Starting phenix.real_space_refine on Tue May 5 09:11:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zec_74099/05_2026/9zec_74099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zec_74099/05_2026/9zec_74099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zec_74099/05_2026/9zec_74099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zec_74099/05_2026/9zec_74099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zec_74099/05_2026/9zec_74099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zec_74099/05_2026/9zec_74099.map" } resolution = 3.61 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= 0.052 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 69 5.49 5 S 138 5.16 5 C 17178 2.51 5 N 4692 2.21 5 O 5333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27413 Number of models: 1 Model: "" Number of chains: 14 Chain: "2" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 781 Classifications: {'RNA': 37} Modifications used: {'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p': 8, 'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "A" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 408 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "A1" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 614 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 66} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1014 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} 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: "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: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 642 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 10, 'rna3p_pyr': 21} Link IDs: {'rna2p': 11, 'rna3p': 20} 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 26064 SG CYS H 11 77.025 93.571 54.268 1.00 83.35 S ATOM 26327 SG CYS H 46 75.964 96.855 52.800 1.00 84.63 S ATOM 26350 SG CYS H 49 74.956 93.751 51.014 1.00 87.85 S ATOM 26621 SG CYS H 85 73.338 94.619 54.400 1.00 86.01 S ATOM 26151 SG CYS H 23 60.968 85.226 48.785 1.00 89.13 S ATOM 26175 SG CYS H 26 61.883 84.544 52.426 1.00 88.83 S ATOM 26422 SG CYS H 58 63.982 86.921 50.155 1.00 86.75 S ATOM 26443 SG CYS H 61 64.006 83.069 49.835 1.00 87.17 S ATOM 26202 SG CYS H 30 62.408 89.646 63.002 1.00 88.43 S ATOM 26223 SG CYS H 33 63.267 87.871 66.412 1.00 89.41 S ATOM 26518 SG CYS H 72 60.762 90.660 66.226 1.00 82.72 S ATOM 26542 SG CYS H 75 64.520 91.298 65.694 1.00 80.52 S Time building chain proxies: 5.21, per 1000 atoms: 0.19 Number of scatterers: 27413 At special positions: 0 Unit cell: (124.3, 179.3, 189.2, 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 138 16.00 P 69 15.00 O 5333 8.00 N 4692 7.00 C 17178 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: 1.99 Conformation dependent library (CDL) restraints added in 991.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 11 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 49 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 85 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 23 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 61 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 26 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 58 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 75 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 33 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 30 " Number of angles added : 18 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6116 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 37 sheets defined 42.6% alpha, 18.3% beta 7 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 686 through 701 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 800 through 815 Processing helix chain 'A1' and resid 248 through 273 Processing helix chain 'A1' and resid 300 through 318 removed outlier: 4.427A pdb=" N GLYA1 305 " --> pdb=" O PROA1 301 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALAA1 306 " --> pdb=" O GLUA1 302 " (cutoff:3.500A) Processing helix chain 'A2' and resid 20 through 36 Processing helix chain 'A2' and resid 65 through 74 removed outlier: 3.940A pdb=" N GLNA2 74 " --> pdb=" O LEUA2 70 " (cutoff:3.500A) Processing helix chain 'A2' and resid 75 through 93 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 393 through 400 removed outlier: 3.518A pdb=" N HISA3 400 " --> pdb=" O LEUA3 396 " (cutoff:3.500A) Processing helix chain 'A3' and resid 418 through 425 removed outlier: 3.507A pdb=" N ARGA3 424 " --> pdb=" O LYSA3 420 " (cutoff:3.500A) 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: 3.597A pdb=" N SERA3 457 " --> pdb=" O GLUA3 453 " (cutoff:3.500A) Processing helix chain 'A3' and resid 488 through 497 removed outlier: 3.517A pdb=" N LYSA3 496 " --> pdb=" O TYRA3 492 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARGA3 497 " --> pdb=" O GLUA3 493 " (cutoff:3.500A) 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: 3.886A pdb=" N ILEB1 472 " --> pdb=" O PROB1 469 " (cutoff:3.500A) Processing helix chain 'B1' and resid 475 through 480 removed outlier: 3.693A pdb=" N LEUB1 479 " --> pdb=" O PHEB1 475 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VALB1 480 " --> pdb=" O ASPB1 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 475 through 480' Processing helix chain 'B1' and resid 488 through 507 removed outlier: 3.554A pdb=" N GLNB1 492 " --> pdb=" O SERB1 488 " (cutoff:3.500A) Processing helix chain 'B1' and resid 508 through 522 removed outlier: 3.737A pdb=" N ALAB1 514 " --> pdb=" O PROB1 510 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARGB1 517 " --> pdb=" O LYSB1 513 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLNB1 518 " --> pdb=" O ALAB1 514 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THRB1 520 " --> pdb=" O LEUB1 516 " (cutoff:3.500A) Processing helix chain 'B1' and resid 522 through 527 removed outlier: 3.601A pdb=" N GLYB1 527 " --> pdb=" O ALAB1 523 " (cutoff:3.500A) Processing helix chain 'B1' and resid 527 through 540 removed outlier: 3.515A pdb=" N LEUB1 531 " --> pdb=" O GLYB1 527 " (cutoff:3.500A) removed outlier: 4.013A 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: 3.647A pdb=" N LYSB1 562 " --> pdb=" O ARGB1 558 " (cutoff:3.500A) Processing helix chain 'B1' and resid 570 through 583 removed outlier: 3.608A pdb=" N VALB1 576 " --> pdb=" O HISB1 572 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VALB1 577 " --> pdb=" O LYSB1 573 " (cutoff:3.500A) Proline residue: B1 580 - end of helix removed outlier: 4.235A pdb=" N ILEB1 583 " --> pdb=" O GLUB1 579 " (cutoff:3.500A) Processing helix chain 'B1' and resid 586 through 605 removed outlier: 3.767A pdb=" N ARGB1 590 " --> pdb=" O ASPB1 586 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALAB1 603 " --> pdb=" O ASNB1 599 " (cutoff:3.500A) Processing helix chain 'B1' and resid 606 through 614 Processing helix chain 'B1' and resid 615 through 619 removed outlier: 3.909A pdb=" N ASPB1 618 " --> pdb=" O PROB1 615 " (cutoff:3.500A) Processing helix chain 'B1' and resid 621 through 640 removed outlier: 3.519A pdb=" N VALB1 634 " --> pdb=" O ARGB1 630 " (cutoff:3.500A) Processing helix chain 'B1' and resid 640 through 654 removed outlier: 4.244A pdb=" N LEUB1 644 " --> pdb=" O GLYB1 640 " (cutoff:3.500A) Proline residue: B1 646 - end of helix Processing helix chain 'B1' and resid 657 through 675 removed outlier: 3.703A pdb=" N ARGB1 661 " --> pdb=" O SERB1 657 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALB1 668 " --> pdb=" O GLYB1 664 " (cutoff:3.500A) Processing helix chain 'B1' and resid 676 through 680 removed outlier: 3.776A pdb=" N ILEB1 679 " --> pdb=" O GLYB1 676 " (cutoff:3.500A) Processing helix chain 'B1' and resid 682 through 692 removed outlier: 3.741A pdb=" N ILEB1 689 " --> pdb=" O SERB1 685 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILEB1 690 " --> pdb=" O LEUB1 686 " (cutoff:3.500A) removed outlier: 4.377A 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: 3.699A pdb=" N LEUB1 728 " --> pdb=" O PHEB1 724 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYSB1 729 " --> pdb=" O ASPB1 725 " (cutoff:3.500A) Proline residue: B1 730 - end of helix removed outlier: 3.710A pdb=" N LYSB1 733 " --> pdb=" O LYSB1 729 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARGB1 736 " --> pdb=" O TRPB1 732 " (cutoff:3.500A) Processing helix chain 'B1' and resid 740 through 754 removed outlier: 3.607A pdb=" N ALAB1 744 " --> pdb=" O GLYB1 740 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALAB1 745 " --> pdb=" O LYSB1 741 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYRB1 752 " --> pdb=" O LYSB1 748 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUB1 753 " --> pdb=" O ALAB1 749 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILEB1 754 " --> pdb=" O ILEB1 750 " (cutoff:3.500A) Processing helix chain 'B1' and resid 758 through 777 removed outlier: 3.813A pdb=" N ASNB1 763 " --> pdb=" O ALAB1 759 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYRB1 764 " --> pdb=" O GLUB1 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLUB1 768 " --> pdb=" O TYRB1 764 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILEB1 772 " --> pdb=" O GLUB1 768 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARGB1 775 " --> pdb=" O LEUB1 771 " (cutoff:3.500A) Processing helix chain 'B1' and resid 781 through 798 removed outlier: 3.514A pdb=" N LYSB1 793 " --> pdb=" O LEUB1 789 " (cutoff:3.500A) Processing helix chain 'B1' and resid 803 through 810 Processing helix chain 'B1' and resid 810 through 817 removed outlier: 3.975A pdb=" N LYSB1 816 " --> pdb=" O PROB1 812 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HISB1 817 " --> pdb=" O PROB1 813 " (cutoff:3.500A) Processing helix chain 'B1' and resid 820 through 825 removed outlier: 3.726A pdb=" N ALAB1 824 " --> pdb=" O HISB1 821 " (cutoff:3.500A) Processing helix chain 'B1' and resid 826 through 845 removed outlier: 3.755A pdb=" N VALB1 834 " --> pdb=" O TYRB1 830 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASNB1 842 " --> pdb=" O VALB1 838 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYSB1 843 " --> pdb=" O GLUB1 839 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VALB1 844 " --> pdb=" O LEUB1 840 " (cutoff:3.500A) Processing helix chain 'B1' and resid 845 through 854 removed outlier: 3.654A pdb=" N ILEB1 849 " --> pdb=" O GLYB1 845 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGB1 852 " --> pdb=" O GLUB1 848 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILEB1 853 " --> pdb=" O ILEB1 849 " (cutoff:3.500A) Processing helix chain 'B1' and resid 855 through 859 Processing helix chain 'B1' and resid 861 through 880 removed outlier: 3.639A pdb=" N LYSB1 866 " --> pdb=" O GLUB1 862 " (cutoff:3.500A) Processing helix chain 'B1' and resid 885 through 903 removed outlier: 3.584A pdb=" N GLNB1 891 " --> pdb=" O LYSB1 887 " (cutoff:3.500A) Processing helix chain 'B1' and resid 908 through 922 Processing helix chain 'B1' and resid 923 through 927 removed outlier: 3.884A 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: 3.520A pdb=" N ARGB1 948 " --> pdb=" O SERB1 944 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILEB1 955 " --> pdb=" O ALAB1 951 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SERB1 956 " --> pdb=" O ALAB1 952 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARGB1 957 " --> pdb=" O ASPB1 953 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VALB1 960 " --> pdb=" O SERB1 956 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VALB1 961 " --> pdb=" O ARGB1 957 " (cutoff:3.500A) Processing helix chain 'B1' and resid 967 through 981 removed outlier: 3.788A 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 removed outlier: 3.559A pdb=" N ASNB11034 " --> pdb=" O LYSB11030 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1047 through 1050 Processing helix chain 'B1' and resid 1051 through 1066 removed outlier: 3.596A pdb=" N LEUB11063 " --> pdb=" O CYSB11059 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLUB11064 " --> pdb=" O PHEB11060 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUB11065 " --> pdb=" O GLUB11061 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUB11066 " --> pdb=" O LEUB11062 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1070 through 1089 removed outlier: 3.507A pdb=" N PHEB11081 " --> pdb=" O THRB11077 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLYB11082 " --> pdb=" O VALB11078 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYRB11083 " --> pdb=" O ASNB11079 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALAB11087 " --> pdb=" O TYRB11083 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1089 through 1100 removed outlier: 4.441A pdb=" N VALB11093 " --> pdb=" O GLYB11089 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALAB11095 " --> pdb=" O HISB11091 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1108 through 1123 Processing helix chain 'B1' and resid 1124 through 1127 Processing helix chain 'B1' and resid 1128 through 1135 removed outlier: 3.528A pdb=" N ASNB11134 " --> pdb=" O PROB11130 " (cutoff:3.500A) removed outlier: 3.580A 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 Processing helix chain 'B1' and resid 1160 through 1164 removed outlier: 3.720A pdb=" N ASPB11164 " --> pdb=" O METB11161 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1165 through 1178 Proline residue: B11171 - end of helix Processing helix chain 'B1' and resid 1181 through 1199 removed outlier: 3.561A pdb=" N ALAB11190 " --> pdb=" O GLNB11186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEUB11197 " --> pdb=" O GLNB11193 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1204 through 1216 removed outlier: 3.964A pdb=" N LEUB11208 " --> pdb=" O CYSB11204 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASNB11213 " --> pdb=" O ASNB11209 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYRB11214 " --> pdb=" O HISB11210 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1217 through 1221 removed outlier: 4.136A pdb=" N PHEB11220 " --> pdb=" O PROB11217 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1223 through 1242 removed outlier: 3.777A pdb=" N VALB11239 " --> pdb=" O GLUB11235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALAB11240 " --> pdb=" O GLYB11236 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1242 through 1251 removed outlier: 3.766A pdb=" N METB11246 " --> pdb=" O GLYB11242 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1258 through 1276 removed outlier: 3.512A pdb=" N ARGB11262 " --> pdb=" O ALAB11258 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VALB11264 " --> pdb=" O LYSB11260 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1278 through 1284 removed outlier: 3.545A pdb=" N ALAB11282 " --> pdb=" O ALAB11279 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYRB11284 " --> pdb=" O ILEB11281 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1297 through 1302 removed outlier: 3.751A pdb=" N ASPB11301 " --> pdb=" O ARGB11297 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.912A pdb=" N ASNB2 458 " --> pdb=" O LEUB2 454 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARGB2 459 " --> pdb=" O ARGB2 455 " (cutoff:3.500A) Processing helix chain 'B2' and resid 461 through 467 removed outlier: 3.564A pdb=" N GLNB2 467 " --> pdb=" O ALAB2 463 " (cutoff:3.500A) Processing helix chain 'B2' and resid 476 through 482 removed outlier: 3.510A pdb=" N ASPB2 479 " --> pdb=" O GLUB2 476 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VALB2 480 " --> pdb=" O METB2 477 " (cutoff:3.500A) Processing helix chain 'B2' and resid 484 through 493 Processing helix chain 'B2' and resid 501 through 505 removed outlier: 3.524A pdb=" N TRPB2 504 " --> pdb=" O PROB2 501 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYSB2 505 " --> pdb=" O ARGB2 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 501 through 505' Processing helix chain 'B2' and resid 525 through 531 removed outlier: 3.761A pdb=" N THRB2 531 " --> pdb=" O PHEB2 527 " (cutoff:3.500A) Processing helix chain 'B2' and resid 532 through 548 Processing helix chain 'B2' and resid 551 through 561 removed outlier: 3.593A pdb=" N ARGB2 558 " --> pdb=" O ARGB2 554 " (cutoff:3.500A) Proline residue: B2 559 - end of helix Processing helix chain 'B2' and resid 567 through 577 removed outlier: 3.522A pdb=" N ALAB2 574 " --> pdb=" O LYSB2 570 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHEB2 575 " --> pdb=" O LEUB2 571 " (cutoff:3.500A) Processing helix chain 'B2' and resid 594 through 603 removed outlier: 3.831A pdb=" N GLUB2 598 " --> pdb=" O GLYB2 594 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARGB2 600 " --> pdb=" O GLUB2 596 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEUB2 601 " --> pdb=" O PHEB2 597 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLUB2 603 " --> pdb=" O THRB2 599 " (cutoff:3.500A) Processing helix chain 'B2' and resid 611 through 617 Processing helix chain 'B2' and resid 622 through 627 removed outlier: 4.484A pdb=" N HISB2 626 " --> pdb=" O PROB2 623 " (cutoff:3.500A) Processing helix chain 'B2' and resid 632 through 639 Processing helix chain 'B3' and resid 198 through 203 removed outlier: 3.958A pdb=" N ALAB3 202 " --> pdb=" O GLYB3 198 " (cutoff:3.500A) Processing helix chain 'B3' and resid 429 through 432 removed outlier: 3.571A 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: 3.958A pdb=" N CYSB3 624 " --> pdb=" O PROB3 621 " (cutoff:3.500A) Processing helix chain 'B3' and resid 808 through 827 removed outlier: 3.632A pdb=" N ALAB3 813 " --> pdb=" O GLUB3 809 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLNB3 814 " --> pdb=" O ALAB3 810 " (cutoff:3.500A) Processing helix chain 'B3' and resid 832 through 845 Processing helix chain 'B3' and resid 848 through 853 Processing helix chain 'B3' and resid 1072 through 1077 removed outlier: 3.892A pdb=" N TRPB31077 " --> pdb=" O ASNB31073 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1134 through 1152 removed outlier: 3.585A pdb=" N HISB31138 " --> pdb=" O SERB31134 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SERB31150 " --> pdb=" O METB31146 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1159 through 1165 Processing helix chain 'B3' and resid 1176 through 1181 Processing helix chain 'B3' and resid 1186 through 1197 Processing helix chain 'B3' and resid 1200 through 1214 removed outlier: 3.642A pdb=" N ILEB31211 " --> pdb=" O LYSB31207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGB31212 " --> pdb=" O LEUB31208 " (cutoff:3.500A) Processing helix chain 'B4' and resid 10 through 12 No H-bonds generated for 'chain 'B4' and resid 10 through 12' Processing helix chain 'B4' and resid 25 through 35 removed outlier: 3.614A pdb=" N GLNB4 35 " --> pdb=" O GLUB4 31 " (cutoff:3.500A) Processing helix chain 'B4' and resid 63 through 75 removed outlier: 3.554A pdb=" N LYSB4 72 " --> pdb=" O ASPB4 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILEB4 73 " --> pdb=" O TYRB4 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASNB4 75 " --> pdb=" O ILEB4 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 112 through 122 removed outlier: 3.534A pdb=" N LEUB4 116 " --> pdb=" O ASPB4 112 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALAB4 122 " --> pdb=" O ASPB4 118 " (cutoff:3.500A) Processing helix chain 'B4' and resid 151 through 163 Processing helix chain 'B4' and resid 189 through 199 Processing helix chain 'B4' and resid 199 through 206 Processing helix chain 'B4' and resid 206 through 211 removed outlier: 3.644A pdb=" N LEUB4 210 " --> pdb=" O ARGB4 206 " (cutoff:3.500A) removed outlier: 4.658A 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: 4.476A pdb=" N GLUB5 12 " --> pdb=" O HISB5 8 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSB5 17 " --> pdb=" O HISB5 13 " (cutoff:3.500A) Processing helix chain 'B5' and resid 27 through 46 removed outlier: 3.582A pdb=" N ASNB5 34 " --> pdb=" O GLUB5 30 " (cutoff:3.500A) Processing helix chain 'B5' and resid 46 through 57 Processing helix chain 'B5' and resid 60 through 72 Processing helix chain 'B6' and resid 5 through 11 Processing helix chain 'B6' and resid 31 through 41 removed outlier: 3.574A pdb=" N LYSB6 41 " --> pdb=" O ASPB6 37 " (cutoff:3.500A) Processing helix chain 'B6' and resid 53 through 57 Processing helix chain 'B6' and resid 66 through 78 removed outlier: 3.658A pdb=" N SERB6 78 " --> pdb=" O CYSB6 74 " (cutoff:3.500A) Processing helix chain 'B6' and resid 93 through 98 removed outlier: 3.511A pdb=" N PHEB6 98 " --> pdb=" O ALAB6 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.770A pdb=" N ARG H 82 " --> pdb=" O GLU H 79 " (cutoff:3.500A) removed outlier: 3.874A 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 sheet with id=AA1, first strand: chain 'A1' and resid 279 through 284 removed outlier: 6.272A pdb=" N VALA1 280 " --> pdb=" O ALAA2 180 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LYSA2 182 " --> pdb=" O VALA1 280 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VALA1 282 " --> pdb=" O LYSA2 182 " (cutoff:3.500A) removed outlier: 11.646A pdb=" N THRA1 284 " --> pdb=" O PROA2 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILEA2 179 " --> pdb=" O META2 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A2' and resid 46 through 47 removed outlier: 3.616A pdb=" N THRA2 61 " --> pdb=" O CYSA2 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.732A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HISA2 211 " --> pdb=" O ASPA2 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A2' and resid 117 through 123 removed outlier: 4.732A pdb=" N GLNA2 130 " --> pdb=" O PHEA2 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A3' and resid 406 through 408 Processing sheet with id=AA6, first strand: chain 'A3' and resid 479 through 480 Processing sheet with id=AA7, first strand: chain 'B1' and resid 412 through 414 removed outlier: 3.659A 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: 3.813A pdb=" N SERB31103 " --> pdb=" O THRB31120 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILEB31126 " --> pdb=" O LEUB3 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B3' and resid 16 through 20 removed outlier: 3.957A pdb=" N PHEB3 16 " --> pdb=" O SERB3 33 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEUB3 54 " --> pdb=" O LEUB3 40 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARGB3 42 " --> pdb=" O THRB3 52 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THRB3 52 " --> pdb=" O ARGB3 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B3' and resid 62 through 68 removed outlier: 3.627A pdb=" N VALB3 80 " --> pdb=" O VALB3 88 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VALB3 88 " --> pdb=" O VALB3 80 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SERB3 82 " --> pdb=" O ARGB3 86 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARGB3 86 " --> pdb=" O SERB3 82 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILEB3 87 " --> pdb=" O GLNB3 104 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLNB3 104 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILEB3 89 " --> pdb=" O ILEB3 102 " (cutoff:3.500A) removed outlier: 3.769A 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: 6.000A pdb=" N VALB3 167 " --> pdb=" O METB3 187 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N METB3 187 " --> pdb=" O VALB3 167 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N HISB3 169 " --> pdb=" O LEUB3 185 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N METB3 181 " --> pdb=" O VALB3 173 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEUB3 208 " --> pdb=" O SERB3 225 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SERB3 225 " --> pdb=" O LEUB3 208 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHEB3 210 " --> pdb=" O LYSB3 223 " (cutoff:3.500A) removed outlier: 3.905A 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: 4.007A pdb=" N PHEB3 234 " --> pdb=" O CYSB3 251 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYB3 247 " --> pdb=" O VALB3 238 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VALB3 248 " --> pdb=" O LYSB3 259 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYRB3 255 " --> pdb=" O SERB3 252 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILEB3 267 " --> pdb=" O TYRB3 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B3' and resid 273 through 274 removed outlier: 6.026A 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 287 through 294 removed outlier: 6.678A pdb=" N GLNB3 304 " --> pdb=" O VALB3 288 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SERB3 290 " --> pdb=" O LEUB3 302 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEUB3 302 " --> pdb=" O SERB3 290 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THRB3 292 " --> pdb=" O PHEB3 300 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHEB3 300 " --> pdb=" O THRB3 292 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHEB3 299 " --> pdb=" O LEUB3 315 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEUB3 315 " --> pdb=" O PHEB3 299 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASPB3 309 " --> pdb=" O THRB3 305 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILEB3 310 " --> pdb=" O PHEB3 330 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLUB3 324 " --> pdb=" O GLUB3 316 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B3' and resid 336 through 342 removed outlier: 7.398A pdb=" N ALAB3 350 " --> pdb=" O ALAB3 337 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N METB3 339 " --> pdb=" O PHEB3 348 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHEB3 348 " --> pdb=" O METB3 339 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VALB3 341 " --> pdb=" O PHEB3 346 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHEB3 346 " --> pdb=" O VALB3 341 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYRB3 357 " --> pdb=" O VALB3 349 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEUB3 358 " --> pdb=" O ASPB3 399 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASPB3 399 " --> pdb=" O LEUB3 358 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLNB3 360 " --> pdb=" O LEUB3 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEUB3 397 " --> pdb=" O GLNB3 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B3' and resid 407 through 413 removed outlier: 3.674A pdb=" N PHEB3 409 " --> pdb=" O ALAB3 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 445 through 450 removed outlier: 5.353A pdb=" N GLUB3 446 " --> pdb=" O ALAB3 766 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALAB3 766 " --> pdb=" O GLUB3 446 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALAB3 448 " --> pdb=" O ILEB3 764 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHEB3 741 " --> pdb=" O ILEB3 757 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 458 through 462 removed outlier: 4.193A pdb=" N VALB3 484 " --> pdb=" O VALB3 494 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 507 through 510 removed outlier: 3.875A pdb=" N HISB3 526 " --> pdb=" O ASNB3 534 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.681A 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: 4.024A pdb=" N CYSB3 589 " --> pdb=" O GLYB3 608 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THRB3 613 " --> pdb=" O LEUB3 609 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VALB3 614 " --> pdb=" O METB3 630 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N METB3 630 " --> pdb=" O VALB3 614 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILEB3 616 " --> pdb=" O LEUB3 628 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SERB3 618 " --> pdb=" O GLNB3 626 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLNB3 626 " --> pdb=" O SERB3 618 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B3' and resid 637 through 643 removed outlier: 4.235A pdb=" N SERB3 639 " --> pdb=" O GLYB3 668 " (cutoff:3.500A) removed outlier: 5.239A 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: 3.714A pdb=" N LYSB3 700 " --> pdb=" O METB3 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 785 through 790 removed outlier: 7.390A pdb=" N ILEB3 800 " --> pdb=" O ARGB3 786 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHEB3 788 " --> pdb=" O ILEB3 798 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILEB3 798 " --> pdb=" O PHEB3 788 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SERB3 864 " --> pdb=" O GLNB3 881 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLNB3 881 " --> pdb=" O SERB3 864 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILEB3 866 " --> pdb=" O LEUB3 879 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEUB3 879 " --> pdb=" O ILEB3 866 " (cutoff:3.500A) removed outlier: 7.147A 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: 5.849A pdb=" N ALAB3 888 " --> pdb=" O ALAB3 910 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALAB3 910 " --> pdb=" O ALAB3 888 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SERB3 890 " --> pdb=" O GLYB3 908 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRPB3 903 " --> pdb=" O LEUB3 930 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HISB3 941 " --> pdb=" O THRB3 927 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYSB3 929 " --> pdb=" O PHEB3 939 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHEB3 939 " --> pdb=" O LYSB3 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B3' and resid 951 through 955 removed outlier: 4.073A pdb=" N ALAB3 951 " --> pdb=" O GLYB3 962 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEUB3 967 " --> pdb=" O GLUB3 982 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLUB3 982 " --> pdb=" O LEUB3 967 " (cutoff:3.500A) removed outlier: 6.389A 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: 3.834A pdb=" N GLYB3 992 " --> pdb=" O SERB31003 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TRPB31011 " --> pdb=" O PHEB31024 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLNB31087 " --> pdb=" O PHEB31024 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B3' and resid 1033 through 1038 removed outlier: 3.816A pdb=" N THRB31035 " --> pdb=" O ALAB31047 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASNB31052 " --> pdb=" O ASPB31048 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILEB31053 " --> pdb=" O ASNB31094 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASNB31094 " --> pdb=" O ILEB31053 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VALB31055 " --> pdb=" O ILEB31092 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B4' and resid 39 through 43 removed outlier: 3.730A pdb=" N ASNB4 41 " --> pdb=" O GLUB4 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VALB4 59 " --> pdb=" O VALB4 15 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B4' and resid 78 through 79 Processing sheet with id=AD6, first strand: chain 'B4' and resid 131 through 134 removed outlier: 7.511A pdb=" N LYSB4 131 " --> pdb=" O TYRB4 144 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYRB4 144 " --> pdb=" O LYSB4 131 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N METB4 133 " --> pdb=" O LYSB4 142 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B6' and resid 81 through 82 Processing sheet with id=AD8, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.208A pdb=" N ALA H 18 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 21 through 22 removed outlier: 3.580A pdb=" N SER H 67 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 39 through 42 removed outlier: 6.478A pdb=" N TYR H 71 " --> pdb=" O CYS H 40 " (cutoff:3.500A) 1131 hydrogen bonds defined for protein. 3180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8372 1.34 - 1.45: 4388 1.45 - 1.57: 15016 1.57 - 1.69: 136 1.69 - 1.81: 219 Bond restraints: 28131 Sorted by residual: bond pdb=" N ILEB2 564 " pdb=" CA ILEB2 564 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.44e+00 bond pdb=" N ILEB2 566 " pdb=" CA ILEB2 566 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 7.99e+00 bond pdb=" N TRPB2 708 " pdb=" CA TRPB2 708 " ideal model delta sigma weight residual 1.454 1.486 -0.031 1.17e-02 7.31e+03 7.22e+00 bond pdb=" N ASPB2 565 " pdb=" CA ASPB2 565 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.59e+00 bond pdb=" N LEUB2 571 " pdb=" CA LEUB2 571 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.29e-02 6.01e+03 6.15e+00 ... (remaining 28126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 37816 1.67 - 3.34: 471 3.34 - 5.01: 74 5.01 - 6.68: 13 6.68 - 8.35: 6 Bond angle restraints: 38380 Sorted by residual: angle pdb=" N GLNB2 569 " pdb=" CA GLNB2 569 " pdb=" C GLNB2 569 " ideal model delta sigma weight residual 111.28 106.43 4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" N LYSB2 570 " pdb=" CA LYSB2 570 " pdb=" C LYSB2 570 " ideal model delta sigma weight residual 111.07 107.25 3.82 1.07e+00 8.73e-01 1.27e+01 angle pdb=" CA GLUB1 802 " pdb=" CB GLUB1 802 " pdb=" CG GLUB1 802 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA LYSB2 570 " pdb=" C LYSB2 570 " pdb=" O LYSB2 570 " ideal model delta sigma weight residual 120.82 117.65 3.17 1.05e+00 9.07e-01 9.13e+00 angle pdb=" C LYSB2 570 " pdb=" N LEUB2 571 " pdb=" CA LEUB2 571 " ideal model delta sigma weight residual 120.63 116.03 4.60 1.61e+00 3.86e-01 8.17e+00 ... (remaining 38375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 16427 35.84 - 71.69: 700 71.69 - 107.53: 43 107.53 - 143.38: 2 143.38 - 179.22: 6 Dihedral angle restraints: 17178 sinusoidal: 7686 harmonic: 9492 Sorted by residual: 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 50.96 -178.96 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 45.13 -173.13 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U R 12 " pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sinusoidal sigma weight residual 200.00 82.11 117.89 1 1.50e+01 4.44e-03 6.26e+01 ... (remaining 17175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3228 0.039 - 0.078: 715 0.078 - 0.116: 295 0.116 - 0.155: 32 0.155 - 0.194: 4 Chirality restraints: 4274 Sorted by residual: chirality pdb=" CA ILEB2 566 " pdb=" N ILEB2 566 " pdb=" C ILEB2 566 " pdb=" CB ILEB2 566 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA ILEB2 564 " pdb=" N ILEB2 564 " pdb=" C ILEB2 564 " pdb=" CB ILEB2 564 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CB ILEB3 764 " pdb=" CA ILEB3 764 " pdb=" CG1 ILEB3 764 " pdb=" CG2 ILEB3 764 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 4271 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRB1 508 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PROB1 509 " -0.090 5.00e-02 4.00e+02 pdb=" CA PROB1 509 " 0.027 5.00e-02 4.00e+02 pdb=" CD PROB1 509 " 0.029 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 4.68e-02 3.50e+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 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PROA3 393 " 0.081 5.00e-02 4.00e+02 pdb=" CA PROA3 393 " -0.024 5.00e-02 4.00e+02 pdb=" CD PROA3 393 " -0.026 5.00e-02 4.00e+02 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6963 2.81 - 3.33: 24624 3.33 - 3.85: 43255 3.85 - 4.38: 49366 4.38 - 4.90: 85042 Nonbonded interactions: 209250 Sorted by model distance: nonbonded pdb=" N2 G 2 33 " pdb=" O2 U R 1 " model vdw 2.282 2.496 nonbonded pdb=" O5' G 2 31 " pdb=" O4' G 2 31 " model vdw 2.498 2.432 nonbonded pdb=" O5' U R 12 " pdb=" O4' U R 12 " model vdw 2.503 2.432 nonbonded pdb=" O5' U 2 46 " pdb=" O4' U 2 46 " model vdw 2.513 2.432 nonbonded pdb=" O5' PSU 2 43 " pdb=" O4' PSU 2 43 " model vdw 2.522 2.432 ... (remaining 209245 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 0.036 28143 Z= 0.115 Angle : 0.490 8.348 38398 Z= 0.264 Chirality : 0.039 0.194 4274 Planarity : 0.003 0.052 4756 Dihedral : 18.304 179.224 11062 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.25 % Allowed : 23.08 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.10 (0.15), residues: 3229 helix: 0.69 (0.15), residues: 1160 sheet: 0.68 (0.22), residues: 611 loop : -0.65 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGB1 549 TYR 0.008 0.001 TYRB3 520 PHE 0.014 0.001 PHEB11126 TRP 0.015 0.001 TRPA1 249 HIS 0.005 0.000 HISB2 572 Details of bonding type rmsd covalent geometry : bond 0.00202 (28131) covalent geometry : angle 0.48601 (38380) hydrogen bonds : bond 0.25847 ( 1126) hydrogen bonds : angle 7.21490 ( 3204) metal coordination : bond 0.00261 ( 12) metal coordination : angle 3.02503 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 608 time to evaluate : 0.965 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: A 700 LYS cc_start: 0.5510 (mttt) cc_final: 0.4293 (mttt) REVERT: A2 29 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7668 (tpt170) REVERT: A2 31 ARG cc_start: 0.7036 (mpt180) cc_final: 0.6276 (mtt-85) REVERT: A2 39 ASP cc_start: 0.6502 (m-30) cc_final: 0.6279 (m-30) REVERT: A2 214 MET cc_start: 0.5066 (mmm) cc_final: 0.3714 (tpt) REVERT: A3 382 ASN cc_start: 0.8711 (t0) cc_final: 0.7841 (p0) REVERT: A3 392 ILE cc_start: 0.8429 (tp) cc_final: 0.7807 (pt) REVERT: A3 428 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7523 (mm-30) REVERT: B1 575 LEU cc_start: 0.8393 (pp) cc_final: 0.8188 (pp) REVERT: B1 796 CYS cc_start: 0.7107 (m) cc_final: 0.6899 (m) REVERT: B1 823 MET cc_start: 0.6724 (tpt) cc_final: 0.6139 (tpp) REVERT: B1 830 TYR cc_start: 0.7284 (t80) cc_final: 0.6981 (t80) REVERT: B1 844 VAL cc_start: 0.8190 (m) cc_final: 0.7457 (p) REVERT: B1 866 LYS cc_start: 0.9035 (ttmm) cc_final: 0.8661 (tttp) REVERT: B1 883 ASP cc_start: 0.7817 (t0) cc_final: 0.7389 (t0) REVERT: B1 939 ARG cc_start: 0.8170 (mtp180) cc_final: 0.6927 (mmt180) REVERT: B1 1161 MET cc_start: 0.7745 (mtp) cc_final: 0.7216 (ttt) REVERT: B1 1246 MET cc_start: 0.8194 (mmm) cc_final: 0.7838 (mmm) REVERT: B2 536 MET cc_start: 0.8068 (ptm) cc_final: 0.7846 (ptm) REVERT: B2 611 ASP cc_start: 0.8078 (m-30) cc_final: 0.7873 (m-30) REVERT: B3 187 MET cc_start: 0.7689 (ttt) cc_final: 0.7367 (ttp) REVERT: B3 285 MET cc_start: 0.7866 (mmm) cc_final: 0.7316 (tpp) REVERT: B3 442 LEU cc_start: 0.8762 (mt) cc_final: 0.8532 (mp) REVERT: B3 516 LEU cc_start: 0.7590 (mt) cc_final: 0.7002 (tt) REVERT: B3 630 MET cc_start: 0.7752 (mmp) cc_final: 0.7546 (mmp) REVERT: B3 713 LEU cc_start: 0.9253 (tp) cc_final: 0.8825 (mp) REVERT: B3 723 TYR cc_start: 0.7300 (p90) cc_final: 0.7050 (p90) REVERT: B3 730 HIS cc_start: 0.7566 (m-70) cc_final: 0.6873 (m90) REVERT: B3 770 LEU cc_start: 0.7523 (pt) cc_final: 0.7169 (pp) REVERT: B3 869 MET cc_start: 0.8892 (ptp) cc_final: 0.8684 (ptm) REVERT: B3 919 SER cc_start: 0.9049 (m) cc_final: 0.8726 (p) REVERT: B3 929 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8065 (mtmm) REVERT: B3 936 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8185 (tttm) REVERT: B3 1053 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7918 (mt) REVERT: B3 1166 TYR cc_start: 0.8753 (t80) cc_final: 0.8439 (t80) REVERT: B4 1 MET cc_start: 0.5202 (tmm) cc_final: 0.4575 (tmm) REVERT: B4 48 ARG cc_start: 0.4067 (ttm-80) cc_final: 0.3659 (ptm160) REVERT: B4 64 GLU cc_start: 0.6458 (mm-30) cc_final: 0.6207 (tm-30) REVERT: B4 85 ARG cc_start: 0.7001 (ptp90) cc_final: 0.6799 (ptm160) REVERT: B4 110 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6482 (pp20) REVERT: B4 115 LEU cc_start: 0.9215 (tp) cc_final: 0.8991 (mm) REVERT: B4 123 PHE cc_start: 0.7518 (m-80) cc_final: 0.6899 (m-80) REVERT: B4 147 ILE cc_start: 0.8032 (mt) cc_final: 0.7541 (mp) REVERT: B4 162 MET cc_start: 0.8573 (mmm) cc_final: 0.8153 (mmm) REVERT: B6 101 MET cc_start: 0.2975 (ptp) cc_final: 0.2526 (mmp) REVERT: H 41 THR cc_start: 0.8494 (m) cc_final: 0.8171 (p) REVERT: H 80 LYS cc_start: 0.8250 (mttt) cc_final: 0.7911 (mtpp) REVERT: H 93 SER cc_start: 0.7184 (m) cc_final: 0.6498 (p) REVERT: H 95 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7938 (mtmt) REVERT: H 101 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7640 (tm-30) outliers start: 7 outliers final: 1 residues processed: 612 average time/residue: 0.2040 time to fit residues: 185.8811 Evaluate side-chains 328 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B2 residue 571 LEU Chi-restraints excluded: chain B3 residue 1053 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.0050 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.0470 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 485 ASN B1 878 ASN B11100 ASN B11256 HIS B2 637 GLN B3 9 GLN B3 97 ASN B3 219 HIS B3 526 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.159137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.117570 restraints weight = 55747.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.113855 restraints weight = 45451.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115224 restraints weight = 40070.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115430 restraints weight = 26046.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117372 restraints weight = 24914.562| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28143 Z= 0.132 Angle : 0.618 10.227 38398 Z= 0.318 Chirality : 0.042 0.172 4274 Planarity : 0.004 0.055 4756 Dihedral : 13.776 179.897 4619 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.71 % Allowed : 23.87 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.32 (0.15), residues: 3229 helix: 1.10 (0.15), residues: 1187 sheet: 0.61 (0.21), residues: 628 loop : -0.70 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGA2 165 TYR 0.021 0.001 TYRA1 271 PHE 0.021 0.001 PHEB4 120 TRP 0.023 0.002 TRPB2 578 HIS 0.010 0.001 HISB1 572 Details of bonding type rmsd covalent geometry : bond 0.00275 (28131) covalent geometry : angle 0.61444 (38380) hydrogen bonds : bond 0.05965 ( 1126) hydrogen bonds : angle 5.36206 ( 3204) metal coordination : bond 0.00265 ( 12) metal coordination : angle 3.05354 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 351 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 ARG cc_start: 0.7150 (ptp-110) cc_final: 0.6003 (mtm-85) REVERT: A2 26 ARG cc_start: 0.5896 (ppt170) cc_final: 0.5696 (ttt180) REVERT: A2 31 ARG cc_start: 0.4161 (mpt180) cc_final: 0.3668 (mtt-85) REVERT: A2 214 MET cc_start: 0.4042 (mmm) cc_final: 0.2718 (tpt) REVERT: A3 382 ASN cc_start: 0.8726 (t0) cc_final: 0.8256 (t0) REVERT: B1 609 MET cc_start: 0.8520 (tpt) cc_final: 0.8302 (tpt) REVERT: B1 850 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8808 (tt) REVERT: B1 883 ASP cc_start: 0.7716 (t0) cc_final: 0.7334 (t0) REVERT: B1 919 ASN cc_start: 0.8098 (m-40) cc_final: 0.7857 (t0) REVERT: B1 939 ARG cc_start: 0.7653 (mtp180) cc_final: 0.6835 (mmt-90) REVERT: B2 454 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6687 (mp) REVERT: B3 460 TRP cc_start: 0.6275 (m-90) cc_final: 0.5547 (m-90) REVERT: B3 516 LEU cc_start: 0.7097 (mt) cc_final: 0.6833 (tt) REVERT: B3 630 MET cc_start: 0.7352 (mmp) cc_final: 0.6944 (mmp) REVERT: B3 770 LEU cc_start: 0.7558 (pt) cc_final: 0.7323 (pp) REVERT: B3 919 SER cc_start: 0.8926 (m) cc_final: 0.8663 (p) REVERT: B3 1166 TYR cc_start: 0.8750 (t80) cc_final: 0.8438 (t80) REVERT: B4 30 TRP cc_start: 0.7665 (t-100) cc_final: 0.7239 (t-100) REVERT: B4 48 ARG cc_start: 0.4004 (ttm-80) cc_final: 0.3615 (ptm160) REVERT: B4 114 LYS cc_start: 0.8709 (tppt) cc_final: 0.8254 (tppt) REVERT: B4 123 PHE cc_start: 0.6347 (m-80) cc_final: 0.6043 (m-80) REVERT: B6 4 GLN cc_start: 0.0848 (OUTLIER) cc_final: -0.1091 (tp40) REVERT: B6 101 MET cc_start: 0.2767 (ptp) cc_final: 0.2172 (mmp) REVERT: H 80 LYS cc_start: 0.8361 (mttt) cc_final: 0.8124 (mtpp) REVERT: H 95 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7647 (mttt) REVERT: H 97 ASP cc_start: 0.8884 (m-30) cc_final: 0.8559 (m-30) REVERT: H 101 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7368 (tm-30) outliers start: 76 outliers final: 33 residues processed: 414 average time/residue: 0.1846 time to fit residues: 118.0242 Evaluate side-chains 323 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 267 GLU Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 396 LEU Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 429 TRP Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 754 ILE Chi-restraints excluded: chain B1 residue 829 ASN Chi-restraints excluded: chain B1 residue 850 ILE Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 469 VAL Chi-restraints excluded: chain B2 residue 571 LEU Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 165 THR Chi-restraints excluded: chain B3 residue 170 VAL Chi-restraints excluded: chain B3 residue 219 HIS Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 363 HIS Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 610 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 284 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 170 optimal weight: 0.0040 chunk 268 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 425 HIS A3 431 HIS B2 637 GLN B3 219 HIS B3 526 HIS ** B3 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B31052 ASN B6 76 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.156007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.114036 restraints weight = 56694.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109404 restraints weight = 49477.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.111009 restraints weight = 42024.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.111470 restraints weight = 28333.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111849 restraints weight = 26631.270| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28143 Z= 0.165 Angle : 0.611 10.293 38398 Z= 0.311 Chirality : 0.042 0.166 4274 Planarity : 0.004 0.053 4756 Dihedral : 13.779 178.707 4617 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.60 % Allowed : 22.51 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.40 (0.15), residues: 3229 helix: 1.28 (0.15), residues: 1187 sheet: 0.74 (0.21), residues: 585 loop : -0.77 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGB3 718 TYR 0.022 0.001 TYRB1 805 PHE 0.016 0.002 PHEB3 22 TRP 0.013 0.001 TRPB31077 HIS 0.010 0.001 HISB3 219 Details of bonding type rmsd covalent geometry : bond 0.00383 (28131) covalent geometry : angle 0.60462 (38380) hydrogen bonds : bond 0.05354 ( 1126) hydrogen bonds : angle 5.07421 ( 3204) metal coordination : bond 0.00475 ( 12) metal coordination : angle 4.07097 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 315 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 ARG cc_start: 0.7300 (ptp-110) cc_final: 0.6193 (mtm-85) REVERT: A2 29 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6526 (tpp-160) REVERT: A2 31 ARG cc_start: 0.4426 (mpt180) cc_final: 0.3829 (mtt-85) REVERT: A2 127 MET cc_start: 0.0638 (ptm) cc_final: 0.0342 (ptm) REVERT: A2 214 MET cc_start: 0.3800 (mmm) cc_final: 0.2883 (tpt) REVERT: B1 498 MET cc_start: 0.7929 (ptm) cc_final: 0.7554 (ptm) REVERT: B1 546 ASP cc_start: 0.8129 (t0) cc_final: 0.7656 (t70) REVERT: B1 563 LEU cc_start: 0.8108 (tp) cc_final: 0.7890 (tp) REVERT: B1 613 MET cc_start: 0.8065 (mmm) cc_final: 0.7381 (mtt) REVERT: B1 818 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: B1 823 MET cc_start: 0.7015 (tpp) cc_final: 0.6596 (tpp) REVERT: B1 850 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B1 883 ASP cc_start: 0.7803 (t0) cc_final: 0.7498 (t0) REVERT: B1 919 ASN cc_start: 0.8161 (m-40) cc_final: 0.7927 (t0) REVERT: B1 939 ARG cc_start: 0.7776 (mtp180) cc_final: 0.6899 (mmt-90) REVERT: B1 1003 VAL cc_start: 0.8756 (m) cc_final: 0.8546 (p) REVERT: B2 619 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.4615 (ttp) REVERT: B3 187 MET cc_start: 0.7746 (ttt) cc_final: 0.7496 (ttp) REVERT: B3 235 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7209 (pp) REVERT: B3 242 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8192 (p) REVERT: B3 516 LEU cc_start: 0.7129 (mt) cc_final: 0.6829 (tt) REVERT: B3 566 PHE cc_start: 0.5579 (m-80) cc_final: 0.5313 (t80) REVERT: B3 630 MET cc_start: 0.7609 (mmp) cc_final: 0.7287 (mmp) REVERT: B3 703 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.6958 (ptm160) REVERT: B3 755 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7914 (m) REVERT: B3 770 LEU cc_start: 0.7683 (pt) cc_final: 0.7482 (pt) REVERT: B3 919 SER cc_start: 0.8954 (m) cc_final: 0.8726 (p) REVERT: B3 1095 TYR cc_start: 0.8168 (t80) cc_final: 0.7766 (t80) REVERT: B3 1166 TYR cc_start: 0.8846 (t80) cc_final: 0.8480 (t80) REVERT: B4 1 MET cc_start: 0.7146 (tmm) cc_final: 0.6480 (tmm) REVERT: B4 30 TRP cc_start: 0.7850 (t-100) cc_final: 0.7262 (t-100) REVERT: B4 48 ARG cc_start: 0.4023 (ttm-80) cc_final: 0.3541 (ptm160) REVERT: B4 114 LYS cc_start: 0.8737 (tppt) cc_final: 0.8458 (tppt) REVERT: B5 25 ASP cc_start: 0.7965 (t0) cc_final: 0.7563 (t0) REVERT: B6 101 MET cc_start: 0.2710 (ptp) cc_final: 0.2120 (mmm) REVERT: H 80 LYS cc_start: 0.8411 (mttt) cc_final: 0.8190 (mtpp) REVERT: H 95 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7677 (mttt) REVERT: H 97 ASP cc_start: 0.8886 (m-30) cc_final: 0.8466 (m-30) REVERT: H 101 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7349 (tm-30) outliers start: 101 outliers final: 54 residues processed: 396 average time/residue: 0.1776 time to fit residues: 110.0131 Evaluate side-chains 337 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 267 GLU Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 407 MET Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 567 VAL Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 707 LEU Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 754 ILE Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 850 ILE Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 1000 ILE Chi-restraints excluded: chain B1 residue 1024 LEU Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 469 VAL Chi-restraints excluded: chain B2 residue 528 ILE Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 571 LEU Chi-restraints excluded: chain B2 residue 619 MET Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 87 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 235 LEU Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 292 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 40 VAL Chi-restraints excluded: chain B4 residue 147 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 27 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 208 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 382 ASN A3 403 ASN B1 626 ASN B1 682 HIS B11100 ASN B2 478 HIS B2 579 GLN B2 637 GLN B3 526 HIS ** B3 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 861 GLN B31147 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.153107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.104037 restraints weight = 56647.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.100917 restraints weight = 41272.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101548 restraints weight = 31870.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101944 restraints weight = 27701.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102106 restraints weight = 25568.400| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 28143 Z= 0.232 Angle : 0.673 11.953 38398 Z= 0.338 Chirality : 0.045 0.167 4274 Planarity : 0.005 0.054 4756 Dihedral : 13.864 178.213 4617 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.35 % Allowed : 22.51 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.18 (0.15), residues: 3229 helix: 1.16 (0.15), residues: 1179 sheet: 0.62 (0.21), residues: 579 loop : -0.94 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGA1 268 TYR 0.045 0.002 TYRA3 416 PHE 0.024 0.002 PHEA2 195 TRP 0.016 0.001 TRPB31077 HIS 0.007 0.001 HISB3 219 Details of bonding type rmsd covalent geometry : bond 0.00559 (28131) covalent geometry : angle 0.66333 (38380) hydrogen bonds : bond 0.05454 ( 1126) hydrogen bonds : angle 5.10780 ( 3204) metal coordination : bond 0.00836 ( 12) metal coordination : angle 5.39036 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 279 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 ARG cc_start: 0.7578 (ptp-110) cc_final: 0.6457 (mtm-85) REVERT: A1 267 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6943 (pt0) REVERT: A2 29 ARG cc_start: 0.7130 (tpt170) cc_final: 0.6622 (tpp-160) REVERT: A2 81 ASN cc_start: 0.7993 (m110) cc_final: 0.7786 (m110) REVERT: A2 127 MET cc_start: 0.1035 (ptm) cc_final: 0.0739 (ptm) REVERT: A2 214 MET cc_start: 0.4052 (mmm) cc_final: 0.3027 (tpt) REVERT: B1 498 MET cc_start: 0.7994 (ptm) cc_final: 0.7736 (ptm) REVERT: B1 563 LEU cc_start: 0.8328 (tp) cc_final: 0.8128 (tp) REVERT: B1 613 MET cc_start: 0.7993 (mmm) cc_final: 0.7667 (mtt) REVERT: B1 818 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: B1 823 MET cc_start: 0.7367 (tpp) cc_final: 0.6638 (tpp) REVERT: B1 883 ASP cc_start: 0.7900 (t0) cc_final: 0.7566 (t0) REVERT: B1 919 ASN cc_start: 0.8373 (m-40) cc_final: 0.8122 (t0) REVERT: B1 939 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7006 (mmt-90) REVERT: B2 619 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5256 (ttp) REVERT: B3 235 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7602 (pp) REVERT: B3 242 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8136 (p) REVERT: B3 566 PHE cc_start: 0.5675 (m-80) cc_final: 0.5349 (t80) REVERT: B3 630 MET cc_start: 0.7635 (mmp) cc_final: 0.7375 (mmp) REVERT: B3 703 ARG cc_start: 0.7286 (ptm-80) cc_final: 0.7000 (ptm160) REVERT: B3 715 MET cc_start: 0.7615 (tpt) cc_final: 0.7341 (tpp) REVERT: B3 723 TYR cc_start: 0.7124 (p90) cc_final: 0.6917 (p90) REVERT: B3 755 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.7999 (m) REVERT: B3 1095 TYR cc_start: 0.8359 (t80) cc_final: 0.7898 (t80) REVERT: B4 48 ARG cc_start: 0.4525 (ttm-80) cc_final: 0.3540 (ptm160) REVERT: B4 114 LYS cc_start: 0.8860 (tppt) cc_final: 0.8617 (tppt) REVERT: B5 25 ASP cc_start: 0.8248 (t0) cc_final: 0.7710 (t0) REVERT: B6 101 MET cc_start: 0.3018 (ptp) cc_final: 0.2444 (mmm) REVERT: H 80 LYS cc_start: 0.8559 (mttt) cc_final: 0.8257 (mtpp) REVERT: H 95 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7671 (mtmt) REVERT: H 97 ASP cc_start: 0.8909 (m-30) cc_final: 0.8520 (m-30) outliers start: 122 outliers final: 74 residues processed: 380 average time/residue: 0.1786 time to fit residues: 106.8767 Evaluate side-chains 338 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 267 GLU Chi-restraints excluded: chain A1 residue 275 ASP Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 382 ASN Chi-restraints excluded: chain A3 residue 403 ASN Chi-restraints excluded: chain A3 residue 415 THR Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 475 THR Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 553 VAL Chi-restraints excluded: chain B1 residue 567 VAL Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 687 VAL Chi-restraints excluded: chain B1 residue 707 LEU Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 754 ILE Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 834 VAL Chi-restraints excluded: chain B1 residue 905 THR Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 1000 ILE Chi-restraints excluded: chain B1 residue 1024 LEU Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 462 VAL Chi-restraints excluded: chain B2 residue 469 VAL Chi-restraints excluded: chain B2 residue 491 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 619 MET Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL Chi-restraints excluded: chain B3 residue 154 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 292 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 834 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 147 ILE Chi-restraints excluded: chain B5 residue 11 LEU Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B6 residue 67 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 280 optimal weight: 0.0020 chunk 155 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 overall best weight: 0.5108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11100 ASN B2 637 GLN B3 138 GLN B3 526 HIS ** B3 553 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 = 0.4267 r_free = 0.4267 target = 0.155770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105716 restraints weight = 55629.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103387 restraints weight = 36459.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104394 restraints weight = 27702.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104781 restraints weight = 23736.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104969 restraints weight = 22236.520| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28143 Z= 0.113 Angle : 0.595 13.746 38398 Z= 0.295 Chirality : 0.042 0.295 4274 Planarity : 0.004 0.056 4756 Dihedral : 13.777 179.967 4615 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.07 % Allowed : 23.69 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.34 (0.15), residues: 3229 helix: 1.33 (0.15), residues: 1181 sheet: 0.72 (0.21), residues: 576 loop : -0.89 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB3 718 TYR 0.023 0.001 TYRA1 271 PHE 0.021 0.001 PHEB4 120 TRP 0.012 0.001 TRPB31032 HIS 0.010 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00250 (28131) covalent geometry : angle 0.58863 (38380) hydrogen bonds : bond 0.04425 ( 1126) hydrogen bonds : angle 4.76993 ( 3204) metal coordination : bond 0.00402 ( 12) metal coordination : angle 4.12481 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 284 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 ARG cc_start: 0.7385 (ptp-110) cc_final: 0.6187 (mtm-85) REVERT: A2 26 ARG cc_start: 0.4607 (ttt180) cc_final: 0.4359 (ppt170) REVERT: A2 29 ARG cc_start: 0.7040 (tpt170) cc_final: 0.6602 (tpp-160) REVERT: A2 81 ASN cc_start: 0.7881 (m110) cc_final: 0.7653 (m110) REVERT: A2 127 MET cc_start: 0.1025 (ptm) cc_final: 0.0740 (ptm) REVERT: A2 214 MET cc_start: 0.4086 (mmm) cc_final: 0.3080 (tpt) REVERT: A3 425 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6697 (t70) REVERT: B1 485 SER cc_start: 0.3632 (OUTLIER) cc_final: 0.3401 (p) REVERT: B1 498 MET cc_start: 0.7942 (ptm) cc_final: 0.7703 (ptm) REVERT: B1 563 LEU cc_start: 0.8209 (tp) cc_final: 0.7736 (tp) REVERT: B1 613 MET cc_start: 0.7939 (mmm) cc_final: 0.7643 (mtt) REVERT: B1 818 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6869 (m-80) REVERT: B1 823 MET cc_start: 0.7411 (tpp) cc_final: 0.6578 (tpp) REVERT: B1 839 GLU cc_start: 0.8202 (tp30) cc_final: 0.7976 (tp30) REVERT: B1 867 MET cc_start: 0.8077 (ppp) cc_final: 0.7503 (ppp) REVERT: B1 883 ASP cc_start: 0.7970 (t0) cc_final: 0.7560 (t0) REVERT: B1 919 ASN cc_start: 0.8387 (m-40) cc_final: 0.8143 (t0) REVERT: B1 939 ARG cc_start: 0.8039 (mtp180) cc_final: 0.6967 (mmt-90) REVERT: B3 235 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7204 (pp) REVERT: B3 298 MET cc_start: 0.7910 (pmm) cc_final: 0.7593 (pmm) REVERT: B3 390 ARG cc_start: 0.7638 (ptt-90) cc_final: 0.7427 (pmt-80) REVERT: B3 460 TRP cc_start: 0.6863 (m-90) cc_final: 0.6410 (m-90) REVERT: B3 569 ASP cc_start: 0.2523 (OUTLIER) cc_final: 0.0385 (p0) REVERT: B3 630 MET cc_start: 0.7679 (mmp) cc_final: 0.7456 (mmp) REVERT: B3 755 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7924 (m) REVERT: B3 823 MET cc_start: 0.8649 (ppp) cc_final: 0.8096 (ppp) REVERT: B3 1087 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6549 (mt0) REVERT: B3 1095 TYR cc_start: 0.8261 (t80) cc_final: 0.7780 (t80) REVERT: B4 1 MET cc_start: 0.7146 (tmm) cc_final: 0.6247 (tmm) REVERT: B4 48 ARG cc_start: 0.4448 (ttm-80) cc_final: 0.3500 (ptm160) REVERT: B4 114 LYS cc_start: 0.8752 (tppt) cc_final: 0.8361 (tppt) REVERT: B5 25 ASP cc_start: 0.8239 (t0) cc_final: 0.7749 (t0) REVERT: B5 57 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.5606 (mp0) REVERT: B6 4 GLN cc_start: 0.0664 (OUTLIER) cc_final: -0.0786 (tp40) REVERT: B6 101 MET cc_start: 0.3011 (ptp) cc_final: 0.2470 (mmm) REVERT: H 80 LYS cc_start: 0.8446 (mttt) cc_final: 0.8134 (mtpp) REVERT: H 97 ASP cc_start: 0.8909 (m-30) cc_final: 0.8464 (m-30) REVERT: H 98 LEU cc_start: 0.7601 (tp) cc_final: 0.7395 (tt) REVERT: H 101 GLU cc_start: 0.8403 (tp30) cc_final: 0.7204 (tm-30) REVERT: H 103 LYS cc_start: 0.7052 (tppt) cc_final: 0.6636 (tppt) outliers start: 86 outliers final: 51 residues processed: 349 average time/residue: 0.1787 time to fit residues: 98.3200 Evaluate side-chains 321 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain B1 residue 485 SER Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 888 LEU Chi-restraints excluded: chain B1 residue 905 THR Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 469 VAL Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 87 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 607 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 729 PHE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 959 VAL Chi-restraints excluded: chain B3 residue 978 LEU Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1087 GLN Chi-restraints excluded: chain B3 residue 1132 PHE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 147 ILE Chi-restraints excluded: chain B4 residue 173 THR Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 2 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 303 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11100 ASN B3 9 GLN ** B3 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.153875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104012 restraints weight = 55822.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102729 restraints weight = 37079.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.103217 restraints weight = 28286.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103788 restraints weight = 25983.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103774 restraints weight = 22827.768| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28143 Z= 0.166 Angle : 0.620 11.333 38398 Z= 0.309 Chirality : 0.043 0.248 4274 Planarity : 0.004 0.057 4756 Dihedral : 13.774 179.389 4615 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.53 % Allowed : 23.51 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.17 (0.15), residues: 3229 helix: 1.24 (0.15), residues: 1186 sheet: 0.45 (0.21), residues: 613 loop : -1.00 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGB3 718 TYR 0.023 0.002 TYRA1 271 PHE 0.019 0.002 PHEB4 120 TRP 0.013 0.001 TRPB31077 HIS 0.009 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00397 (28131) covalent geometry : angle 0.61218 (38380) hydrogen bonds : bond 0.04703 ( 1126) hydrogen bonds : angle 4.78617 ( 3204) metal coordination : bond 0.00572 ( 12) metal coordination : angle 4.66822 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 273 time to evaluate : 1.044 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: A 702 ARG cc_start: 0.7322 (ptp-110) cc_final: 0.6216 (mtm-85) REVERT: A2 29 ARG cc_start: 0.7063 (tpt170) cc_final: 0.6610 (tpp-160) REVERT: A2 81 ASN cc_start: 0.7945 (m110) cc_final: 0.7731 (m110) REVERT: A2 146 MET cc_start: 0.7231 (mmp) cc_final: 0.6520 (ttp) REVERT: A2 152 MET cc_start: 0.5953 (mtm) cc_final: 0.5739 (mpp) REVERT: A2 214 MET cc_start: 0.4044 (mmm) cc_final: 0.3117 (tpt) REVERT: A3 425 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7215 (t70) REVERT: B1 498 MET cc_start: 0.7970 (ptm) cc_final: 0.7735 (ptm) REVERT: B1 563 LEU cc_start: 0.8270 (tp) cc_final: 0.7805 (tp) REVERT: B1 609 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: B1 613 MET cc_start: 0.7943 (mmm) cc_final: 0.7688 (mtt) REVERT: B1 818 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: B1 823 MET cc_start: 0.7330 (tpp) cc_final: 0.6272 (tpp) REVERT: B1 839 GLU cc_start: 0.8102 (tp30) cc_final: 0.7871 (tp30) REVERT: B1 867 MET cc_start: 0.8089 (ppp) cc_final: 0.7629 (ppp) REVERT: B1 883 ASP cc_start: 0.7936 (t0) cc_final: 0.7558 (t0) REVERT: B1 919 ASN cc_start: 0.8319 (m-40) cc_final: 0.8053 (t0) REVERT: B1 939 ARG cc_start: 0.8009 (mtp180) cc_final: 0.6952 (mmt-90) REVERT: B1 1028 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6585 (t-90) REVERT: B1 1246 MET cc_start: 0.7944 (mmm) cc_final: 0.7424 (mmm) REVERT: B3 187 MET cc_start: 0.7851 (ttt) cc_final: 0.7596 (ttp) REVERT: B3 235 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7387 (pp) REVERT: B3 390 ARG cc_start: 0.7732 (ptt-90) cc_final: 0.7420 (pmt-80) REVERT: B3 392 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6077 (pp) REVERT: B3 460 TRP cc_start: 0.6712 (m-90) cc_final: 0.6288 (m-90) REVERT: B3 569 ASP cc_start: 0.2422 (OUTLIER) cc_final: 0.1542 (m-30) REVERT: B3 630 MET cc_start: 0.7594 (mmp) cc_final: 0.7340 (mmp) REVERT: B3 703 ARG cc_start: 0.7284 (ptm-80) cc_final: 0.7003 (ptm160) REVERT: B3 755 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7950 (m) REVERT: B3 1087 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6472 (mt0) REVERT: B3 1095 TYR cc_start: 0.8505 (t80) cc_final: 0.8073 (t80) REVERT: B4 48 ARG cc_start: 0.4403 (ttm-80) cc_final: 0.3271 (ptm160) REVERT: B4 114 LYS cc_start: 0.8525 (tppt) cc_final: 0.8289 (tppt) REVERT: B4 133 MET cc_start: 0.8108 (mmp) cc_final: 0.7589 (mmp) REVERT: B5 25 ASP cc_start: 0.8336 (t0) cc_final: 0.7951 (t0) REVERT: B5 57 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: B6 101 MET cc_start: 0.2952 (ptp) cc_final: 0.2409 (mmm) REVERT: H 80 LYS cc_start: 0.8505 (mttt) cc_final: 0.8303 (ttmm) REVERT: H 97 ASP cc_start: 0.8885 (m-30) cc_final: 0.8483 (m-30) outliers start: 99 outliers final: 70 residues processed: 352 average time/residue: 0.1773 time to fit residues: 98.9941 Evaluate side-chains 342 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 262 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 392 ILE Chi-restraints excluded: chain A3 residue 415 THR Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 475 THR Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 707 LEU Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 795 CYS Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 850 ILE Chi-restraints excluded: chain B1 residue 905 THR Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 1024 LEU Chi-restraints excluded: chain B1 residue 1028 HIS Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 9 GLN Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 131 MET Chi-restraints excluded: chain B3 residue 154 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 392 LEU Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 607 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 729 PHE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 919 SER Chi-restraints excluded: chain B3 residue 943 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 1079 ARG Chi-restraints excluded: chain B3 residue 1087 GLN Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1132 PHE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 147 ILE Chi-restraints excluded: chain B4 residue 173 THR Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 chunk 201 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 403 ASN ** B1 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 878 ASN B1 903 GLN B11100 ASN B3 776 GLN ** B4 165 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 = 0.4256 r_free = 0.4256 target = 0.154738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105516 restraints weight = 56297.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.104027 restraints weight = 37948.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104417 restraints weight = 29381.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.104776 restraints weight = 26649.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104945 restraints weight = 24422.861| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28143 Z= 0.125 Angle : 0.598 11.276 38398 Z= 0.296 Chirality : 0.042 0.216 4274 Planarity : 0.004 0.060 4756 Dihedral : 13.742 179.926 4615 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.64 % Allowed : 23.97 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.22 (0.15), residues: 3229 helix: 1.30 (0.15), residues: 1185 sheet: 0.40 (0.21), residues: 617 loop : -0.95 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB3 718 TYR 0.022 0.001 TYRA1 271 PHE 0.032 0.001 PHEA2 151 TRP 0.010 0.001 TRPB31032 HIS 0.010 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00291 (28131) covalent geometry : angle 0.59089 (38380) hydrogen bonds : bond 0.04312 ( 1126) hydrogen bonds : angle 4.66380 ( 3204) metal coordination : bond 0.00439 ( 12) metal coordination : angle 4.36202 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 270 time to evaluate : 0.958 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: A 702 ARG cc_start: 0.7415 (ptp-110) cc_final: 0.6288 (mtm-85) REVERT: A2 29 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6658 (tpp-160) REVERT: A2 81 ASN cc_start: 0.7952 (m110) cc_final: 0.7713 (m110) REVERT: A2 127 MET cc_start: 0.0516 (ptm) cc_final: 0.0097 (ptm) REVERT: A2 146 MET cc_start: 0.7298 (mmp) cc_final: 0.6502 (ttp) REVERT: A2 214 MET cc_start: 0.3999 (mmm) cc_final: 0.3222 (tpt) REVERT: A3 425 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.7172 (t70) REVERT: B1 532 PHE cc_start: 0.8082 (m-80) cc_final: 0.7748 (t80) REVERT: B1 563 LEU cc_start: 0.8262 (tp) cc_final: 0.7823 (tp) REVERT: B1 609 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7702 (mtt) REVERT: B1 613 MET cc_start: 0.7974 (mmm) cc_final: 0.7730 (mtt) REVERT: B1 818 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: B1 839 GLU cc_start: 0.8153 (tp30) cc_final: 0.7908 (tp30) REVERT: B1 867 MET cc_start: 0.8147 (ppp) cc_final: 0.7763 (ppp) REVERT: B1 883 ASP cc_start: 0.7983 (t0) cc_final: 0.7591 (t0) REVERT: B1 919 ASN cc_start: 0.8274 (m-40) cc_final: 0.8039 (t0) REVERT: B1 939 ARG cc_start: 0.8005 (mtp180) cc_final: 0.6883 (mmt-90) REVERT: B1 1028 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.6474 (t-90) REVERT: B1 1204 CYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7536 (t) REVERT: B2 636 MET cc_start: 0.7327 (mpp) cc_final: 0.7124 (mpp) REVERT: B3 235 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7451 (pp) REVERT: B3 298 MET cc_start: 0.7912 (pmm) cc_final: 0.7563 (pmm) REVERT: B3 342 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7703 (mp) REVERT: B3 390 ARG cc_start: 0.7714 (ptt-90) cc_final: 0.7384 (pmt-80) REVERT: B3 392 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6103 (pp) REVERT: B3 460 TRP cc_start: 0.6692 (m-90) cc_final: 0.6302 (m-90) REVERT: B3 566 PHE cc_start: 0.5986 (OUTLIER) cc_final: 0.5366 (t80) REVERT: B3 569 ASP cc_start: 0.2441 (OUTLIER) cc_final: 0.0745 (p0) REVERT: B3 630 MET cc_start: 0.7612 (mmp) cc_final: 0.7390 (mmp) REVERT: B3 706 MET cc_start: 0.7817 (tmm) cc_final: 0.7579 (tmm) REVERT: B3 715 MET cc_start: 0.7478 (tpp) cc_final: 0.6932 (tpp) REVERT: B3 755 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7940 (m) REVERT: B3 770 LEU cc_start: 0.7539 (pp) cc_final: 0.6841 (mp) REVERT: B3 1087 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6332 (mt0) REVERT: B3 1095 TYR cc_start: 0.8461 (t80) cc_final: 0.7978 (t80) REVERT: B4 1 MET cc_start: 0.6944 (tmm) cc_final: 0.6009 (tmm) REVERT: B4 48 ARG cc_start: 0.4419 (ttm-80) cc_final: 0.3274 (ptm160) REVERT: B4 114 LYS cc_start: 0.8528 (tppt) cc_final: 0.8154 (tppt) REVERT: B5 25 ASP cc_start: 0.8353 (t0) cc_final: 0.7973 (t0) REVERT: B5 57 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: B6 4 GLN cc_start: 0.0615 (OUTLIER) cc_final: -0.0885 (tp40) REVERT: B6 101 MET cc_start: 0.2964 (ptp) cc_final: 0.2437 (mmm) REVERT: H 97 ASP cc_start: 0.8885 (m-30) cc_final: 0.8425 (m-30) REVERT: H 101 GLU cc_start: 0.8322 (tp30) cc_final: 0.7229 (tm-30) outliers start: 102 outliers final: 70 residues processed: 351 average time/residue: 0.1705 time to fit residues: 95.3507 Evaluate side-chains 333 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 249 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 254 GLU Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 403 ASN Chi-restraints excluded: chain A3 residue 415 THR Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 707 LEU Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 905 THR Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 970 LEU Chi-restraints excluded: chain B1 residue 1024 LEU Chi-restraints excluded: chain B1 residue 1028 HIS Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1204 CYS Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 ILE Chi-restraints excluded: chain B3 residue 116 VAL 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 342 LEU Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 392 LEU Chi-restraints excluded: chain B3 residue 404 LEU Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 566 PHE Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 607 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 729 PHE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 919 SER Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1079 ARG Chi-restraints excluded: chain B3 residue 1087 GLN Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1132 PHE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 173 THR Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 85 CYS Chi-restraints excluded: chain H residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 288 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11100 ASN B3 422 GLN ** B4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.155465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.114017 restraints weight = 56556.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110447 restraints weight = 49370.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.112459 restraints weight = 46882.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.112072 restraints weight = 31050.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112343 restraints weight = 27621.120| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28143 Z= 0.111 Angle : 0.595 11.114 38398 Z= 0.294 Chirality : 0.041 0.200 4274 Planarity : 0.004 0.061 4756 Dihedral : 13.699 179.461 4615 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.21 % Allowed : 24.55 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.30 (0.15), residues: 3229 helix: 1.38 (0.15), residues: 1186 sheet: 0.45 (0.21), residues: 617 loop : -0.92 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGB1 822 TYR 0.025 0.001 TYRA1 271 PHE 0.022 0.001 PHEB3 702 TRP 0.012 0.001 TRPB1 819 HIS 0.010 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00250 (28131) covalent geometry : angle 0.58877 (38380) hydrogen bonds : bond 0.04083 ( 1126) hydrogen bonds : angle 4.55328 ( 3204) metal coordination : bond 0.00353 ( 12) metal coordination : angle 4.00865 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 276 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 ARG cc_start: 0.7166 (ptp-110) cc_final: 0.6008 (mtm-85) REVERT: A2 29 ARG cc_start: 0.7150 (tpt170) cc_final: 0.6683 (tpp-160) REVERT: A2 127 MET cc_start: -0.0114 (ptm) cc_final: -0.0340 (ptm) REVERT: A2 146 MET cc_start: 0.6978 (mmp) cc_final: 0.6388 (ttp) REVERT: A2 214 MET cc_start: 0.3617 (mmm) cc_final: 0.2975 (tpt) REVERT: A3 425 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7196 (t70) REVERT: B1 540 MET cc_start: 0.7917 (tpp) cc_final: 0.7212 (ppp) REVERT: B1 563 LEU cc_start: 0.8329 (tp) cc_final: 0.8047 (tp) REVERT: B1 609 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7443 (mtt) REVERT: B1 613 MET cc_start: 0.7836 (mmm) cc_final: 0.7628 (mtt) REVERT: B1 818 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: B1 867 MET cc_start: 0.7659 (ppp) cc_final: 0.7366 (ppp) REVERT: B1 883 ASP cc_start: 0.7695 (t0) cc_final: 0.7379 (t0) REVERT: B1 911 LEU cc_start: 0.8951 (mm) cc_final: 0.8726 (mp) REVERT: B1 919 ASN cc_start: 0.8034 (m-40) cc_final: 0.7797 (t0) REVERT: B1 939 ARG cc_start: 0.7720 (mtp180) cc_final: 0.6834 (mmt-90) REVERT: B1 1028 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.6386 (t-90) REVERT: B1 1204 CYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7472 (t) REVERT: B2 619 MET cc_start: 0.6148 (mpp) cc_final: 0.5325 (mtm) REVERT: B3 40 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8297 (tt) REVERT: B3 235 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7115 (pp) REVERT: B3 298 MET cc_start: 0.7851 (pmm) cc_final: 0.7549 (pmm) REVERT: B3 390 ARG cc_start: 0.7629 (ptt-90) cc_final: 0.7363 (pmt-80) REVERT: B3 392 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5997 (pp) REVERT: B3 566 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4787 (t80) REVERT: B3 569 ASP cc_start: 0.2611 (OUTLIER) cc_final: 0.0756 (p0) REVERT: B3 630 MET cc_start: 0.7502 (mmp) cc_final: 0.7223 (mmp) REVERT: B3 715 MET cc_start: 0.7698 (tpp) cc_final: 0.7193 (tpp) REVERT: B3 755 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7802 (m) REVERT: B3 770 LEU cc_start: 0.7481 (pp) cc_final: 0.6846 (mp) REVERT: B3 1087 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5944 (mt0) REVERT: B3 1095 TYR cc_start: 0.8581 (t80) cc_final: 0.8020 (t80) REVERT: B4 1 MET cc_start: 0.6886 (tmm) cc_final: 0.5916 (tmm) REVERT: B4 30 TRP cc_start: 0.7706 (t-100) cc_final: 0.7141 (t-100) REVERT: B4 48 ARG cc_start: 0.4345 (ttm-80) cc_final: 0.3268 (ptm160) REVERT: B4 114 LYS cc_start: 0.8342 (tppt) cc_final: 0.8116 (tppt) REVERT: B5 17 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7437 (mtmt) REVERT: B5 25 ASP cc_start: 0.8434 (t0) cc_final: 0.8131 (t0) REVERT: B5 57 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.5659 (mp0) REVERT: B6 4 GLN cc_start: 0.0579 (OUTLIER) cc_final: -0.1091 (tp40) REVERT: B6 101 MET cc_start: 0.3041 (ptp) cc_final: 0.2460 (mmm) REVERT: H 97 ASP cc_start: 0.8781 (m-30) cc_final: 0.8329 (m-30) REVERT: H 101 GLU cc_start: 0.8279 (tp30) cc_final: 0.7208 (tm-30) outliers start: 90 outliers final: 61 residues processed: 347 average time/residue: 0.1704 time to fit residues: 94.9130 Evaluate side-chains 332 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 254 GLU Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 415 THR Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 970 LEU Chi-restraints excluded: chain B1 residue 1028 HIS Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1204 CYS Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 40 LEU Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 392 LEU Chi-restraints excluded: chain B3 residue 404 LEU Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 566 PHE Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 607 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 729 PHE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1020 GLN Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1079 ARG Chi-restraints excluded: chain B3 residue 1087 GLN Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1132 PHE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 173 THR Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 17 LYS Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 29 optimal weight: 8.9990 chunk 291 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 112 optimal weight: 0.0670 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 319 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 403 ASN ** B1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11100 ASN B3 138 GLN ** B4 165 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 = 0.4269 r_free = 0.4269 target = 0.155803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114486 restraints weight = 56650.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.110734 restraints weight = 51374.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112075 restraints weight = 45678.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113752 restraints weight = 29678.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113740 restraints weight = 27127.703| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28143 Z= 0.109 Angle : 0.602 12.885 38398 Z= 0.296 Chirality : 0.041 0.189 4274 Planarity : 0.004 0.061 4756 Dihedral : 13.667 179.417 4615 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.03 % Allowed : 25.12 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.31 (0.15), residues: 3229 helix: 1.35 (0.15), residues: 1190 sheet: 0.46 (0.21), residues: 619 loop : -0.89 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGB1 822 TYR 0.029 0.001 TYRA1 271 PHE 0.033 0.001 PHEA2 195 TRP 0.040 0.001 TRPB3 460 HIS 0.010 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00244 (28131) covalent geometry : angle 0.59650 (38380) hydrogen bonds : bond 0.04000 ( 1126) hydrogen bonds : angle 4.53543 ( 3204) metal coordination : bond 0.00332 ( 12) metal coordination : angle 3.85542 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 276 time to evaluate : 0.981 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: A 702 ARG cc_start: 0.7132 (ptp-110) cc_final: 0.5943 (mtm-85) REVERT: A 811 PHE cc_start: 0.5906 (t80) cc_final: 0.5654 (t80) REVERT: A2 29 ARG cc_start: 0.7115 (tpt170) cc_final: 0.6550 (ttt180) REVERT: A2 127 MET cc_start: -0.0099 (ptm) cc_final: -0.0302 (ptm) REVERT: A2 146 MET cc_start: 0.7034 (mmp) cc_final: 0.6361 (ttp) REVERT: A2 214 MET cc_start: 0.3551 (mmm) cc_final: 0.2944 (tpt) REVERT: A3 425 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.7083 (t70) REVERT: B1 534 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B1 540 MET cc_start: 0.7902 (tpp) cc_final: 0.7392 (ppp) REVERT: B1 546 ASP cc_start: 0.8004 (t0) cc_final: 0.7496 (t70) REVERT: B1 563 LEU cc_start: 0.8331 (tp) cc_final: 0.8078 (tp) REVERT: B1 609 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7438 (mtt) REVERT: B1 818 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: B1 839 GLU cc_start: 0.7777 (tt0) cc_final: 0.7475 (tp30) REVERT: B1 867 MET cc_start: 0.7674 (ppp) cc_final: 0.7388 (ppp) REVERT: B1 883 ASP cc_start: 0.7536 (t0) cc_final: 0.7222 (t0) REVERT: B1 919 ASN cc_start: 0.8070 (m-40) cc_final: 0.7750 (t0) REVERT: B1 939 ARG cc_start: 0.7674 (mtp180) cc_final: 0.6837 (mmt-90) REVERT: B1 962 MET cc_start: 0.8652 (mtp) cc_final: 0.8376 (mtp) REVERT: B1 1028 HIS cc_start: 0.6561 (OUTLIER) cc_final: 0.6292 (t-90) REVERT: B1 1204 CYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7441 (t) REVERT: B2 619 MET cc_start: 0.6162 (mpp) cc_final: 0.5490 (mtm) REVERT: B3 40 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B3 235 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7040 (pp) REVERT: B3 298 MET cc_start: 0.7845 (pmm) cc_final: 0.7546 (pmm) REVERT: B3 342 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7741 (mp) REVERT: B3 390 ARG cc_start: 0.7589 (ptt-90) cc_final: 0.7358 (pmt-80) REVERT: B3 392 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6033 (pp) REVERT: B3 566 PHE cc_start: 0.5490 (OUTLIER) cc_final: 0.4724 (t80) REVERT: B3 569 ASP cc_start: 0.2584 (OUTLIER) cc_final: 0.0799 (p0) REVERT: B3 630 MET cc_start: 0.7430 (mmp) cc_final: 0.7148 (mmp) REVERT: B3 703 ARG cc_start: 0.7232 (ptm-80) cc_final: 0.6965 (ptm160) REVERT: B3 715 MET cc_start: 0.7721 (tpp) cc_final: 0.7224 (tpp) REVERT: B3 755 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7817 (m) REVERT: B3 770 LEU cc_start: 0.7402 (pp) cc_final: 0.6780 (mp) REVERT: B3 842 PHE cc_start: 0.8775 (t80) cc_final: 0.8455 (t80) REVERT: B3 1087 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5755 (mt0) REVERT: B3 1095 TYR cc_start: 0.8561 (t80) cc_final: 0.7970 (t80) REVERT: B4 1 MET cc_start: 0.6821 (tmm) cc_final: 0.5821 (tmm) REVERT: B4 30 TRP cc_start: 0.7659 (t-100) cc_final: 0.7110 (t-100) REVERT: B4 48 ARG cc_start: 0.4504 (ttm-80) cc_final: 0.3350 (ptm160) REVERT: B4 114 LYS cc_start: 0.8259 (tppt) cc_final: 0.8056 (tppt) REVERT: B5 17 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7390 (mtmt) REVERT: B5 25 ASP cc_start: 0.8413 (t0) cc_final: 0.8100 (t0) REVERT: B5 57 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.5536 (mp0) REVERT: B6 4 GLN cc_start: 0.0585 (OUTLIER) cc_final: -0.1085 (tp40) REVERT: B6 101 MET cc_start: 0.2860 (ptp) cc_final: 0.2503 (mmm) REVERT: H 97 ASP cc_start: 0.8772 (m-30) cc_final: 0.8330 (m-30) REVERT: H 101 GLU cc_start: 0.8280 (tp30) cc_final: 0.7220 (tm-30) outliers start: 85 outliers final: 62 residues processed: 345 average time/residue: 0.1673 time to fit residues: 92.5094 Evaluate side-chains 334 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 256 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 403 ASN Chi-restraints excluded: chain A3 residue 415 THR Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 750 ILE Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 840 LEU Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 970 LEU Chi-restraints excluded: chain B1 residue 1024 LEU Chi-restraints excluded: chain B1 residue 1028 HIS Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1204 CYS Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 40 LEU Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 71 THR Chi-restraints excluded: chain B3 residue 87 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 342 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 392 LEU Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 566 PHE Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 607 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 729 PHE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 919 SER Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1079 ARG Chi-restraints excluded: chain B3 residue 1087 GLN Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1132 PHE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 173 THR Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 17 LYS Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 101 optimal weight: 5.9990 chunk 280 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 248 optimal weight: 0.0060 chunk 317 optimal weight: 0.5980 chunk 267 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 403 ASN ** B1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11100 ASN ** B4 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.107124 restraints weight = 55910.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.104455 restraints weight = 37541.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.104897 restraints weight = 28954.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.105302 restraints weight = 25815.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.105536 restraints weight = 23856.049| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28143 Z= 0.111 Angle : 0.616 11.731 38398 Z= 0.302 Chirality : 0.042 0.248 4274 Planarity : 0.004 0.061 4756 Dihedral : 13.646 179.443 4615 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.03 % Allowed : 25.26 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.34 (0.15), residues: 3229 helix: 1.38 (0.15), residues: 1184 sheet: 0.48 (0.21), residues: 613 loop : -0.86 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARGB1 822 TYR 0.029 0.001 TYRA1 271 PHE 0.032 0.001 PHEA2 151 TRP 0.029 0.001 TRPB3 460 HIS 0.010 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00249 (28131) covalent geometry : angle 0.61053 (38380) hydrogen bonds : bond 0.03978 ( 1126) hydrogen bonds : angle 4.52044 ( 3204) metal coordination : bond 0.00315 ( 12) metal coordination : angle 3.74272 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6458 Ramachandran restraints generated. 3229 Oldfield, 0 Emsley, 3229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 266 time to evaluate : 0.944 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: A 702 ARG cc_start: 0.7444 (ptp-110) cc_final: 0.6218 (mtm-85) REVERT: A2 29 ARG cc_start: 0.6882 (tpt170) cc_final: 0.6462 (ttt180) REVERT: A2 127 MET cc_start: 0.0605 (ptm) cc_final: 0.0171 (ptm) REVERT: A2 146 MET cc_start: 0.7430 (mmp) cc_final: 0.6559 (ttp) REVERT: A2 214 MET cc_start: 0.4346 (mmm) cc_final: 0.3504 (tpt) REVERT: A3 425 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6976 (t70) REVERT: B1 511 MET cc_start: 0.8350 (ptp) cc_final: 0.8060 (tmm) REVERT: B1 532 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7797 (t80) REVERT: B1 534 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B1 540 MET cc_start: 0.8450 (tpp) cc_final: 0.7436 (ppp) REVERT: B1 546 ASP cc_start: 0.8372 (t0) cc_final: 0.7876 (t70) REVERT: B1 563 LEU cc_start: 0.8446 (tp) cc_final: 0.8163 (tp) REVERT: B1 609 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7823 (mtt) REVERT: B1 818 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: B1 839 GLU cc_start: 0.8226 (tt0) cc_final: 0.7462 (tp30) REVERT: B1 867 MET cc_start: 0.7877 (ppp) cc_final: 0.7507 (ppp) REVERT: B1 883 ASP cc_start: 0.8082 (t0) cc_final: 0.7606 (t0) REVERT: B1 919 ASN cc_start: 0.8408 (m-40) cc_final: 0.8116 (t0) REVERT: B1 939 ARG cc_start: 0.8001 (mtp180) cc_final: 0.6975 (mmt-90) REVERT: B1 989 VAL cc_start: 0.8159 (t) cc_final: 0.7736 (t) REVERT: B1 1028 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6265 (t-90) REVERT: B1 1204 CYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7525 (t) REVERT: B2 619 MET cc_start: 0.6651 (mpp) cc_final: 0.5899 (mtm) REVERT: B3 40 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B3 235 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7102 (pp) REVERT: B3 242 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8179 (p) REVERT: B3 342 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7781 (mp) REVERT: B3 390 ARG cc_start: 0.7656 (ptt-90) cc_final: 0.7359 (pmt-80) REVERT: B3 392 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5964 (pp) REVERT: B3 566 PHE cc_start: 0.5198 (OUTLIER) cc_final: 0.4457 (t80) REVERT: B3 569 ASP cc_start: 0.2804 (OUTLIER) cc_final: 0.1002 (p0) REVERT: B3 675 LEU cc_start: 0.8966 (tp) cc_final: 0.8603 (tt) REVERT: B3 703 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6993 (ptm160) REVERT: B3 715 MET cc_start: 0.7458 (tpp) cc_final: 0.6788 (tpp) REVERT: B3 718 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.8356 (ttp80) REVERT: B3 755 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7856 (m) REVERT: B3 770 LEU cc_start: 0.7235 (pp) cc_final: 0.6781 (mp) REVERT: B3 1087 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6178 (mt0) REVERT: B3 1095 TYR cc_start: 0.8454 (t80) cc_final: 0.7845 (t80) REVERT: B4 30 TRP cc_start: 0.7921 (t-100) cc_final: 0.7221 (t-100) REVERT: B4 48 ARG cc_start: 0.4649 (ttm-80) cc_final: 0.3386 (ptm160) REVERT: B5 17 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7386 (mtmt) REVERT: B5 25 ASP cc_start: 0.8418 (t0) cc_final: 0.8025 (t0) REVERT: B5 57 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.5624 (mp0) REVERT: B6 4 GLN cc_start: 0.0765 (OUTLIER) cc_final: -0.0665 (tp40) REVERT: B6 101 MET cc_start: 0.3097 (ptp) cc_final: 0.2728 (mmm) REVERT: H 97 ASP cc_start: 0.8902 (m-30) cc_final: 0.8465 (m-30) REVERT: H 101 GLU cc_start: 0.8244 (tp30) cc_final: 0.7307 (tm-30) outliers start: 85 outliers final: 57 residues processed: 335 average time/residue: 0.1688 time to fit residues: 90.7362 Evaluate side-chains 331 residues out of total 2825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 256 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 MET Chi-restraints excluded: chain A1 residue 282 VAL Chi-restraints excluded: chain A3 residue 403 ASN Chi-restraints excluded: chain A3 residue 415 THR Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 480 GLU Chi-restraints excluded: chain B1 residue 532 PHE Chi-restraints excluded: chain B1 residue 538 LEU Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 634 VAL Chi-restraints excluded: chain B1 residue 674 LEU Chi-restraints excluded: chain B1 residue 692 HIS Chi-restraints excluded: chain B1 residue 727 VAL Chi-restraints excluded: chain B1 residue 801 VAL Chi-restraints excluded: chain B1 residue 818 PHE Chi-restraints excluded: chain B1 residue 947 VAL Chi-restraints excluded: chain B1 residue 970 LEU Chi-restraints excluded: chain B1 residue 1024 LEU Chi-restraints excluded: chain B1 residue 1028 HIS Chi-restraints excluded: chain B1 residue 1065 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1101 LEU Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1204 CYS Chi-restraints excluded: chain B1 residue 1206 ASP Chi-restraints excluded: chain B1 residue 1304 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B2 residue 686 VAL Chi-restraints excluded: chain B2 residue 711 LEU Chi-restraints excluded: chain B3 residue 40 LEU Chi-restraints excluded: chain B3 residue 64 SER Chi-restraints excluded: chain B3 residue 87 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 213 LEU Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 242 SER Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 257 THR Chi-restraints excluded: chain B3 residue 333 VAL Chi-restraints excluded: chain B3 residue 342 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 392 LEU Chi-restraints excluded: chain B3 residue 408 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 479 VAL Chi-restraints excluded: chain B3 residue 509 SER Chi-restraints excluded: chain B3 residue 566 PHE Chi-restraints excluded: chain B3 residue 569 ASP Chi-restraints excluded: chain B3 residue 607 VAL Chi-restraints excluded: chain B3 residue 666 ASN Chi-restraints excluded: chain B3 residue 729 PHE Chi-restraints excluded: chain B3 residue 755 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 789 VAL Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1053 ILE Chi-restraints excluded: chain B3 residue 1079 ARG Chi-restraints excluded: chain B3 residue 1087 GLN Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1132 PHE Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 173 THR Chi-restraints excluded: chain B5 residue 16 SER Chi-restraints excluded: chain B5 residue 17 LYS Chi-restraints excluded: chain B5 residue 26 THR Chi-restraints excluded: chain B5 residue 57 GLU Chi-restraints excluded: chain B6 residue 4 GLN Chi-restraints excluded: chain B6 residue 90 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 35 optimal weight: 0.0060 chunk 47 optimal weight: 7.9990 chunk 57 optimal weight: 0.0070 chunk 272 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 294 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11100 ASN ** B4 165 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 = 0.4278 r_free = 0.4278 target = 0.156507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.115178 restraints weight = 55817.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112150 restraints weight = 49385.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114114 restraints weight = 44715.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.113809 restraints weight = 29817.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116266 restraints weight = 26526.888| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28143 Z= 0.106 Angle : 0.614 11.324 38398 Z= 0.299 Chirality : 0.042 0.282 4274 Planarity : 0.004 0.072 4756 Dihedral : 13.625 179.340 4615 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.60 % Allowed : 25.47 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % 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: 0.38 (0.15), residues: 3229 helix: 1.43 (0.15), residues: 1185 sheet: 0.48 (0.21), residues: 613 loop : -0.84 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGB4 134 TYR 0.028 0.001 TYRA1 271 PHE 0.025 0.001 PHEA2 151 TRP 0.033 0.001 TRPB3 460 HIS 0.010 0.001 HISA3 425 Details of bonding type rmsd covalent geometry : bond 0.00237 (28131) covalent geometry : angle 0.60900 (38380) hydrogen bonds : bond 0.03881 ( 1126) hydrogen bonds : angle 4.50675 ( 3204) metal coordination : bond 0.00289 ( 12) metal coordination : angle 3.59778 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4633.69 seconds wall clock time: 80 minutes 41.12 seconds (4841.12 seconds total)