" O CYSB11204 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASNB11213 " --> pdb=" O ASNB11209 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYRB11214 " --> pdb=" O HISB11210 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VALB11215 " --> pdb=" O LEUB11211 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1217 through 1221 removed outlier: 3.951A pdb=" N PHEB11220 " --> pdb=" O PROB11217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLUB11221 " --> pdb=" O ASNB11218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1217 through 1221' Processing helix chain 'B1' and resid 1223 through 1242 removed outlier: 3.616A pdb=" N VALB11239 " --> pdb=" O GLUB11235 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1242 through 1251 removed outlier: 4.050A pdb=" N METB11246 " --> pdb=" O GLYB11242 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1258 through 1276 removed outlier: 4.348A pdb=" N VALB11264 " --> pdb=" O LYSB11260 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1297 through 1302 removed outlier: 3.574A pdb=" N ASPB11301 " --> pdb=" O ARGB11297 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYRB11302 " --> pdb=" O TYRB11298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1297 through 1302' Processing helix chain 'B2' and resid 452 through 459 removed outlier: 3.851A pdb=" N ASNB2 458 " --> pdb=" O LEUB2 454 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARGB2 459 " --> pdb=" O ARGB2 455 " (cutoff:3.500A) Processing helix chain 'B2' and resid 461 through 467 removed outlier: 3.632A pdb=" N GLNB2 467 " --> pdb=" O ALAB2 463 " (cutoff:3.500A) Processing helix chain 'B2' and resid 471 through 475 removed outlier: 3.680A pdb=" N VALB2 474 " --> pdb=" O ARGB2 471 " (cutoff:3.500A) Processing helix chain 'B2' and resid 478 through 482 Processing helix chain 'B2' and resid 484 through 493 Processing helix chain 'B2' and resid 525 through 530 Processing helix chain 'B2' and resid 532 through 547 Processing helix chain 'B2' and resid 551 through 561 removed outlier: 3.730A 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 577 removed outlier: 3.637A pdb=" N HISB2 572 " --> pdb=" O TYRB2 568 " (cutoff:3.500A) Processing helix chain 'B2' and resid 594 through 603 removed outlier: 3.949A pdb=" N GLUB2 598 " --> pdb=" O GLYB2 594 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARGB2 600 " --> pdb=" O GLUB2 596 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEUB2 601 " --> pdb=" O PHEB2 597 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLUB2 603 " --> pdb=" O THRB2 599 " (cutoff:3.500A) Processing helix chain 'B2' and resid 610 through 617 removed outlier: 4.218A pdb=" N ARGB2 614 " --> pdb=" O SERB2 610 " (cutoff:3.500A) Processing helix chain 'B2' and resid 624 through 628 removed outlier: 4.169A pdb=" N VALB2 628 " --> pdb=" O ALAB2 625 " (cutoff:3.500A) Processing helix chain 'B2' and resid 632 through 640 Processing helix chain 'B3' and resid 190 through 194 Processing helix chain 'B3' and resid 429 through 432 removed outlier: 3.712A 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: 3.876A pdb=" N CYSB3 624 " --> pdb=" O PROB3 621 " (cutoff:3.500A) Processing helix chain 'B3' and resid 808 through 827 removed outlier: 3.768A 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 removed outlier: 3.864A pdb=" N GLYB3 853 " --> pdb=" O GLUB3 849 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1072 through 1077 removed outlier: 3.540A pdb=" N LEUB31076 " --> pdb=" O GLYB31072 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRPB31077 " --> pdb=" O ASNB31073 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 1072 through 1077' Processing helix chain 'B3' and resid 1134 through 1152 removed outlier: 4.057A pdb=" N HISB31138 " --> pdb=" O SERB31134 " (cutoff:3.500A) removed outlier: 3.801A 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 1182 through 1184 No H-bonds generated for 'chain 'B3' and resid 1182 through 1184' Processing helix chain 'B3' and resid 1186 through 1197 Processing helix chain 'B3' and resid 1200 through 1216 removed outlier: 3.586A pdb=" N ILEB31211 " --> pdb=" O LYSB31207 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARGB31212 " --> pdb=" O LEUB31208 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYRB31215 " --> pdb=" O ILEB31211 " (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 removed outlier: 3.885A pdb=" N GLNB4 35 " --> pdb=" O GLUB4 31 " (cutoff:3.500A) Processing helix chain 'B4' and resid 63 through 75 removed outlier: 3.557A pdb=" N ILEB4 73 " --> pdb=" O TYRB4 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASNB4 75 " --> pdb=" O ILEB4 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 112 through 122 removed outlier: 3.718A 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 198 Processing helix chain 'B4' and resid 199 through 206 Processing helix chain 'B4' and resid 206 through 211 removed outlier: 3.577A pdb=" N LEUB4 210 " --> pdb=" O ARGB4 206 " (cutoff:3.500A) removed outlier: 4.663A 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 8 through 18 removed outlier: 4.430A pdb=" N GLUB5 12 " --> pdb=" O HISB5 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUB5 14 " --> pdb=" O GLNB5 10 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSB5 17 " --> pdb=" O HISB5 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYRB5 18 " --> pdb=" O LEUB5 14 " (cutoff:3.500A) Processing helix chain 'B5' and resid 27 through 46 removed outlier: 3.699A pdb=" N ASNB5 34 " --> pdb=" O GLUB5 30 " (cutoff:3.500A) Processing helix chain 'B5' and resid 46 through 57 removed outlier: 3.575A pdb=" N LEUB5 50 " --> pdb=" O HISB5 46 " (cutoff:3.500A) Processing helix chain 'B5' and resid 60 through 71 Processing helix chain 'B6' and resid 5 through 11 Processing helix chain 'B6' and resid 31 through 41 removed outlier: 3.646A pdb=" N LYSB6 41 " --> pdb=" O ASPB6 37 " (cutoff:3.500A) Processing helix chain 'B6' and resid 66 through 78 removed outlier: 3.606A 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: 6.619A pdb=" N ARGA1 179 " --> pdb=" O ALAA1 175 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLNA1 180 " --> pdb=" O ARGA1 176 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHEA1 181 " --> pdb=" O ASNA1 177 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEUA1 182 " --> pdb=" O GLYA1 178 " (cutoff:3.500A) Processing helix chain 'A1' and resid 192 through 199 removed outlier: 4.648A 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 238 through 244 Processing helix chain 'A1' and resid 244 through 273 removed outlier: 4.965A pdb=" N ALAA1 250 " --> pdb=" O ARGA1 246 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYSA1 251 " --> pdb=" O VALA1 247 " (cutoff:3.500A) Processing helix chain 'A1' and resid 303 through 318 Processing helix chain 'A2' and resid 20 through 36 removed outlier: 3.560A pdb=" N GLUA2 36 " --> pdb=" O GLNA2 32 " (cutoff:3.500A) Processing helix chain 'A2' and resid 65 through 74 removed outlier: 3.912A pdb=" N GLNA2 74 " --> pdb=" O LEUA2 70 " (cutoff:3.500A) Processing helix chain 'A2' and resid 75 through 92 Processing helix chain 'A2' and resid 155 through 157 No H-bonds generated for 'chain 'A2' and resid 155 through 157' 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: 4.316A pdb=" N GLUA3 109 " --> pdb=" O PROA3 105 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHEA3 110 " --> pdb=" O META3 106 " (cutoff:3.500A) Processing helix chain 'A3' and resid 119 through 124 removed outlier: 3.532A pdb=" N ALAA3 124 " --> pdb=" O PROA3 120 " (cutoff:3.500A) 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: 3.877A 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 223 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 Processing helix chain 'A3' and resid 418 through 425 Processing helix chain 'A3' and resid 428 through 439 Processing helix chain 'A3' and resid 443 through 447 Processing helix chain 'A3' and resid 451 through 470 removed outlier: 3.670A pdb=" N SERA3 457 " --> pdb=" O GLUA3 453 " (cutoff:3.500A) Processing helix chain 'A3' and resid 488 through 497 removed outlier: 3.811A pdb=" N ARGA3 497 " --> pdb=" O GLUA3 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 643 Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 226 removed outlier: 6.897A pdb=" N GLY B 218 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 237 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER B 220 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY B 187 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE B 258 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 189 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.292A pdb=" N GLU B 320 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG B 483 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE B 322 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 434 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 482 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 436 " --> pdb=" O PHE B 482 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP B 351 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 437 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 353 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 352 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER B 420 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 354 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 441 through 448 removed outlier: 3.573A pdb=" N LEU B 741 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN B 745 " --> pdb=" O VAL B 718 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 21 through 22 removed outlier: 3.584A pdb=" N SER H 67 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 39 through 42 removed outlier: 6.475A pdb=" N TYR H 71 " --> pdb=" O CYS H 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B1' and resid 412 through 414 removed outlier: 3.646A pdb=" N GLNB6 47 " --> pdb=" O VALB6 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B3' and resid 1101 through 1107 removed outlier: 3.628A pdb=" N SERB31103 " --> pdb=" O THRB31120 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THRB31120 " --> pdb=" O SERB31103 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYRB31119 " --> pdb=" O GLYB31127 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILEB31126 " --> pdb=" O LEUB3 8 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEUB3 3 " --> pdb=" O ILEB31174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B3' and resid 16 through 20 removed outlier: 4.145A pdb=" N PHEB3 16 " --> pdb=" O SERB3 33 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEUB3 38 " --> pdb=" O THRB3 55 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THRB3 55 " --> pdb=" O LEUB3 38 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEUB3 40 " --> pdb=" O LEUB3 53 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HISB3 51 " --> pdb=" O ARGB3 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B3' and resid 64 through 69 removed outlier: 7.730A pdb=" N ASPB3 76 " --> pdb=" O TYRB3 92 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYRB3 92 " --> pdb=" O ASPB3 76 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VALB3 88 " --> pdb=" O VALB3 80 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILEB3 87 " --> pdb=" O GLNB3 104 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLNB3 104 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILEB3 89 " --> pdb=" O ILEB3 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLNB3 93 " --> pdb=" O METB3 98 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N METB3 98 " --> pdb=" O GLNB3 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B3' and resid 120 through 123 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 166 through 173 removed outlier: 6.022A pdb=" N VALB3 167 " --> pdb=" O METB3 187 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N METB3 187 " --> pdb=" O VALB3 167 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HISB3 169 " --> pdb=" O LEUB3 185 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N METB3 181 " --> pdb=" O VALB3 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEUB3 208 " --> pdb=" O SERB3 225 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SERB3 225 " --> pdb=" O LEUB3 208 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHEB3 210 " --> pdb=" O LYSB3 223 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASPB3 214 " --> pdb=" O HISB3 219 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HISB3 219 " --> pdb=" O ASPB3 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B3' and resid 232 through 238 removed outlier: 3.900A pdb=" N PHEB3 234 " --> pdb=" O CYSB3 251 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLYB3 247 " --> pdb=" O VALB3 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYRB3 255 " --> pdb=" O SERB3 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B3' and resid 273 through 274 removed outlier: 5.769A pdb=" N ARGB3 273 " --> pdb=" O PHEB3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B3' and resid 289 through 294 removed outlier: 3.937A pdb=" N CYSB3 289 " --> pdb=" O GLNB3 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHEB3 300 " --> pdb=" O HISB3 293 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHEB3 299 " --> pdb=" O LEUB3 315 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEUB3 315 " --> pdb=" O PHEB3 299 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILEB3 310 " --> pdb=" O PHEB3 330 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLUB3 324 " --> pdb=" O GLUB3 316 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B3' and resid 340 through 342 removed outlier: 3.571A pdb=" N CYSB3 340 " --> pdb=" O PHEB3 348 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHEB3 348 " --> pdb=" O CYSB3 340 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHEB3 346 " --> pdb=" O LEUB3 342 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYRB3 357 " --> pdb=" O VALB3 349 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEUB3 358 " --> pdb=" O VALB3 398 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VALB3 398 " --> pdb=" O LEUB3 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B3' and resid 407 through 413 removed outlier: 4.017A pdb=" N PHEB3 409 " --> pdb=" O ALAB3 426 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALAB3 413 " --> pdb=" O GLNB3 422 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 445 through 450 removed outlier: 5.321A pdb=" N GLUB3 446 " --> pdb=" O ALAB3 766 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALAB3 766 " --> pdb=" O GLUB3 446 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALAB3 448 " --> pdb=" O ILEB3 764 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 458 through 462 removed outlier: 4.102A pdb=" N VALB3 484 " --> pdb=" O VALB3 494 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLUB3 492 " --> pdb=" O SERB3 486 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 507 through 510 removed outlier: 3.734A pdb=" N HISB3 526 " --> pdb=" O ASNB3 534 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASNB3 534 " --> pdb=" O HISB3 526 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B3' and resid 544 through 548 removed outlier: 3.606A pdb=" N ASNB3 575 " --> pdb=" O GLUB3 567 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B3' and resid 587 through 592 removed outlier: 4.047A pdb=" N CYSB3 589 " --> pdb=" O GLYB3 608 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THRB3 613 " --> pdb=" O LEUB3 609 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SERB3 629 " --> pdb=" O ILEB3 616 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SERB3 618 " --> pdb=" O PROB3 627 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B3' and resid 637 through 643 removed outlier: 3.943A pdb=" N SERB3 639 " --> pdb=" O GLYB3 668 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VALB3 673 " --> pdb=" O LEUB3 669 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B3' and resid 700 through 706 removed outlier: 3.841A pdb=" N LYSB3 700 " --> pdb=" O METB3 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALB3 712 " --> pdb=" O SERB3 722 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 784 through 790 removed outlier: 6.475A pdb=" N THRB3 802 " --> pdb=" O PROB3 785 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYSB3 787 " --> pdb=" O ILEB3 800 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILEB3 800 " --> pdb=" O LYSB3 787 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILEB3 866 " --> pdb=" O LEUB3 879 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEUB3 879 " --> pdb=" O ILEB3 866 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VALB3 868 " --> pdb=" O LEUB3 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 886 through 894 removed outlier: 6.171A pdb=" N ALAB3 888 " --> pdb=" O ALAB3 910 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALAB3 910 " --> pdb=" O ALAB3 888 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SERB3 890 " --> pdb=" O GLYB3 908 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALB3 907 " --> pdb=" O TYRB3 926 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLYB3 923 " --> pdb=" O PROB3 944 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VALB3 925 " --> pdb=" O LYSB3 942 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYSB3 942 " --> pdb=" O VALB3 925 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THRB3 927 " --> pdb=" O LEUB3 940 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 959 through 961 removed outlier: 3.560A pdb=" N VALB3 959 " --> pdb=" O TYRB3 970 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEUB3 967 " --> pdb=" O GLUB3 982 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLUB3 982 " --> pdb=" O LEUB3 967 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VALB3 969 " --> pdb=" O LYSB3 980 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B3' and resid 990 through 995 removed outlier: 3.739A pdb=" N GLYB3 992 " --> pdb=" O SERB31003 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRPB31011 " --> pdb=" O PHEB31024 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHEB31024 " --> pdb=" O TRPB31011 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 1033 through 1038 removed outlier: 3.891A pdb=" N THRB31035 " --> pdb=" O ALAB31047 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASNB31052 " --> pdb=" O ASPB31048 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILEB31053 " --> pdb=" O ASNB31094 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASNB31094 " --> pdb=" O ILEB31053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VALB31055 " --> pdb=" O ILEB31092 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B4' and resid 39 through 41 removed outlier: 4.000A pdb=" N ASNB4 41 " --> pdb=" O GLUB4 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALB4 59 " --> pdb=" O VALB4 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASNB4 87 " --> pdb=" O TYRB4 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEB4 77 " --> pdb=" O ILEB4 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B4' and resid 131 through 134 removed outlier: 7.558A pdb=" N LYSB4 131 " --> pdb=" O TYRB4 144 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYRB4 144 " --> pdb=" O LYSB4 131 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N METB4 133 " --> pdb=" O LYSB4 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B6' and resid 81 through 82 Processing sheet with id=AD7, first strand: chain 'A1' and resid 279 through 284 removed outlier: 6.307A pdb=" N VALA1 280 " --> pdb=" O ALAA2 180 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LYSA2 182 " --> pdb=" O VALA1 280 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VALA1 282 " --> pdb=" O LYSA2 182 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N THRA1 284 " --> pdb=" O PROA2 184 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILEA2 179 " --> pdb=" O META2 171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARGA2 148 " --> pdb=" O ALAA2 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A2' and resid 46 through 48 removed outlier: 3.511A pdb=" N THRA2 61 " --> pdb=" O CYSA2 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.711A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N HISA2 211 " --> pdb=" O ASPA2 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.711A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A3' and resid 406 through 408 Processing sheet with id=AE3, first strand: chain 'A3' and resid 479 through 480 1716 hydrogen bonds defined for protein. 4884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 9.71 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11453 1.34 - 1.46: 6653 1.46 - 1.58: 20353 1.58 - 1.70: 160 1.70 - 1.82: 316 Bond restraints: 38935 Sorted by residual: bond pdb=" N TRPB2 708 " pdb=" CA TRPB2 708 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.18e-02 7.18e+03 7.18e+00 bond pdb=" N GLUB2 710 " pdb=" CA GLUB2 710 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.86e+00 bond pdb=" N ASNB3 988 " pdb=" CA ASNB3 988 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N PROB2 707 " pdb=" CD PROB2 707 " ideal model delta sigma weight residual 1.473 1.440 0.033 1.40e-02 5.10e+03 5.48e+00 bond pdb=" C4' PSU 2 43 " pdb=" O4' PSU 2 43 " ideal model delta sigma weight residual 1.410 1.455 -0.045 2.00e-02 2.50e+03 5.05e+00 ... (remaining 38930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 52198 2.01 - 4.01: 662 4.01 - 6.02: 79 6.02 - 8.02: 13 8.02 - 10.03: 18 Bond angle restraints: 52970 Sorted by residual: angle pdb=" CA GLUB1 809 " pdb=" CB GLUB1 809 " pdb=" CG GLUB1 809 " ideal model delta sigma weight residual 114.10 122.50 -8.40 2.00e+00 2.50e-01 1.76e+01 angle pdb=" CB GLUB1 809 " pdb=" CG GLUB1 809 " pdb=" CD GLUB1 809 " ideal model delta sigma weight residual 112.60 119.41 -6.81 1.70e+00 3.46e-01 1.60e+01 angle pdb=" N PROB2 707 " pdb=" CD PROB2 707 " pdb=" CG PROB2 707 " ideal model delta sigma weight residual 103.20 97.27 5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" C THRB1 808 " pdb=" N GLUB1 809 " pdb=" CA GLUB1 809 " ideal model delta sigma weight residual 121.99 115.91 6.08 1.56e+00 4.11e-01 1.52e+01 angle pdb=" N PROB2 707 " pdb=" CA PROB2 707 " pdb=" CB PROB2 707 " ideal model delta sigma weight residual 103.25 99.19 4.06 1.05e+00 9.07e-01 1.50e+01 ... (remaining 52965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 22959 35.71 - 71.42: 818 71.42 - 107.13: 44 107.13 - 142.85: 2 142.85 - 178.56: 7 Dihedral angle restraints: 23830 sinusoidal: 10598 harmonic: 13232 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 -128.00 50.56 -178.56 1 1.70e+01 3.46e-03 6.64e+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 50.41 -178.41 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 49.17 -177.17 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5088 0.058 - 0.116: 700 0.116 - 0.174: 87 0.174 - 0.232: 1 0.232 - 0.290: 8 Chirality restraints: 5884 Sorted by residual: chirality pdb=" C3' PSU 2 43 " pdb=" C4' PSU 2 43 " pdb=" O3' PSU 2 43 " pdb=" C2' PSU 2 43 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2' PSU 2 37 " pdb=" C3' PSU 2 37 " pdb=" O2' PSU 2 37 " pdb=" C1' PSU 2 37 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C2' PSU 2 58 " pdb=" C3' PSU 2 58 " pdb=" O2' PSU 2 58 " pdb=" C1' PSU 2 58 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 5881 not shown) Planarity restraints: 6617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRB1 508 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PROB1 509 " -0.085 5.00e-02 4.00e+02 pdb=" CA PROB1 509 " 0.025 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 ASPB3 680 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PROB3 681 " -0.081 5.00e-02 4.00e+02 pdb=" CA PROB3 681 " 0.024 5.00e-02 4.00e+02 pdb=" CD PROB3 681 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEA3 392 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PROA3 393 " 0.078 5.00e-02 4.00e+02 pdb=" CA PROA3 393 " -0.023 5.00e-02 4.00e+02 pdb=" CD PROA3 393 " -0.025 5.00e-02 4.00e+02 ... (remaining 6614 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 12920 2.86 - 3.37: 35273 3.37 - 3.88: 62039 3.88 - 4.39: 68511 4.39 - 4.90: 116257 Nonbonded interactions: 295000 Sorted by model distance: nonbonded pdb=" N2 G 2 33 " pdb=" O2 U R 1 " model vdw 2.351 2.496 nonbonded pdb=" O THRB2 706 " pdb=" OG1 THRB2 706 " model vdw 2.388 3.040 nonbonded pdb=" O5' G 2 31 " pdb=" O4' G 2 31 " model vdw 2.487 2.432 nonbonded pdb=" OD1 ASPB11290 " pdb=" N ASPB11291 " model vdw 2.502 3.120 nonbonded pdb=" O5' U 2 46 " pdb=" O4' U 2 46 " model vdw 2.518 2.432 ... (remaining 294995 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 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: 0.050 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 44.020 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 38947 Z= 0.128 Angle : 0.570 10.027 52988 Z= 0.318 Chirality : 0.042 0.290 5884 Planarity : 0.004 0.049 6617 Dihedral : 17.169 178.556 15292 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 18.10 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 1.15 (0.13), residues: 4485 helix: 1.90 (0.12), residues: 1861 sheet: 0.49 (0.21), residues: 702 loop : -0.21 (0.15), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGB6 85 TYR 0.016 0.001 TYRB1 830 PHE 0.014 0.001 PHEB1 818 TRP 0.014 0.001 TRPB2 708 HIS 0.003 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (38935) covalent geometry : angle 0.56401 / 0.32 (52970) hydrogen bonds : bond 0.18003 / 12.29 ( 1711) hydrogen bonds : angle 6.13341 / 4.36 ( 4908) metal coordination : bond 0.01193 / 0.80 ( 12) metal coordination : angle 4.32615 / 2.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 601 time to evaluate : 1.464 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ILE cc_start: 0.8795 (mm) cc_final: 0.8498 (pt) REVERT: H 77 ILE cc_start: 0.8873 (pt) cc_final: 0.8641 (tp) REVERT: B1 575 LEU cc_start: 0.9080 (mm) cc_final: 0.8798 (tt) REVERT: B1 613 MET cc_start: 0.8404 (mmm) cc_final: 0.7930 (mtm) REVERT: B1 834 VAL cc_start: 0.8812 (t) cc_final: 0.7655 (t) REVERT: B1 954 LEU cc_start: 0.8872 (tp) cc_final: 0.8474 (tt) REVERT: B1 1133 MET cc_start: 0.5936 (mtt) cc_final: 0.5670 (mtt) REVERT: B2 602 LYS cc_start: 0.7121 (tppt) cc_final: 0.6880 (mttm) REVERT: B2 619 MET cc_start: 0.3912 (tmm) cc_final: 0.3679 (mtp) REVERT: B3 39 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7419 (tt0) REVERT: B3 329 TYR cc_start: 0.7876 (t80) cc_final: 0.6861 (t80) REVERT: B3 630 MET cc_start: 0.5994 (mmp) cc_final: 0.5532 (mmm) REVERT: B3 765 LEU cc_start: 0.9072 (pp) cc_final: 0.8565 (mm) REVERT: B3 823 MET cc_start: 0.8834 (ttm) cc_final: 0.8314 (tmm) REVERT: B4 1 MET cc_start: 0.5253 (tmm) cc_final: 0.4496 (tmm) REVERT: B5 9 SER cc_start: 0.7770 (p) cc_final: 0.7464 (t) REVERT: A2 65 ASN cc_start: 0.6352 (p0) cc_final: 0.6011 (p0) REVERT: A3 1 MET cc_start: -0.1273 (ttt) cc_final: -0.2153 (tmm) REVERT: A3 392 ILE cc_start: 0.8629 (tp) cc_final: 0.8163 (mp) outliers start: 2 outliers final: 1 residues processed: 603 average time/residue: 0.2717 time to fit residues: 258.3374 Evaluate side-chains 310 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B2 residue 712 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN B 647 ASN H 78 GLN B11108 ASN ** B11193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B11228 GLN B2 541 GLN B3 422 GLN B3 526 HIS B3 861 GLN B3 985 HIS B31052 ASN A1 187 GLN A1 288 GLN A3 431 HIS A3 445 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.167404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.138068 restraints weight = 138349.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.132588 restraints weight = 177943.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.130027 restraints weight = 130464.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.129323 restraints weight = 118928.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.129635 restraints weight = 127314.537| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 38947 Z= 0.213 Angle : 0.678 13.317 52988 Z= 0.342 Chirality : 0.044 0.247 5884 Planarity : 0.005 0.072 6617 Dihedral : 13.201 178.713 6187 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.10 % Allowed : 19.14 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.90 (0.13), residues: 4485 helix: 1.59 (0.12), residues: 1917 sheet: 0.51 (0.20), residues: 694 loop : -0.35 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 702 TYR 0.030 0.002 TYRB1 830 PHE 0.022 0.002 PHEA2 181 TRP 0.021 0.002 TRPB1 819 HIS 0.007 0.001 HISB11194 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (38935) covalent geometry : angle 0.67242 / 0.34 (52970) hydrogen bonds : bond 0.05172 / 3.51 ( 1711) hydrogen bonds : angle 5.08321 / 3.62 ( 4908) metal coordination : bond 0.01119 / 0.75 ( 12) metal coordination : angle 4.63666 / 2.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 314 time to evaluate : 1.320 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: B 550 ASN cc_start: 0.6901 (m-40) cc_final: 0.6296 (t0) REVERT: B 749 THR cc_start: 0.3804 (OUTLIER) cc_final: 0.3582 (m) REVERT: C 630 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8477 (mm) REVERT: C 641 LEU cc_start: 0.7395 (pt) cc_final: 0.6722 (mt) REVERT: H 19 ILE cc_start: 0.8796 (mm) cc_final: 0.8589 (pt) REVERT: H 34 ASP cc_start: 0.8104 (t0) cc_final: 0.7690 (t0) REVERT: B1 575 LEU cc_start: 0.9183 (mm) cc_final: 0.8822 (pp) REVERT: B1 853 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B1 864 TYR cc_start: 0.7732 (t80) cc_final: 0.7317 (t80) REVERT: B1 1133 MET cc_start: 0.6187 (mtt) cc_final: 0.5915 (mtt) REVERT: B1 1181 ASP cc_start: 0.7759 (t0) cc_final: 0.7540 (t70) REVERT: B3 1 MET cc_start: 0.8178 (ptp) cc_final: 0.7502 (ptm) REVERT: B3 39 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7182 (tt0) REVERT: B3 508 CYS cc_start: 0.5561 (OUTLIER) cc_final: 0.3671 (m) REVERT: B3 765 LEU cc_start: 0.8703 (pp) cc_final: 0.8349 (mm) REVERT: B3 1020 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: B4 1 MET cc_start: 0.5588 (tmm) cc_final: 0.4576 (tmm) REVERT: B5 9 SER cc_start: 0.7913 (p) cc_final: 0.7688 (t) REVERT: A1 186 MET cc_start: 0.3137 (mmp) cc_final: 0.2512 (mpp) REVERT: A2 47 MET cc_start: 0.7812 (ptm) cc_final: 0.7591 (ptp) REVERT: A2 65 ASN cc_start: 0.8348 (p0) cc_final: 0.8028 (p0) REVERT: A2 85 ARG cc_start: 0.6680 (mmp80) cc_final: 0.5946 (mmp80) REVERT: A3 1 MET cc_start: -0.1201 (ttt) cc_final: -0.2175 (tmm) REVERT: A3 392 ILE cc_start: 0.8473 (tp) cc_final: 0.8081 (mp) outliers start: 122 outliers final: 55 residues processed: 403 average time/residue: 0.2019 time to fit residues: 135.9996 Evaluate side-chains 323 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain B1 residue 540 MET Chi-restraints excluded: chain B1 residue 619 ASN Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 651 VAL Chi-restraints excluded: chain B1 residue 689 ILE Chi-restraints excluded: chain B1 residue 757 MET Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 821 HIS Chi-restraints excluded: chain B1 residue 853 ILE Chi-restraints excluded: chain B1 residue 889 GLU Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 989 VAL Chi-restraints excluded: chain B1 residue 1001 VAL Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 567 ASP Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 628 VAL Chi-restraints excluded: chain B2 residue 678 THR Chi-restraints excluded: chain B2 residue 712 GLU Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 131 MET Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 175 VAL Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 305 THR Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 437 VAL Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 573 GLN Chi-restraints excluded: chain B3 residue 610 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 701 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1076 LEU Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1144 VAL Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 59 VAL Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 30 LEU Chi-restraints excluded: chain A2 residue 197 THR Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 449 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 340 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 430 optimal weight: 9.9990 chunk 343 optimal weight: 1.9990 chunk 411 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 688 ASN B1 492 GLN B11100 ASN B11194 HIS ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 541 GLN ** B3 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 526 HIS B3 636 GLN B6 95 ASN ** A2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 98 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.166854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.137098 restraints weight = 138448.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.133483 restraints weight = 180578.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.129856 restraints weight = 125969.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.128924 restraints weight = 135086.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.129561 restraints weight = 119250.196| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38947 Z= 0.193 Angle : 0.650 13.454 52988 Z= 0.326 Chirality : 0.043 0.240 5884 Planarity : 0.005 0.076 6617 Dihedral : 12.949 178.841 6187 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.36 % Allowed : 18.89 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.76 (0.13), residues: 4485 helix: 1.50 (0.12), residues: 1925 sheet: 0.40 (0.20), residues: 678 loop : -0.45 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 649 TYR 0.033 0.002 TYRB1 761 PHE 0.024 0.002 PHEA2 181 TRP 0.020 0.001 TRPA2 166 HIS 0.007 0.001 HISB3 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (38935) covalent geometry : angle 0.64390 / 0.33 (52970) hydrogen bonds : bond 0.04519 / 3.06 ( 1711) hydrogen bonds : angle 4.86362 / 3.47 ( 4908) metal coordination : bond 0.01084 / 0.72 ( 12) metal coordination : angle 4.70260 / 2.50 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 279 time to evaluate : 1.454 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: B 550 ASN cc_start: 0.6921 (m-40) cc_final: 0.6360 (t0) REVERT: C 630 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (mm) REVERT: C 641 LEU cc_start: 0.7394 (pt) cc_final: 0.6675 (mt) REVERT: H 34 ASP cc_start: 0.8219 (t0) cc_final: 0.7734 (t0) REVERT: H 60 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B1 609 MET cc_start: 0.7313 (mtt) cc_final: 0.7084 (mtp) REVERT: B1 613 MET cc_start: 0.8573 (mmm) cc_final: 0.8090 (mtm) REVERT: B1 853 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B1 864 TYR cc_start: 0.7729 (t80) cc_final: 0.7342 (t80) REVERT: B1 962 MET cc_start: 0.8330 (mmm) cc_final: 0.8011 (mpp) REVERT: B1 981 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: B2 639 TYR cc_start: 0.6811 (m-10) cc_final: 0.6547 (m-10) REVERT: B2 712 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6058 (mt-10) REVERT: B3 1 MET cc_start: 0.8290 (ptp) cc_final: 0.7831 (ptm) REVERT: B3 39 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7067 (tt0) REVERT: B3 508 CYS cc_start: 0.5329 (OUTLIER) cc_final: 0.3496 (m) REVERT: B3 630 MET cc_start: 0.5110 (mmp) cc_final: 0.4590 (mmp) REVERT: B3 765 LEU cc_start: 0.8578 (pp) cc_final: 0.8182 (mt) REVERT: B3 1020 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: B4 1 MET cc_start: 0.5716 (tmm) cc_final: 0.4557 (tmm) REVERT: B5 9 SER cc_start: 0.7955 (p) cc_final: 0.7734 (t) REVERT: A1 186 MET cc_start: 0.3014 (mmp) cc_final: 0.2034 (mtt) REVERT: A2 65 ASN cc_start: 0.8424 (p0) cc_final: 0.8067 (p0) REVERT: A2 81 ASN cc_start: 0.7889 (m-40) cc_final: 0.6674 (m-40) REVERT: A2 85 ARG cc_start: 0.6728 (mmp80) cc_final: 0.6062 (mmp80) REVERT: A3 1 MET cc_start: -0.1683 (ttt) cc_final: -0.2544 (tmm) REVERT: A3 392 ILE cc_start: 0.8459 (tp) cc_final: 0.8081 (mp) outliers start: 132 outliers final: 72 residues processed: 387 average time/residue: 0.2010 time to fit residues: 132.9616 Evaluate side-chains 340 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 261 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 570 TYR Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 651 VAL Chi-restraints excluded: chain B1 residue 689 ILE Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 853 ILE Chi-restraints excluded: chain B1 residue 889 GLU Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1001 VAL Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1093 VAL Chi-restraints excluded: chain B1 residue 1111 CYS Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 712 GLU Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 131 MET Chi-restraints excluded: chain B3 residue 143 ILE Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 175 VAL Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 305 THR Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 437 VAL Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 517 VAL Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 573 GLN Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1076 LEU Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1144 VAL Chi-restraints excluded: chain B3 residue 1174 ILE Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 59 VAL Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 30 LEU Chi-restraints excluded: chain A2 residue 197 THR Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 487 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 399 optimal weight: 8.9990 chunk 265 optimal weight: 0.0970 chunk 301 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 688 ASN B11134 ASN ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 541 GLN B3 219 HIS B3 526 HIS B3 956 GLN ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 211 HIS ** 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 = 0.4639 r_free = 0.4639 target = 0.166490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.136664 restraints weight = 137791.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.131706 restraints weight = 175971.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.128005 restraints weight = 119041.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.127989 restraints weight = 125429.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.128413 restraints weight = 105655.516| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38947 Z= 0.182 Angle : 0.632 14.426 52988 Z= 0.316 Chirality : 0.043 0.260 5884 Planarity : 0.005 0.081 6617 Dihedral : 12.813 179.057 6187 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.48 % Allowed : 19.57 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.67 (0.13), residues: 4485 helix: 1.46 (0.12), residues: 1925 sheet: 0.29 (0.20), residues: 680 loop : -0.51 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 649 TYR 0.021 0.002 TYRA1 271 PHE 0.019 0.002 PHEA2 210 TRP 0.018 0.001 TRPB31032 HIS 0.005 0.001 HISB3 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (38935) covalent geometry : angle 0.62617 / 0.32 (52970) hydrogen bonds : bond 0.04268 / 2.89 ( 1711) hydrogen bonds : angle 4.74480 / 3.38 ( 4908) metal coordination : bond 0.01023 / 0.67 ( 12) metal coordination : angle 4.58821 / 2.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 274 time to evaluate : 1.297 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: B 550 ASN cc_start: 0.7014 (m-40) cc_final: 0.6467 (t0) REVERT: B 749 THR cc_start: 0.3805 (OUTLIER) cc_final: 0.3585 (m) REVERT: C 630 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8492 (mm) REVERT: C 641 LEU cc_start: 0.7339 (pt) cc_final: 0.6623 (mt) REVERT: H 23 CYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7748 (p) REVERT: H 60 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8366 (mt) REVERT: B1 613 MET cc_start: 0.8587 (mmm) cc_final: 0.7898 (mtm) REVERT: B1 853 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8648 (mt) REVERT: B1 864 TYR cc_start: 0.7760 (t80) cc_final: 0.7352 (t80) REVERT: B1 954 LEU cc_start: 0.9149 (mm) cc_final: 0.8885 (mp) REVERT: B1 981 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: B2 457 MET cc_start: 0.8516 (tmm) cc_final: 0.8174 (mtt) REVERT: B2 647 ASN cc_start: 0.5974 (OUTLIER) cc_final: 0.5252 (p0) REVERT: B2 712 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6300 (mt-10) REVERT: B3 1 MET cc_start: 0.8404 (ptp) cc_final: 0.7999 (ptm) REVERT: B3 39 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7445 (tt0) REVERT: B3 508 CYS cc_start: 0.5513 (OUTLIER) cc_final: 0.3644 (m) REVERT: B3 762 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8059 (pp) REVERT: B3 765 LEU cc_start: 0.8600 (pp) cc_final: 0.8128 (mt) REVERT: B3 1020 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: B3 1185 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5244 (ttm) REVERT: B4 1 MET cc_start: 0.5765 (tmm) cc_final: 0.4560 (tmm) REVERT: B5 9 SER cc_start: 0.7921 (p) cc_final: 0.7698 (t) REVERT: A1 186 MET cc_start: 0.3313 (mmp) cc_final: 0.2211 (mtt) REVERT: A2 65 ASN cc_start: 0.8402 (p0) cc_final: 0.8068 (p0) REVERT: A2 81 ASN cc_start: 0.7990 (m-40) cc_final: 0.6722 (m-40) REVERT: A2 85 ARG cc_start: 0.6688 (mmp80) cc_final: 0.6104 (mmp80) REVERT: A3 1 MET cc_start: -0.1586 (ttt) cc_final: -0.2040 (tmm) REVERT: A3 392 ILE cc_start: 0.8394 (tp) cc_final: 0.7993 (mp) outliers start: 137 outliers final: 91 residues processed: 387 average time/residue: 0.1883 time to fit residues: 126.1931 Evaluate side-chains 359 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 256 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain B1 residue 566 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 570 TYR Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 651 VAL Chi-restraints excluded: chain B1 residue 701 VAL Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 853 ILE Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1001 VAL Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1111 CYS Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1169 VAL Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1178 MET Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 491 LEU Chi-restraints excluded: chain B2 residue 494 THR Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 647 ASN Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B2 residue 712 GLU Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 131 MET Chi-restraints excluded: chain B3 residue 143 ILE Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 175 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 305 THR Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 420 THR Chi-restraints excluded: chain B3 residue 437 VAL Chi-restraints excluded: chain B3 residue 494 VAL 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 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 573 GLN Chi-restraints excluded: chain B3 residue 587 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 824 VAL Chi-restraints excluded: chain B3 residue 876 THR Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1035 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1144 VAL Chi-restraints excluded: chain B3 residue 1174 ILE Chi-restraints excluded: chain B3 residue 1185 MET Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 30 LEU Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 425 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 288 optimal weight: 20.0000 chunk 372 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 257 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 412 optimal weight: 8.9990 chunk 310 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 ASN B 688 ASN ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 526 HIS ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.166750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.137210 restraints weight = 137888.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.133218 restraints weight = 178762.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.129036 restraints weight = 128316.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.128905 restraints weight = 139576.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.129421 restraints weight = 117424.664| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38947 Z= 0.146 Angle : 0.614 13.882 52988 Z= 0.303 Chirality : 0.042 0.285 5884 Planarity : 0.004 0.064 6617 Dihedral : 12.712 178.697 6187 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.46 % Allowed : 20.46 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.69 (0.13), residues: 4485 helix: 1.47 (0.12), residues: 1932 sheet: 0.28 (0.20), residues: 664 loop : -0.48 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 649 TYR 0.020 0.001 TYRA1 271 PHE 0.020 0.001 PHEA2 206 TRP 0.017 0.001 TRPB31032 HIS 0.005 0.001 HISB3 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (38935) covalent geometry : angle 0.60885 / 0.30 (52970) hydrogen bonds : bond 0.04023 / 2.73 ( 1711) hydrogen bonds : angle 4.63107 / 3.31 ( 4908) metal coordination : bond 0.00749 / 0.47 ( 12) metal coordination : angle 4.33976 / 2.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 268 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 MET cc_start: 0.1471 (ptm) cc_final: 0.1238 (ttp) REVERT: B 528 MET cc_start: 0.2011 (mpp) cc_final: 0.1189 (mpp) REVERT: B 550 ASN cc_start: 0.6964 (m-40) cc_final: 0.6429 (t0) REVERT: C 630 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (mm) REVERT: B1 532 PHE cc_start: 0.7140 (m-80) cc_final: 0.6829 (m-80) REVERT: B1 609 MET cc_start: 0.7339 (mtt) cc_final: 0.7064 (mtp) REVERT: B1 613 MET cc_start: 0.8458 (mmm) cc_final: 0.7910 (mtm) REVERT: B1 954 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (mp) REVERT: B1 981 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: B1 1006 MET cc_start: 0.8772 (tmm) cc_final: 0.7801 (tpt) REVERT: B2 647 ASN cc_start: 0.6021 (OUTLIER) cc_final: 0.5275 (p0) REVERT: B3 1 MET cc_start: 0.8431 (ptp) cc_final: 0.7997 (ptm) REVERT: B3 39 GLU cc_start: 0.7734 (mt-10) cc_final: 0.6930 (tt0) REVERT: B3 285 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7351 (ttm) REVERT: B3 508 CYS cc_start: 0.5469 (OUTLIER) cc_final: 0.3617 (m) REVERT: B3 762 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8054 (pp) REVERT: B3 765 LEU cc_start: 0.8560 (pp) cc_final: 0.8106 (mt) REVERT: B3 1020 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: B3 1185 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.5196 (ttm) REVERT: B4 1 MET cc_start: 0.5731 (tmm) cc_final: 0.4540 (tmm) REVERT: B4 211 PHE cc_start: 0.4051 (OUTLIER) cc_final: 0.3230 (t80) REVERT: B5 9 SER cc_start: 0.8093 (p) cc_final: 0.7878 (t) REVERT: B5 55 ILE cc_start: 0.8998 (mm) cc_final: 0.8745 (mt) REVERT: A1 186 MET cc_start: 0.3236 (mmp) cc_final: 0.2094 (mtt) REVERT: A2 65 ASN cc_start: 0.8410 (p0) cc_final: 0.8030 (p0) REVERT: A2 81 ASN cc_start: 0.8127 (m-40) cc_final: 0.6786 (m110) REVERT: A2 85 ARG cc_start: 0.6645 (mmp80) cc_final: 0.6096 (mmp80) REVERT: A3 1 MET cc_start: -0.1795 (ttt) cc_final: -0.2124 (tmm) REVERT: A3 392 ILE cc_start: 0.8420 (tp) cc_final: 0.8005 (mp) REVERT: A3 462 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7602 (mt) outliers start: 136 outliers final: 88 residues processed: 373 average time/residue: 0.1923 time to fit residues: 123.1258 Evaluate side-chains 356 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 257 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain B1 residue 531 LEU Chi-restraints excluded: chain B1 residue 566 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 570 TYR Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 651 VAL Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 787 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 949 GLN Chi-restraints excluded: chain B1 residue 954 LEU Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1093 VAL Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1147 VAL Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1169 VAL Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 491 LEU Chi-restraints excluded: chain B2 residue 494 THR Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 647 ASN Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 58 VAL Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 143 ILE Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 285 MET Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 420 THR Chi-restraints excluded: chain B3 residue 437 VAL Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 494 VAL 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 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 587 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 800 ILE Chi-restraints excluded: chain B3 residue 824 VAL Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1035 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1144 VAL Chi-restraints excluded: chain B3 residue 1174 ILE Chi-restraints excluded: chain B3 residue 1185 MET Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 211 PHE Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 462 LEU Chi-restraints excluded: chain A3 residue 487 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 362 optimal weight: 0.0470 chunk 326 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 424 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 422 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 ASN B 688 ASN ** B1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 9 GLN B3 28 GLN B3 526 HIS ** B31094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 135 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 = 0.4654 r_free = 0.4654 target = 0.167524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.138059 restraints weight = 137753.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134458 restraints weight = 171998.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.129653 restraints weight = 114978.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.129618 restraints weight = 134615.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.129980 restraints weight = 123479.951| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 38947 Z= 0.112 Angle : 0.592 14.258 52988 Z= 0.290 Chirality : 0.041 0.226 5884 Planarity : 0.004 0.056 6617 Dihedral : 12.564 178.805 6184 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.05 % Allowed : 20.87 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.80 (0.13), residues: 4485 helix: 1.60 (0.12), residues: 1925 sheet: 0.27 (0.20), residues: 684 loop : -0.45 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 649 TYR 0.040 0.001 TYRB4 166 PHE 0.018 0.001 PHEA2 210 TRP 0.016 0.001 TRPB31032 HIS 0.004 0.001 HISA2 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (38935) covalent geometry : angle 0.58829 / 0.29 (52970) hydrogen bonds : bond 0.03757 / 2.55 ( 1711) hydrogen bonds : angle 4.49639 / 3.23 ( 4908) metal coordination : bond 0.00516 / 0.28 ( 12) metal coordination : angle 3.85796 / 2.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 275 time to evaluate : 0.943 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: B 273 MET cc_start: 0.1650 (ptm) cc_final: 0.1362 (ttp) REVERT: B 528 MET cc_start: 0.2781 (mpp) cc_final: 0.1865 (mpp) REVERT: B 550 ASN cc_start: 0.7023 (m-40) cc_final: 0.6490 (t0) REVERT: B 749 THR cc_start: 0.3822 (OUTLIER) cc_final: 0.3595 (m) REVERT: C 630 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8479 (mm) REVERT: H 60 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B1 499 LYS cc_start: 0.7833 (mttt) cc_final: 0.7130 (mmmt) REVERT: B1 532 PHE cc_start: 0.7201 (m-80) cc_final: 0.6970 (m-80) REVERT: B1 609 MET cc_start: 0.7295 (mtt) cc_final: 0.7037 (mtp) REVERT: B1 613 MET cc_start: 0.8474 (mmm) cc_final: 0.7947 (mtm) REVERT: B1 839 GLU cc_start: 0.7803 (tp30) cc_final: 0.7490 (tm-30) REVERT: B1 954 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8895 (mp) REVERT: B1 981 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: B1 1006 MET cc_start: 0.8618 (tmm) cc_final: 0.7984 (tmm) REVERT: B1 1081 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: B1 1108 ASN cc_start: 0.6813 (OUTLIER) cc_final: 0.6313 (t0) REVERT: B2 457 MET cc_start: 0.8497 (tmm) cc_final: 0.8210 (mtt) REVERT: B3 1 MET cc_start: 0.8466 (ptp) cc_final: 0.8065 (ptm) REVERT: B3 39 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7323 (tt0) REVERT: B3 508 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.3612 (m) REVERT: B3 762 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B3 765 LEU cc_start: 0.8563 (pp) cc_final: 0.8160 (mt) REVERT: B3 1093 MET cc_start: 0.8138 (tmm) cc_final: 0.7171 (tmm) REVERT: B3 1185 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.5133 (ttm) REVERT: B4 1 MET cc_start: 0.5518 (tmm) cc_final: 0.4389 (tmm) REVERT: B4 211 PHE cc_start: 0.3939 (OUTLIER) cc_final: 0.3249 (t80) REVERT: B5 9 SER cc_start: 0.7995 (p) cc_final: 0.7763 (t) REVERT: B5 55 ILE cc_start: 0.8885 (mm) cc_final: 0.8632 (mt) REVERT: A1 186 MET cc_start: 0.3299 (mmp) cc_final: 0.2253 (mtt) REVERT: A2 65 ASN cc_start: 0.8413 (p0) cc_final: 0.8013 (p0) REVERT: A2 81 ASN cc_start: 0.8133 (m-40) cc_final: 0.6777 (m-40) REVERT: A2 85 ARG cc_start: 0.6634 (mmp80) cc_final: 0.6097 (mmp80) REVERT: A3 1 MET cc_start: -0.1756 (ttt) cc_final: -0.2086 (tmm) REVERT: A3 392 ILE cc_start: 0.8440 (tp) cc_final: 0.7994 (mp) outliers start: 120 outliers final: 82 residues processed: 370 average time/residue: 0.1905 time to fit residues: 121.0686 Evaluate side-chains 356 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 263 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain B1 residue 522 LYS Chi-restraints excluded: chain B1 residue 566 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 570 TYR Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 641 ILE Chi-restraints excluded: chain B1 residue 689 ILE Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 787 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 823 MET Chi-restraints excluded: chain B1 residue 907 ASP Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 949 GLN Chi-restraints excluded: chain B1 residue 954 LEU Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1081 PHE Chi-restraints excluded: chain B1 residue 1108 ASN Chi-restraints excluded: chain B1 residue 1111 CYS Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1169 VAL Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1178 MET Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 404 LEU Chi-restraints excluded: chain B3 residue 494 VAL 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 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 587 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 876 THR Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1035 THR Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1091 VAL Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1185 MET Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 211 PHE Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 168 TYR Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 425 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 152 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 ASN ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 526 HIS ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 130 GLN ** A2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 198 HIS ** A2 211 HIS ** 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 = 0.4622 r_free = 0.4622 target = 0.165420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.135255 restraints weight = 137522.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129198 restraints weight = 182380.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.126664 restraints weight = 133526.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.125778 restraints weight = 135243.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.126222 restraints weight = 131626.845| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 38947 Z= 0.219 Angle : 0.673 14.250 52988 Z= 0.336 Chirality : 0.044 0.221 5884 Planarity : 0.005 0.070 6617 Dihedral : 12.522 179.767 6184 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.58 % Allowed : 20.64 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.53 (0.13), residues: 4485 helix: 1.40 (0.12), residues: 1924 sheet: -0.02 (0.20), residues: 671 loop : -0.55 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 804 TYR 0.024 0.002 TYRB3 189 PHE 0.022 0.002 PHEB31217 TRP 0.013 0.002 TRPB31032 HIS 0.008 0.001 HIS H 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (38935) covalent geometry : angle 0.66710 / 0.34 (52970) hydrogen bonds : bond 0.04272 / 2.88 ( 1711) hydrogen bonds : angle 4.72415 / 3.38 ( 4908) metal coordination : bond 0.01280 / 0.85 ( 12) metal coordination : angle 4.98436 / 2.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 259 time to evaluate : 1.358 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: B 528 MET cc_start: 0.2471 (mpp) cc_final: 0.1682 (mpp) REVERT: B 550 ASN cc_start: 0.7146 (m-40) cc_final: 0.6573 (t0) REVERT: B 749 THR cc_start: 0.3728 (OUTLIER) cc_final: 0.3491 (m) REVERT: C 630 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8482 (mm) REVERT: H 23 CYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7875 (p) REVERT: H 60 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8411 (mt) REVERT: B1 511 MET cc_start: 0.7240 (ppp) cc_final: 0.6835 (ppp) REVERT: B1 609 MET cc_start: 0.7515 (mtt) cc_final: 0.7204 (mtp) REVERT: B1 613 MET cc_start: 0.8580 (mmm) cc_final: 0.8016 (mtm) REVERT: B1 853 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B1 981 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: B1 1006 MET cc_start: 0.8492 (tmm) cc_final: 0.7861 (tmm) REVERT: B1 1081 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7973 (m-10) REVERT: B2 647 ASN cc_start: 0.6225 (OUTLIER) cc_final: 0.5468 (p0) REVERT: B3 1 MET cc_start: 0.8395 (ptp) cc_final: 0.8056 (ptm) REVERT: B3 39 GLU cc_start: 0.7912 (mt-10) cc_final: 0.6972 (tt0) REVERT: B3 508 CYS cc_start: 0.5891 (OUTLIER) cc_final: 0.3790 (m) REVERT: B3 509 SER cc_start: 0.7335 (OUTLIER) cc_final: 0.7051 (t) REVERT: B3 762 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8214 (pp) REVERT: B3 765 LEU cc_start: 0.8674 (pp) cc_final: 0.8111 (mt) REVERT: B3 1145 GLU cc_start: 0.7092 (tt0) cc_final: 0.6694 (mt-10) REVERT: B4 1 MET cc_start: 0.5985 (tmm) cc_final: 0.4843 (tmm) REVERT: B4 211 PHE cc_start: 0.4195 (OUTLIER) cc_final: 0.3194 (t80) REVERT: B5 9 SER cc_start: 0.8026 (p) cc_final: 0.7814 (t) REVERT: A1 186 MET cc_start: 0.3316 (mmp) cc_final: 0.2315 (mtt) REVERT: A2 81 ASN cc_start: 0.8381 (m-40) cc_final: 0.7097 (m110) REVERT: A2 85 ARG cc_start: 0.6860 (mmp80) cc_final: 0.6239 (mmp80) REVERT: A3 1 MET cc_start: -0.1321 (ttt) cc_final: -0.1813 (tmm) REVERT: A3 392 ILE cc_start: 0.8313 (tp) cc_final: 0.7871 (mp) outliers start: 141 outliers final: 105 residues processed: 377 average time/residue: 0.1844 time to fit residues: 120.8969 Evaluate side-chains 367 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 250 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 ARG Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain B1 residue 522 LYS Chi-restraints excluded: chain B1 residue 566 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 570 TYR Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 680 LEU Chi-restraints excluded: chain B1 residue 701 VAL Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 787 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 853 ILE Chi-restraints excluded: chain B1 residue 907 ASP Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 949 GLN Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1081 PHE Chi-restraints excluded: chain B1 residue 1111 CYS Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1147 VAL Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1169 VAL Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1178 MET Chi-restraints excluded: chain B1 residue 1195 MET Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 491 LEU Chi-restraints excluded: chain B2 residue 494 THR Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 647 ASN Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B3 residue 14 ILE Chi-restraints excluded: chain B3 residue 58 VAL Chi-restraints excluded: chain B3 residue 62 ILE Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 143 ILE Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 175 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 420 THR Chi-restraints excluded: chain B3 residue 422 GLN Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 494 VAL 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 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 587 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 797 LEU Chi-restraints excluded: chain B3 residue 824 VAL Chi-restraints excluded: chain B3 residue 876 THR Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 995 THR Chi-restraints excluded: chain B3 residue 1035 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1091 VAL Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1144 VAL Chi-restraints excluded: chain B3 residue 1174 ILE Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 211 PHE Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain A1 residue 280 VAL Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 30 LEU Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 462 LEU Chi-restraints excluded: chain A3 residue 487 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 50 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 412 optimal weight: 40.0000 chunk 178 optimal weight: 0.9980 chunk 400 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 192 optimal weight: 0.5980 chunk 449 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 496 ASN B3 526 HIS B31094 ASN A2 32 GLN ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 135 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 = 0.4651 r_free = 0.4651 target = 0.167298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.138052 restraints weight = 138149.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.132688 restraints weight = 185407.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.128841 restraints weight = 137715.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.128417 restraints weight = 129262.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.128877 restraints weight = 117300.419| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38947 Z= 0.113 Angle : 0.608 14.768 52988 Z= 0.297 Chirality : 0.042 0.278 5884 Planarity : 0.004 0.054 6617 Dihedral : 12.401 179.065 6184 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 21.86 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.71 (0.13), residues: 4485 helix: 1.56 (0.12), residues: 1925 sheet: 0.12 (0.20), residues: 675 loop : -0.47 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGB31199 TYR 0.023 0.001 TYRA1 271 PHE 0.065 0.001 PHE A 808 TRP 0.029 0.001 TRP C 657 HIS 0.003 0.001 HISB11283 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (38935) covalent geometry : angle 0.60336 / 0.30 (52970) hydrogen bonds : bond 0.03705 / 2.51 ( 1711) hydrogen bonds : angle 4.47183 / 3.22 ( 4908) metal coordination : bond 0.00531 / 0.27 ( 12) metal coordination : angle 4.01679 / 2.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 273 time to evaluate : 1.127 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 550 ASN cc_start: 0.7089 (m-40) cc_final: 0.6537 (t0) REVERT: B 749 THR cc_start: 0.3719 (OUTLIER) cc_final: 0.3490 (m) REVERT: C 630 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8499 (mm) REVERT: B1 511 MET cc_start: 0.7008 (ppp) cc_final: 0.6663 (ppp) REVERT: B1 609 MET cc_start: 0.7359 (mtt) cc_final: 0.7091 (mtp) REVERT: B1 613 MET cc_start: 0.8559 (mmm) cc_final: 0.8036 (mtm) REVERT: B1 879 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7334 (mm) REVERT: B1 954 LEU cc_start: 0.9220 (mm) cc_final: 0.8896 (mp) REVERT: B1 981 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: B1 1006 MET cc_start: 0.8449 (tmm) cc_final: 0.7930 (tmm) REVERT: B1 1081 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: B1 1299 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7197 (pm20) REVERT: B2 457 MET cc_start: 0.8563 (tmm) cc_final: 0.8219 (mtt) REVERT: B2 605 LYS cc_start: 0.6653 (ptmt) cc_final: 0.6187 (mmtt) REVERT: B2 647 ASN cc_start: 0.6180 (OUTLIER) cc_final: 0.5412 (p0) REVERT: B3 1 MET cc_start: 0.8426 (ptp) cc_final: 0.8062 (ptm) REVERT: B3 39 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7036 (tt0) REVERT: B3 508 CYS cc_start: 0.5626 (OUTLIER) cc_final: 0.3614 (m) REVERT: B3 509 SER cc_start: 0.7322 (OUTLIER) cc_final: 0.7028 (t) REVERT: B3 630 MET cc_start: 0.5820 (mmp) cc_final: 0.5128 (mmp) REVERT: B3 762 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8130 (pp) REVERT: B3 765 LEU cc_start: 0.8604 (pp) cc_final: 0.8127 (mt) REVERT: B3 1093 MET cc_start: 0.8282 (tmm) cc_final: 0.7338 (tmm) REVERT: B3 1145 GLU cc_start: 0.7052 (tt0) cc_final: 0.6726 (mt-10) REVERT: B4 1 MET cc_start: 0.5583 (tmm) cc_final: 0.4471 (tmm) REVERT: B4 74 MET cc_start: 0.9081 (mmt) cc_final: 0.8518 (mmm) REVERT: B5 9 SER cc_start: 0.8035 (p) cc_final: 0.7793 (t) REVERT: A2 33 LEU cc_start: 0.4768 (tt) cc_final: 0.4506 (tp) REVERT: A2 81 ASN cc_start: 0.8224 (m-40) cc_final: 0.6856 (m-40) REVERT: A2 85 ARG cc_start: 0.6731 (mmp80) cc_final: 0.6188 (mmp80) REVERT: A3 1 MET cc_start: -0.1566 (ttt) cc_final: -0.1958 (tmm) REVERT: A3 392 ILE cc_start: 0.8257 (tp) cc_final: 0.7947 (mm) outliers start: 95 outliers final: 74 residues processed: 350 average time/residue: 0.1943 time to fit residues: 115.3332 Evaluate side-chains 343 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain B1 residue 566 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 570 TYR Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 787 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 823 MET Chi-restraints excluded: chain B1 residue 879 LEU Chi-restraints excluded: chain B1 residue 907 ASP Chi-restraints excluded: chain B1 residue 949 GLN Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1081 PHE Chi-restraints excluded: chain B1 residue 1093 VAL Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1178 MET Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 494 THR Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 647 ASN Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 494 VAL 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 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 587 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 876 THR Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 79 optimal weight: 20.0000 chunk 286 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 339 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 408 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 117 optimal weight: 0.0770 chunk 446 optimal weight: 5.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN B1 682 HIS ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 541 GLN B3 526 HIS B3 804 HIS ** B4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 36 HIS ** A2 122 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 = 0.4624 r_free = 0.4624 target = 0.165560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.135336 restraints weight = 138439.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130855 restraints weight = 173964.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.126757 restraints weight = 120864.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.126303 restraints weight = 114778.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.126577 restraints weight = 107178.562| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38947 Z= 0.191 Angle : 0.676 14.595 52988 Z= 0.334 Chirality : 0.043 0.203 5884 Planarity : 0.005 0.080 6617 Dihedral : 12.375 179.442 6184 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.02 % Allowed : 21.40 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.49 (0.13), residues: 4485 helix: 1.38 (0.12), residues: 1932 sheet: -0.05 (0.20), residues: 672 loop : -0.58 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGB3 552 TYR 0.027 0.002 TYRA1 271 PHE 0.060 0.002 PHE A 808 TRP 0.019 0.002 TRP C 657 HIS 0.008 0.001 HISB1 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (38935) covalent geometry : angle 0.66998 / 0.33 (52970) hydrogen bonds : bond 0.04079 / 2.75 ( 1711) hydrogen bonds : angle 4.67610 / 3.35 ( 4908) metal coordination : bond 0.01090 / 0.72 ( 12) metal coordination : angle 4.73326 / 2.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 256 time to evaluate : 1.142 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: B 550 ASN cc_start: 0.7080 (m-40) cc_final: 0.6564 (t0) REVERT: B 749 THR cc_start: 0.3776 (OUTLIER) cc_final: 0.3555 (m) REVERT: C 630 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8470 (mm) REVERT: H 60 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B1 511 MET cc_start: 0.6944 (ppp) cc_final: 0.6620 (ppp) REVERT: B1 609 MET cc_start: 0.7392 (mtt) cc_final: 0.7155 (mtp) REVERT: B1 879 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7516 (mm) REVERT: B1 954 LEU cc_start: 0.9263 (mm) cc_final: 0.8963 (mp) REVERT: B1 981 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: B1 1006 MET cc_start: 0.8438 (tmm) cc_final: 0.7837 (tmm) REVERT: B1 1081 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: B1 1108 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6442 (t0) REVERT: B2 457 MET cc_start: 0.8502 (tmm) cc_final: 0.8080 (mtt) REVERT: B2 647 ASN cc_start: 0.6179 (OUTLIER) cc_final: 0.5376 (p0) REVERT: B3 1 MET cc_start: 0.8446 (ptp) cc_final: 0.8080 (ptm) REVERT: B3 39 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7047 (tt0) REVERT: B3 508 CYS cc_start: 0.5817 (OUTLIER) cc_final: 0.3867 (m) REVERT: B3 509 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7121 (t) REVERT: B3 762 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8190 (pp) REVERT: B3 765 LEU cc_start: 0.8534 (pp) cc_final: 0.8026 (mt) REVERT: B3 1095 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7737 (t80) REVERT: B3 1145 GLU cc_start: 0.7079 (tt0) cc_final: 0.6738 (mt-10) REVERT: B4 1 MET cc_start: 0.5795 (tmm) cc_final: 0.4536 (tmm) REVERT: B4 211 PHE cc_start: 0.4141 (OUTLIER) cc_final: 0.3254 (t80) REVERT: B5 9 SER cc_start: 0.8146 (p) cc_final: 0.7901 (t) REVERT: B5 44 MET cc_start: 0.8300 (mmm) cc_final: 0.7792 (mmt) REVERT: A1 186 MET cc_start: 0.3051 (mmp) cc_final: 0.1992 (mtt) REVERT: A2 33 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4852 (tp) REVERT: A2 81 ASN cc_start: 0.8390 (m-40) cc_final: 0.7066 (m110) REVERT: A2 85 ARG cc_start: 0.6821 (mmp80) cc_final: 0.6228 (mmp80) REVERT: A3 1 MET cc_start: -0.1612 (ttt) cc_final: -0.1981 (tmm) REVERT: A3 392 ILE cc_start: 0.8273 (tp) cc_final: 0.7963 (mm) outliers start: 119 outliers final: 91 residues processed: 354 average time/residue: 0.1880 time to fit residues: 114.9041 Evaluate side-chains 356 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 251 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain B1 residue 466 PHE Chi-restraints excluded: chain B1 residue 566 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 682 HIS Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 787 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 823 MET Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 879 LEU Chi-restraints excluded: chain B1 residue 907 ASP Chi-restraints excluded: chain B1 residue 949 GLN Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1081 PHE Chi-restraints excluded: chain B1 residue 1093 VAL Chi-restraints excluded: chain B1 residue 1108 ASN Chi-restraints excluded: chain B1 residue 1111 CYS Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1169 VAL Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1178 MET Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 491 LEU Chi-restraints excluded: chain B2 residue 494 THR Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 647 ASN Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 175 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 214 ASP Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 420 THR Chi-restraints excluded: chain B3 residue 422 GLN Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 494 VAL 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 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 876 THR Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1035 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1095 TYR Chi-restraints excluded: chain B3 residue 1174 ILE Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B4 residue 211 PHE Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 30 LEU Chi-restraints excluded: chain A2 residue 33 LEU Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 161 ILE Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 462 LEU Chi-restraints excluded: chain A3 residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 281 optimal weight: 5.9990 chunk 256 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 412 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 285 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 526 HIS B3 804 HIS ** B4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.165860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136000 restraints weight = 137441.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.130315 restraints weight = 179767.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126791 restraints weight = 135877.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.126498 restraints weight = 134892.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.126725 restraints weight = 119448.239| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38947 Z= 0.163 Angle : 0.655 15.406 52988 Z= 0.322 Chirality : 0.043 0.194 5884 Planarity : 0.004 0.067 6617 Dihedral : 12.335 179.100 6184 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.85 % Allowed : 21.43 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.50 (0.13), residues: 4485 helix: 1.39 (0.12), residues: 1928 sheet: -0.06 (0.20), residues: 679 loop : -0.58 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGB2 638 TYR 0.022 0.001 TYRA1 271 PHE 0.050 0.002 PHEB1 532 TRP 0.016 0.001 TRP C 657 HIS 0.021 0.001 HISB1 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (38935) covalent geometry : angle 0.64981 / 0.32 (52970) hydrogen bonds : bond 0.03949 / 2.65 ( 1711) hydrogen bonds : angle 4.60183 / 3.30 ( 4908) metal coordination : bond 0.00851 / 0.55 ( 12) metal coordination : angle 4.66486 / 2.54 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8970 Ramachandran restraints generated. 4485 Oldfield, 0 Emsley, 4485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 257 time to evaluate : 1.224 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: B 550 ASN cc_start: 0.6999 (m-40) cc_final: 0.6509 (t0) REVERT: B 749 THR cc_start: 0.3732 (OUTLIER) cc_final: 0.3507 (m) REVERT: H 60 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8355 (mt) REVERT: B1 511 MET cc_start: 0.6952 (ppp) cc_final: 0.6657 (ppp) REVERT: B1 609 MET cc_start: 0.7456 (mtt) cc_final: 0.7196 (mtp) REVERT: B1 613 MET cc_start: 0.8650 (mmm) cc_final: 0.8200 (mtm) REVERT: B1 873 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7786 (tp30) REVERT: B1 949 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: B1 954 LEU cc_start: 0.9274 (mm) cc_final: 0.8977 (mp) REVERT: B1 962 MET cc_start: 0.8427 (mmm) cc_final: 0.7872 (mpp) REVERT: B1 981 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: B1 1006 MET cc_start: 0.8452 (tmm) cc_final: 0.8008 (tmm) REVERT: B1 1081 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: B1 1108 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6541 (t0) REVERT: B2 457 MET cc_start: 0.8535 (tmm) cc_final: 0.8093 (mtt) REVERT: B2 605 LYS cc_start: 0.6365 (ptmt) cc_final: 0.5736 (mptt) REVERT: B2 647 ASN cc_start: 0.6204 (OUTLIER) cc_final: 0.5439 (p0) REVERT: B3 1 MET cc_start: 0.8386 (ptp) cc_final: 0.8056 (ptm) REVERT: B3 39 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7129 (tt0) REVERT: B3 508 CYS cc_start: 0.5893 (OUTLIER) cc_final: 0.3937 (m) REVERT: B3 509 SER cc_start: 0.7555 (OUTLIER) cc_final: 0.7277 (t) REVERT: B3 630 MET cc_start: 0.6201 (mmp) cc_final: 0.5836 (mmm) REVERT: B3 762 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8227 (pp) REVERT: B3 765 LEU cc_start: 0.8524 (pp) cc_final: 0.7993 (mp) REVERT: B3 1095 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7948 (t80) REVERT: B3 1145 GLU cc_start: 0.7084 (tt0) cc_final: 0.6688 (mt-10) REVERT: B4 1 MET cc_start: 0.5774 (tmm) cc_final: 0.4568 (tmm) REVERT: B5 9 SER cc_start: 0.8121 (p) cc_final: 0.7886 (t) REVERT: A1 186 MET cc_start: 0.3099 (mmp) cc_final: 0.1987 (mtt) REVERT: A2 81 ASN cc_start: 0.8219 (m-40) cc_final: 0.6870 (m110) REVERT: A2 85 ARG cc_start: 0.6880 (mmp80) cc_final: 0.6287 (mmp80) REVERT: A3 1 MET cc_start: -0.1635 (ttt) cc_final: -0.1988 (tmm) REVERT: A3 392 ILE cc_start: 0.8250 (tp) cc_final: 0.7942 (mm) outliers start: 112 outliers final: 92 residues processed: 346 average time/residue: 0.1830 time to fit residues: 109.4302 Evaluate side-chains 356 residues out of total 3957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 253 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 722 HIS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain B1 residue 531 LEU Chi-restraints excluded: chain B1 residue 568 ARG Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 787 ILE Chi-restraints excluded: chain B1 residue 805 TYR Chi-restraints excluded: chain B1 residue 821 HIS Chi-restraints excluded: chain B1 residue 823 MET Chi-restraints excluded: chain B1 residue 870 GLU Chi-restraints excluded: chain B1 residue 907 ASP Chi-restraints excluded: chain B1 residue 949 GLN Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 981 TYR Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1081 PHE Chi-restraints excluded: chain B1 residue 1093 VAL Chi-restraints excluded: chain B1 residue 1108 ASN Chi-restraints excluded: chain B1 residue 1111 CYS Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1147 VAL Chi-restraints excluded: chain B1 residue 1148 LEU Chi-restraints excluded: chain B1 residue 1169 VAL Chi-restraints excluded: chain B1 residue 1170 THR Chi-restraints excluded: chain B1 residue 1178 MET Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1274 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 491 LEU Chi-restraints excluded: chain B2 residue 494 THR Chi-restraints excluded: chain B2 residue 585 THR Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B2 residue 647 ASN Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B3 residue 58 VAL Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 130 VAL Chi-restraints excluded: chain B3 residue 159 GLU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 175 VAL Chi-restraints excluded: chain B3 residue 204 THR Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 214 ASP Chi-restraints excluded: chain B3 residue 226 GLU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 290 SER Chi-restraints excluded: chain B3 residue 315 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 420 THR Chi-restraints excluded: chain B3 residue 422 GLN Chi-restraints excluded: chain B3 residue 437 VAL Chi-restraints excluded: chain B3 residue 479 VAL 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 526 HIS Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 564 VAL Chi-restraints excluded: chain B3 residue 664 TYR Chi-restraints excluded: chain B3 residue 665 LEU Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 876 THR Chi-restraints excluded: chain B3 residue 878 ASP Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1035 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1081 LEU Chi-restraints excluded: chain B3 residue 1095 TYR Chi-restraints excluded: chain B3 residue 1174 ILE Chi-restraints excluded: chain B4 residue 28 LEU Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 194 LEU Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain A1 residue 285 VAL Chi-restraints excluded: chain A2 residue 151 PHE Chi-restraints excluded: chain A2 residue 168 TYR Chi-restraints excluded: chain A2 residue 210 PHE Chi-restraints excluded: chain A3 residue 161 ILE Chi-restraints excluded: chain A3 residue 411 CYS Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 14 optimal weight: 0.0770 chunk 341 optimal weight: 0.9980 chunk 254 optimal weight: 0.6980 chunk 411 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 406 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN ** B1 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B11283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4646 r_free = 0.4646 target = 0.166922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.137635 restraints weight = 137965.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.133249 restraints weight = 179959.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.129806 restraints weight = 126191.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.129493 restraints weight = 121347.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.129624 restraints weight = 122617.911| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38947 Z= 0.115 Angle : 0.633 14.822 52988 Z= 0.310 Chirality : 0.042 0.228 5884 Planarity : 0.004 0.058 6617 Dihedral : 12.230 179.551 6184 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.52 % Allowed : 21.91 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.63 (0.13), residues: 4485 helix: 1.50 (0.12), residues: 1922 sheet: 0.03 (0.20), residues: 681 loop : -0.51 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGB3 525 TYR 0.029 0.001 TYRB1 570 PHE 0.080 0.001 PHE A 808 TRP 0.055 0.001 TRP C 660 HIS 0.041 0.001 HISB3 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (38935) covalent geometry : angle 0.62962 / 0.31 (52970) hydrogen bonds : bond 0.03658 / 2.48 ( 1711) hydrogen bonds : angle 4.46604 / 3.21 ( 4908) metal coordination : bond 0.00601 / 0.34 ( 12) metal coordination : angle 3.73064 / 2.03 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6950.01 seconds wall clock time: 120 minutes 35.71 seconds (7235.71 seconds total)