Starting phenix.real_space_refine on Sat Aug 8 02:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ze2_74089/08_2026/9ze2_74089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ze2_74089/08_2026/9ze2_74089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ze2_74089/08_2026/9ze2_74089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ze2_74089/08_2026/9ze2_74089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ze2_74089/08_2026/9ze2_74089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ze2_74089/08_2026/9ze2_74089.map" } resolution = 3.26 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= 0.076 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 129 5.16 5 C 15341 2.51 5 N 4186 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24516 Number of models: 1 Model: "" Number of chains: 13 Chain: "2" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 781 Classifications: {'RNA': 29, 'RNAv2': 8} Modifications used: {'rna2p': 3, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p': 8, 'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "H" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "R" Number of atoms: 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: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 258 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain breaks: 1 Chain: "B1" Number of atoms: 7142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7142 Classifications: {'peptide': 895} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 849} Chain breaks: 1 Chain: "B2" Number of atoms: 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 698 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} 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: "A2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 407 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} 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: "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 871 SG CYS H 11 67.703 64.451 53.658 1.00 62.13 S ATOM 1134 SG CYS H 46 66.852 67.711 51.932 1.00 60.19 S ATOM 1157 SG CYS H 49 65.363 64.590 50.612 1.00 58.09 S ATOM 1428 SG CYS H 85 64.206 65.939 54.055 1.00 79.57 S ATOM 958 SG CYS H 23 50.357 57.979 49.984 1.00 71.91 S ATOM 982 SG CYS H 26 51.404 57.328 53.591 1.00 80.93 S ATOM 1229 SG CYS H 58 53.594 59.429 51.128 1.00 58.73 S ATOM 1250 SG CYS H 61 53.215 55.565 50.985 1.00 78.84 S ATOM 1009 SG CYS H 30 53.915 62.839 63.702 1.00 65.10 S ATOM 1030 SG CYS H 33 54.434 60.945 67.133 1.00 78.50 S ATOM 1325 SG CYS H 72 52.614 64.235 66.922 1.00 57.98 S ATOM 1349 SG CYS H 75 56.408 63.962 66.412 1.00 67.29 S Time building chain proxies: 5.00, per 1000 atoms: 0.20 Number of scatterers: 24516 At special positions: 0 Unit cell: (125.4, 156.2, 159.5, 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 129 16.00 P 69 15.00 O 4788 8.00 N 4186 7.00 C 15341 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: 1.87 Conformation dependent library (CDL) restraints added in 972.1 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 26 " 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 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 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5446 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 32 sheets defined 43.4% alpha, 17.9% beta 7 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'H' and resid 23 through 27 removed outlier: 3.665A pdb=" N ASP H 27 " --> pdb=" O GLU H 24 " (cutoff:3.500A) 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: 3.533A pdb=" N ARG H 82 " --> pdb=" O GLU H 79 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP H 83 " --> pdb=" O LYS H 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 79 through 83' Processing helix chain 'H' and resid 93 through 103 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.523A pdb=" N GLU A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 815 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: 3.623A pdb=" N ILEB1 472 " --> pdb=" O PROB1 469 " (cutoff:3.500A) Processing helix chain 'B1' and resid 488 through 506 Processing helix chain 'B1' and resid 508 through 522 removed outlier: 3.560A pdb=" N ALAB1 514 " --> pdb=" O PROB1 510 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLNB1 518 " --> pdb=" O ALAB1 514 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THRB1 520 " --> pdb=" O LEUB1 516 " (cutoff:3.500A) Processing helix chain 'B1' and resid 522 through 527 Processing helix chain 'B1' and resid 527 through 540 removed outlier: 4.120A 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: 3.775A pdb=" N LYSB1 562 " --> pdb=" O ARGB1 558 " (cutoff:3.500A) Processing helix chain 'B1' and resid 567 through 569 No H-bonds generated for 'chain 'B1' and resid 567 through 569' Processing helix chain 'B1' and resid 570 through 579 removed outlier: 3.830A pdb=" N VALB1 577 " --> pdb=" O LYSB1 573 " (cutoff:3.500A) Processing helix chain 'B1' and resid 580 through 584 removed outlier: 3.583A pdb=" N ILEB1 583 " --> pdb=" O PROB1 580 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASPB1 584 " --> pdb=" O LEUB1 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 580 through 584' Processing helix chain 'B1' and resid 586 through 604 removed outlier: 3.814A pdb=" N ARGB1 590 " --> pdb=" O ASPB1 586 " (cutoff:3.500A) Processing helix chain 'B1' and resid 606 through 614 Processing helix chain 'B1' and resid 615 through 619 removed outlier: 3.938A pdb=" N ASPB1 618 " --> pdb=" O PROB1 615 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASNB1 619 " --> pdb=" O ASPB1 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 615 through 619' Processing helix chain 'B1' and resid 621 through 640 removed outlier: 3.528A pdb=" N ALAB1 633 " --> pdb=" O ALAB1 629 " (cutoff:3.500A) Processing helix chain 'B1' and resid 640 through 654 removed outlier: 4.226A pdb=" N LEUB1 644 " --> pdb=" O GLYB1 640 " (cutoff:3.500A) Proline residue: B1 646 - end of helix removed outlier: 3.508A pdb=" N ALAB1 650 " --> pdb=" O PROB1 646 " (cutoff:3.500A) Processing helix chain 'B1' and resid 657 through 675 removed outlier: 3.667A pdb=" N ARGB1 661 " --> pdb=" O SERB1 657 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VALB1 668 " --> pdb=" O GLYB1 664 " (cutoff:3.500A) Processing helix chain 'B1' and resid 676 through 680 removed outlier: 3.761A pdb=" N ILEB1 679 " --> pdb=" O GLYB1 676 " (cutoff:3.500A) Processing helix chain 'B1' and resid 682 through 692 removed outlier: 3.536A pdb=" N GLUB1 688 " --> pdb=" O ARGB1 684 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILEB1 689 " --> pdb=" O SERB1 685 " (cutoff:3.500A) removed outlier: 4.358A 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 721 through 723 No H-bonds generated for 'chain 'B1' and resid 721 through 723' Processing helix chain 'B1' and resid 724 through 736 removed outlier: 3.640A pdb=" N LEUB1 728 " --> pdb=" O PHEB1 724 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYSB1 729 " --> pdb=" O ASPB1 725 " (cutoff:3.500A) Proline residue: B1 730 - end of helix removed outlier: 4.054A pdb=" N ARGB1 736 " --> pdb=" O TRPB1 732 " (cutoff:3.500A) Processing helix chain 'B1' and resid 740 through 754 removed outlier: 3.736A pdb=" N TYRB1 752 " --> pdb=" O LYSB1 748 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILEB1 754 " --> pdb=" O ILEB1 750 " (cutoff:3.500A) Processing helix chain 'B1' and resid 755 through 757 No H-bonds generated for 'chain 'B1' and resid 755 through 757' Processing helix chain 'B1' and resid 758 through 776 removed outlier: 3.770A pdb=" N ASNB1 763 " --> pdb=" O ALAB1 759 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYRB1 764 " --> pdb=" O GLUB1 760 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLUB1 768 " --> pdb=" O TYRB1 764 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEUB1 771 " --> pdb=" O ARGB1 767 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILEB1 772 " --> pdb=" O GLUB1 768 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARGB1 775 " --> pdb=" O LEUB1 771 " (cutoff:3.500A) Processing helix chain 'B1' and resid 777 through 779 No H-bonds generated for 'chain 'B1' and resid 777 through 779' Processing helix chain 'B1' and resid 781 through 798 removed outlier: 3.502A pdb=" N THRB1 798 " --> pdb=" O GLNB1 794 " (cutoff:3.500A) Processing helix chain 'B1' and resid 802 through 810 removed outlier: 3.827A pdb=" N ILEB1 806 " --> pdb=" O GLUB1 802 " (cutoff:3.500A) Processing helix chain 'B1' and resid 810 through 817 removed outlier: 3.965A pdb=" N LYSB1 816 " --> pdb=" O PROB1 812 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HISB1 817 " --> pdb=" O PROB1 813 " (cutoff:3.500A) Processing helix chain 'B1' and resid 821 through 825 removed outlier: 3.516A pdb=" N ALAB1 824 " --> pdb=" O HISB1 821 " (cutoff:3.500A) Processing helix chain 'B1' and resid 826 through 845 removed outlier: 3.736A pdb=" N ASNB1 842 " --> pdb=" O VALB1 838 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYSB1 843 " --> pdb=" O GLUB1 839 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VALB1 844 " --> pdb=" O LEUB1 840 " (cutoff:3.500A) Processing helix chain 'B1' and resid 845 through 854 removed outlier: 3.746A pdb=" N ILEB1 849 " --> pdb=" O GLYB1 845 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARGB1 852 " --> pdb=" O GLUB1 848 " (cutoff:3.500A) removed outlier: 3.562A 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 879 Processing helix chain 'B1' and resid 885 through 903 Processing helix chain 'B1' and resid 908 through 922 Processing helix chain 'B1' and resid 923 through 927 Proline residue: B1 927 - end of helix Processing helix chain 'B1' and resid 928 through 939 Processing helix chain 'B1' and resid 944 through 958 removed outlier: 3.649A pdb=" N ARGB1 948 " --> pdb=" O SERB1 944 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARGB1 957 " --> pdb=" O ASPB1 953 " (cutoff:3.500A) Processing helix chain 'B1' and resid 958 through 965 removed outlier: 3.502A pdb=" N LYSB1 963 " --> pdb=" O ALAB1 959 " (cutoff:3.500A) Processing helix chain 'B1' and resid 967 through 980 removed outlier: 3.850A pdb=" N METB1 971 " --> pdb=" O GLUB1 967 " (cutoff:3.500A) Processing helix chain 'B1' and resid 986 through 1005 removed outlier: 3.538A pdb=" N SERB1 992 " --> pdb=" O GLUB1 988 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1012 through 1024 Proline residue: B11018 - end of helix removed outlier: 3.533A pdb=" N THRB11021 " --> pdb=" O LEUB11017 " (cutoff:3.500A) Proline residue: B11022 - end of helix Processing helix chain 'B1' and resid 1028 through 1046 Processing helix chain 'B1' and resid 1047 through 1050 removed outlier: 3.651A pdb=" N VALB11050 " --> pdb=" O ALAB11047 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1047 through 1050' Processing helix chain 'B1' and resid 1051 through 1065 removed outlier: 3.531A pdb=" N TRPB11055 " --> pdb=" O SERB11051 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEUB11063 " --> pdb=" O CYSB11059 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLUB11064 " --> pdb=" O PHEB11060 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1066 through 1068 No H-bonds generated for 'chain 'B1' and resid 1066 through 1068' Processing helix chain 'B1' and resid 1070 through 1089 removed outlier: 3.604A pdb=" N GLYB11082 " --> pdb=" O VALB11078 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1090 through 1100 removed outlier: 3.632A pdb=" N ASNB11100 " --> pdb=" O THRB11096 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1108 through 1123 Processing helix chain 'B1' and resid 1124 through 1127 Processing helix chain 'B1' and resid 1128 through 1136 removed outlier: 3.687A pdb=" N TYRB11136 " --> pdb=" O LEUB11132 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1140 through 1159 removed outlier: 3.516A pdb=" N GLUB11156 " --> pdb=" O SERB11152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLYB11159 " --> pdb=" O PHEB11155 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1160 through 1164 removed outlier: 3.591A pdb=" N LYSB11163 " --> pdb=" O GLUB11160 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1165 through 1179 removed outlier: 3.521A pdb=" N VALB11169 " --> pdb=" O TYRB11165 " (cutoff:3.500A) Proline residue: B11171 - end of helix removed outlier: 3.566A pdb=" N ASPB11179 " --> pdb=" O ASPB11175 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1181 through 1199 Processing helix chain 'B1' and resid 1204 through 1216 removed outlier: 3.946A pdb=" N LEUB11208 " --> pdb=" O CYSB11204 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASNB11213 " --> pdb=" O ASNB11209 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYRB11214 " --> pdb=" O HISB11210 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1217 through 1221 removed outlier: 4.194A pdb=" N PHEB11220 " --> pdb=" O PROB11217 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLUB11221 " --> pdb=" O ASNB11218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 1217 through 1221' Processing helix chain 'B1' and resid 1223 through 1242 removed outlier: 3.688A pdb=" N VALB11239 " --> pdb=" O GLUB11235 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1242 through 1251 removed outlier: 3.756A pdb=" N METB11246 " --> pdb=" O GLYB11242 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1258 through 1276 removed outlier: 3.543A pdb=" N VALB11264 " --> pdb=" O LYSB11260 " (cutoff:3.500A) Processing helix chain 'B1' and resid 1278 through 1284 removed outlier: 3.569A pdb=" N ILEB11281 " --> pdb=" O ASPB11278 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALAB11282 " --> pdb=" O ALAB11279 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYRB11284 " --> pdb=" O ILEB11281 " (cutoff:3.500A) Processing helix chain 'B2' and resid 452 through 459 removed outlier: 3.804A pdb=" N ASNB2 458 " --> pdb=" O LEUB2 454 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARGB2 459 " --> pdb=" O ARGB2 455 " (cutoff:3.500A) Processing helix chain 'B2' and resid 461 through 467 removed outlier: 3.528A pdb=" N GLNB2 467 " --> pdb=" O ALAB2 463 " (cutoff:3.500A) Processing helix chain 'B2' and resid 471 through 475 removed outlier: 3.908A pdb=" N VALB2 474 " --> pdb=" O ARGB2 471 " (cutoff:3.500A) Processing helix chain 'B2' and resid 476 through 482 removed outlier: 3.576A pdb=" N ASPB2 479 " --> pdb=" O GLUB2 476 " (cutoff:3.500A) removed outlier: 4.061A 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: 3.805A pdb=" N TRPB2 504 " --> pdb=" O PROB2 501 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYSB2 505 " --> pdb=" O ARGB2 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 501 through 505' Processing helix chain 'B2' and resid 525 through 530 Processing helix chain 'B2' and resid 532 through 547 Processing helix chain 'B2' and resid 551 through 561 removed outlier: 3.546A 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 578 removed outlier: 3.969A pdb=" N PHEB2 575 " --> pdb=" O LEUB2 571 " (cutoff:3.500A) Processing helix chain 'B2' and resid 594 through 603 removed outlier: 3.750A pdb=" N GLUB2 598 " --> pdb=" O GLYB2 594 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARGB2 600 " --> pdb=" O GLUB2 596 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEUB2 601 " --> pdb=" O PHEB2 597 " (cutoff:3.500A) removed outlier: 3.710A 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 624 through 628 removed outlier: 4.176A pdb=" N VALB2 628 " --> pdb=" O ALAB2 625 " (cutoff:3.500A) Processing helix chain 'B2' and resid 630 through 640 removed outlier: 4.382A pdb=" N ILEB2 634 " --> pdb=" O PROB2 630 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALAB2 635 " --> pdb=" O PROB2 631 " (cutoff:3.500A) Processing helix chain 'B3' and resid 429 through 432 removed outlier: 3.585A 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: 3.956A pdb=" N CYSB3 624 " --> pdb=" O PROB3 621 " (cutoff:3.500A) Processing helix chain 'B3' and resid 808 through 827 removed outlier: 3.510A pdb=" N ALAB3 813 " --> pdb=" O GLUB3 809 " (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: 3.770A pdb=" N TRPB31077 " --> pdb=" O ASNB31073 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1134 through 1152 removed outlier: 3.876A pdb=" N HISB31138 " --> pdb=" O SERB31134 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASPB31139 " --> pdb=" O HISB31135 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SERB31150 " --> pdb=" O METB31146 " (cutoff:3.500A) Processing helix chain 'B3' and resid 1159 through 1165 Processing helix chain 'B3' and resid 1176 through 1181 Processing helix chain 'B3' and resid 1182 through 1184 No H-bonds generated for 'chain 'B3' and resid 1182 through 1184' Processing helix chain 'B3' and resid 1186 through 1197 Processing helix chain 'B3' and resid 1200 through 1216 removed outlier: 3.724A pdb=" N ILEB31211 " --> pdb=" O LYSB31207 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARGB31212 " --> pdb=" O LEUB31208 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYRB31215 " --> pdb=" O ILEB31211 " (cutoff:3.500A) Processing helix chain 'B4' and resid 10 through 12 No H-bonds generated for 'chain 'B4' and resid 10 through 12' Processing helix chain 'B4' and resid 25 through 35 removed outlier: 3.531A pdb=" N GLNB4 35 " --> pdb=" O GLUB4 31 " (cutoff:3.500A) Processing helix chain 'B4' and resid 63 through 75 removed outlier: 3.615A pdb=" N ALAB4 67 " --> pdb=" O SERB4 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYSB4 72 " --> pdb=" O ASPB4 68 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEB4 73 " --> pdb=" O TYRB4 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASNB4 75 " --> pdb=" O ILEB4 71 " (cutoff:3.500A) Processing helix chain 'B5' and resid 8 through 18 removed outlier: 4.241A pdb=" N GLUB5 12 " --> pdb=" O HISB5 8 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYSB5 17 " --> pdb=" O HISB5 13 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYRB5 18 " --> pdb=" O LEUB5 14 " (cutoff:3.500A) Processing helix chain 'B5' and resid 27 through 46 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: 3.597A pdb=" N LYSB6 41 " --> pdb=" O ASPB6 37 " (cutoff:3.500A) Processing helix chain 'B6' and resid 66 through 78 Processing helix chain 'B6' and resid 93 through 98 removed outlier: 3.546A pdb=" N PHEB6 98 " --> pdb=" O ALAB6 94 " (cutoff:3.500A) Processing helix chain 'A2' and resid 65 through 74 removed outlier: 3.799A pdb=" N GLNA2 74 " --> pdb=" O LEUA2 70 " (cutoff:3.500A) Processing helix chain 'A2' and resid 75 through 93 Processing helix chain 'A3' and resid 393 through 400 removed outlier: 3.564A pdb=" N HISA3 400 " --> pdb=" O LEUA3 396 " (cutoff:3.500A) Processing helix chain 'A3' and resid 418 through 425 removed outlier: 3.581A 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 removed outlier: 3.506A pdb=" N PHEA3 446 " --> pdb=" O THRA3 443 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAA3 447 " --> pdb=" O ALAA3 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'A3' and resid 443 through 447' Processing helix chain 'A3' and resid 451 through 470 Processing helix chain 'A3' and resid 488 through 497 removed outlier: 4.355A pdb=" N ARGA3 497 " --> pdb=" O GLUA3 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.118A pdb=" N ALA H 18 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'H' and resid 39 through 42 removed outlier: 6.414A pdb=" N TYR H 71 " --> pdb=" O CYS H 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B1' and resid 412 through 414 removed outlier: 3.690A pdb=" N GLNB6 47 " --> pdb=" O VALB6 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B3' and resid 1101 through 1107 removed outlier: 4.024A pdb=" N SERB31103 " --> pdb=" O THRB31120 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILEB31126 " --> pdb=" O LEUB3 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B3' and resid 16 through 20 removed outlier: 4.181A pdb=" N PHEB3 16 " --> pdb=" O SERB3 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEUB3 54 " --> pdb=" O LEUB3 40 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARGB3 42 " --> pdb=" O THRB3 52 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THRB3 52 " --> pdb=" O ARGB3 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B3' and resid 62 through 68 removed outlier: 3.541A pdb=" N VALB3 80 " --> pdb=" O VALB3 88 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VALB3 88 " --> pdb=" O VALB3 80 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SERB3 82 " --> pdb=" O ARGB3 86 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARGB3 86 " --> pdb=" O SERB3 82 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILEB3 87 " --> pdb=" O GLNB3 104 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLNB3 104 " --> pdb=" O ILEB3 87 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILEB3 89 " --> pdb=" O ILEB3 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLNB3 93 " --> pdb=" O METB3 98 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N METB3 98 " --> pdb=" O GLNB3 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B3' and resid 120 through 123 Processing sheet with id=AA9, first strand: chain 'B3' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain 'B3' and resid 165 through 173 removed outlier: 6.666A pdb=" N LEUB3 185 " --> pdb=" O TYRB3 168 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VALB3 170 " --> pdb=" O ALAB3 183 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALAB3 183 " --> pdb=" O VALB3 170 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLYB3 172 " --> pdb=" O METB3 181 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N METB3 181 " --> pdb=" O GLYB3 172 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEUB3 208 " --> pdb=" O SERB3 225 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SERB3 225 " --> pdb=" O LEUB3 208 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHEB3 210 " --> pdb=" O LYSB3 223 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HISB3 219 " --> pdb=" O ASPB3 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B3' and resid 232 through 238 removed outlier: 3.908A pdb=" N PHEB3 234 " --> pdb=" O CYSB3 251 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLYB3 247 " --> pdb=" O VALB3 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VALB3 248 " --> pdb=" O LYSB3 259 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYRB3 255 " --> pdb=" O SERB3 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B3' and resid 273 through 274 removed outlier: 5.991A pdb=" N ARGB3 273 " --> pdb=" O PHEB3 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B3' and resid 287 through 294 removed outlier: 6.698A pdb=" N GLNB3 304 " --> pdb=" O VALB3 288 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SERB3 290 " --> pdb=" O LEUB3 302 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEUB3 302 " --> pdb=" O SERB3 290 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THRB3 292 " --> pdb=" O PHEB3 300 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHEB3 300 " --> pdb=" O THRB3 292 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHEB3 299 " --> pdb=" O LEUB3 315 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEUB3 315 " --> pdb=" O PHEB3 299 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASPB3 309 " --> pdb=" O THRB3 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASPB3 331 " --> pdb=" O ILEB3 310 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYSB3 312 " --> pdb=" O TYRB3 329 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYRB3 329 " --> pdb=" O LYSB3 312 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THRB3 314 " --> pdb=" O LEUB3 327 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEUB3 327 " --> pdb=" O THRB3 314 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLUB3 316 " --> pdb=" O ILEB3 325 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILEB3 325 " --> pdb=" O GLUB3 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B3' and resid 336 through 342 removed outlier: 7.219A pdb=" N ALAB3 350 " --> pdb=" O ALAB3 337 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N METB3 339 " --> pdb=" O PHEB3 348 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHEB3 348 " --> pdb=" O METB3 339 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VALB3 341 " --> pdb=" O PHEB3 346 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHEB3 346 " --> pdb=" O VALB3 341 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUB3 358 " --> pdb=" O ASPB3 399 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASPB3 399 " --> pdb=" O LEUB3 358 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLNB3 360 " --> pdb=" O LEUB3 397 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEUB3 397 " --> pdb=" O GLNB3 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B3' and resid 407 through 413 removed outlier: 3.575A pdb=" N PHEB3 409 " --> pdb=" O ALAB3 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B3' and resid 445 through 450 removed outlier: 5.244A pdb=" N GLUB3 446 " --> pdb=" O ALAB3 766 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALAB3 766 " --> pdb=" O GLUB3 446 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALAB3 448 " --> pdb=" O ILEB3 764 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHEB3 741 " --> pdb=" O ILEB3 757 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B3' and resid 458 through 462 removed outlier: 3.509A pdb=" N ILEB3 475 " --> pdb=" O TRPB3 460 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VALB3 484 " --> pdb=" O VALB3 494 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLUB3 492 " --> pdb=" O SERB3 486 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B3' and resid 507 through 509 removed outlier: 3.846A pdb=" N HISB3 526 " --> pdb=" O ASNB3 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B3' and resid 544 through 548 removed outlier: 3.647A pdb=" N ASNB3 575 " --> pdb=" O GLUB3 567 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B3' and resid 587 through 592 removed outlier: 4.104A pdb=" N CYSB3 589 " --> pdb=" O GLYB3 608 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THRB3 613 " --> pdb=" O LEUB3 609 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VALB3 614 " --> pdb=" O METB3 630 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N METB3 630 " --> pdb=" O VALB3 614 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILEB3 616 " --> pdb=" O LEUB3 628 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SERB3 618 " --> pdb=" O GLNB3 626 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLNB3 626 " --> pdb=" O SERB3 618 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B3' and resid 637 through 643 removed outlier: 4.565A pdb=" N SERB3 639 " --> pdb=" O GLYB3 668 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B3' and resid 700 through 706 removed outlier: 3.737A pdb=" N LYSB3 700 " --> pdb=" O METB3 715 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B3' and resid 785 through 790 removed outlier: 7.358A pdb=" N ILEB3 800 " --> pdb=" O ARGB3 786 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHEB3 788 " --> pdb=" O ILEB3 798 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILEB3 798 " --> pdb=" O PHEB3 788 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SERB3 864 " --> pdb=" O GLNB3 881 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLNB3 881 " --> pdb=" O SERB3 864 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILEB3 866 " --> pdb=" O LEUB3 879 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUB3 879 " --> pdb=" O ILEB3 866 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VALB3 868 " --> pdb=" O LEUB3 877 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B3' and resid 886 through 894 removed outlier: 5.693A pdb=" N ALAB3 888 " --> pdb=" O ALAB3 910 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALAB3 910 " --> pdb=" O ALAB3 888 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SERB3 890 " --> pdb=" O GLYB3 908 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TRPB3 903 " --> pdb=" O LEUB3 930 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HISB3 941 " --> pdb=" O THRB3 927 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYSB3 929 " --> pdb=" O PHEB3 939 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHEB3 939 " --> pdb=" O LYSB3 929 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B3' and resid 951 through 955 removed outlier: 3.930A pdb=" N ALAB3 951 " --> pdb=" O GLYB3 962 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEUB3 967 " --> pdb=" O GLUB3 982 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLUB3 982 " --> pdb=" O LEUB3 967 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VALB3 969 " --> pdb=" O LYSB3 980 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYB3 973 " --> pdb=" O LYSB3 976 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYSB3 976 " --> pdb=" O GLYB3 973 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B3' and resid 990 through 995 removed outlier: 3.798A pdb=" N GLYB3 992 " --> pdb=" O SERB31003 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRPB31011 " --> pdb=" O PHEB31024 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B3' and resid 1033 through 1038 removed outlier: 3.913A pdb=" N THRB31035 " --> pdb=" O ALAB31047 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASNB31052 " --> pdb=" O ASPB31048 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILEB31053 " --> pdb=" O ASNB31094 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASNB31094 " --> pdb=" O ILEB31053 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VALB31055 " --> pdb=" O ILEB31092 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B4' and resid 39 through 41 removed outlier: 3.644A pdb=" N ASNB4 41 " --> pdb=" O GLUB4 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VALB4 59 " --> pdb=" O VALB4 15 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASNB4 87 " --> pdb=" O TYRB4 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILEB4 77 " --> pdb=" O ILEB4 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B6' and resid 81 through 82 Processing sheet with id=AD3, first strand: chain 'A2' and resid 46 through 48 removed outlier: 3.643A pdb=" N THRA2 61 " --> pdb=" O CYSA2 56 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A3' and resid 406 through 408 Processing sheet with id=AD5, first strand: chain 'A3' and resid 479 through 480 990 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6773 1.33 - 1.45: 4527 1.45 - 1.57: 13526 1.57 - 1.69: 137 1.69 - 1.82: 202 Bond restraints: 25165 Sorted by residual: bond pdb=" N GLUB2 710 " pdb=" CA GLUB2 710 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.19e-02 7.06e+03 6.54e+00 bond pdb=" N TRPB2 708 " pdb=" CA TRPB2 708 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.50e+00 bond pdb=" N LEUB2 711 " pdb=" CA LEUB2 711 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.27e-02 6.20e+03 5.51e+00 bond pdb=" CA LYSB11102 " pdb=" CB LYSB11102 " ideal model delta sigma weight residual 1.528 1.587 -0.059 2.61e-02 1.47e+03 5.07e+00 bond pdb=" P C 2 45 " pdb=" O5' C 2 45 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.00e-02 1.00e+04 4.95e+00 ... (remaining 25160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 33938 2.36 - 4.72: 335 4.72 - 7.07: 45 7.07 - 9.43: 19 9.43 - 11.79: 5 Bond angle restraints: 34342 Sorted by residual: angle pdb=" C3' U R -13 " pdb=" O3' U R -13 " pdb=" P U R -12 " ideal model delta sigma weight residual 119.70 125.77 -6.07 1.20e+00 6.94e-01 2.55e+01 angle pdb=" N LYSB3 137 " pdb=" CA LYSB3 137 " pdb=" CB LYSB3 137 " ideal model delta sigma weight residual 114.17 109.31 4.86 1.14e+00 7.69e-01 1.82e+01 angle pdb=" O5' A 2 59 " pdb=" C5' A 2 59 " pdb=" C4' A 2 59 " ideal model delta sigma weight residual 109.40 112.63 -3.23 8.00e-01 1.56e+00 1.63e+01 angle pdb=" C3' PSU 2 44 " pdb=" O3' PSU 2 44 " pdb=" P C 2 45 " ideal model delta sigma weight residual 119.70 124.53 -4.83 1.20e+00 6.94e-01 1.62e+01 angle pdb=" C3' PSU 2 43 " pdb=" C2' PSU 2 43 " pdb=" C1' PSU 2 43 " ideal model delta sigma weight residual 111.00 99.21 11.79 3.00e+00 1.11e-01 1.54e+01 ... (remaining 34337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 14604 35.93 - 71.85: 677 71.85 - 107.78: 40 107.78 - 143.70: 0 143.70 - 179.63: 7 Dihedral angle restraints: 15328 sinusoidal: 6867 harmonic: 8461 Sorted by residual: dihedral pdb=" O4' U R 12 " pdb=" C1' U R 12 " pdb=" N1 U R 12 " pdb=" C2 U R 12 " ideal model delta sinusoidal sigma weight residual 200.00 50.49 149.51 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U R 9 " pdb=" C1' U R 9 " pdb=" N1 U R 9 " pdb=" C2 U R 9 " ideal model delta sinusoidal sigma weight residual -128.00 51.63 -179.63 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 232.00 53.67 178.33 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3737 0.106 - 0.212: 120 0.212 - 0.319: 8 0.319 - 0.425: 1 0.425 - 0.531: 4 Chirality restraints: 3870 Sorted by residual: chirality pdb=" P C 2 45 " pdb=" OP1 C 2 45 " pdb=" OP2 C 2 45 " pdb=" O5' C 2 45 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" P U R -11 " pdb=" OP1 U R -11 " pdb=" OP2 U R -11 " pdb=" O5' U R -11 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" P U R -9 " pdb=" OP1 U R -9 " pdb=" OP2 U R -9 " pdb=" O5' U R -9 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 3867 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILEA3 392 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PROA3 393 " 0.089 5.00e-02 4.00e+02 pdb=" CA PROA3 393 " -0.027 5.00e-02 4.00e+02 pdb=" CD PROA3 393 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U R 2 " 0.026 2.00e-02 2.50e+03 1.27e-02 3.63e+00 pdb=" N1 U R 2 " -0.024 2.00e-02 2.50e+03 pdb=" C2 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" O2 U R 2 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U R 2 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U R 2 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U R 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U R 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U R 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THRB1 508 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PROB1 509 " 0.082 5.00e-02 4.00e+02 pdb=" CA PROB1 509 " -0.025 5.00e-02 4.00e+02 pdb=" CD PROB1 509 " -0.026 5.00e-02 4.00e+02 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7008 2.82 - 3.34: 21541 3.34 - 3.86: 38257 3.86 - 4.38: 44074 4.38 - 4.90: 75936 Nonbonded interactions: 186816 Sorted by model distance: nonbonded pdb=" O2' PSU 2 44 " pdb=" O5' C 2 45 " model vdw 2.299 3.040 nonbonded pdb=" O2' C 2 45 " pdb=" OP1 U 2 46 " model vdw 2.403 3.040 nonbonded pdb=" N2 G 2 31 " pdb=" O2 U R 3 " model vdw 2.446 2.496 nonbonded pdb=" O THRB2 706 " pdb=" OG1 THRB2 706 " model vdw 2.496 3.040 nonbonded pdb=" O5' G 2 31 " pdb=" O4' G 2 31 " model vdw 2.498 2.432 ... (remaining 186811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 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: 0.050 Set scattering table: 0.040 Process input model: 25.590 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 0.059 25177 Z= 0.129 Angle : 0.608 11.789 34360 Z= 0.327 Chirality : 0.047 0.531 3870 Planarity : 0.004 0.052 4220 Dihedral : 18.802 179.625 9882 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.12 % Allowed : 23.94 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: -0.54 (0.15), residues: 2881 helix: 0.25 (0.16), residues: 1047 sheet: 0.51 (0.24), residues: 483 loop : -1.14 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGB3 580 TYR 0.014 0.001 TYRB11302 PHE 0.019 0.001 PHEB11126 TRP 0.015 0.001 TRPB31032 HIS 0.003 0.001 HISB3 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (25165) covalent geometry : angle 0.60295 / 0.33 (34342) hydrogen bonds : bond 0.24198 / 22.67 ( 998) hydrogen bonds : angle 7.12502 / 7.30 ( 2829) metal coordination : bond 0.00386 / 0.29 ( 12) metal coordination : angle 3.43935 / 5.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 462 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 78 GLN cc_start: 0.8624 (mt0) cc_final: 0.8387 (mt0) REVERT: B1 579 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6669 (mm-30) REVERT: B1 623 TYR cc_start: 0.6533 (m-10) cc_final: 0.6185 (m-10) REVERT: B1 627 THR cc_start: 0.8286 (p) cc_final: 0.7571 (p) REVERT: B1 790 LYS cc_start: 0.8804 (tptt) cc_final: 0.8302 (ttmt) REVERT: B1 830 TYR cc_start: 0.7243 (t80) cc_final: 0.6866 (t80) REVERT: B1 856 ASP cc_start: 0.7248 (m-30) cc_final: 0.6945 (m-30) REVERT: B1 866 LYS cc_start: 0.8417 (ttmm) cc_final: 0.7934 (tptt) REVERT: B1 876 MET cc_start: 0.9007 (tpp) cc_final: 0.8771 (mmt) REVERT: B1 973 HIS cc_start: 0.7257 (t70) cc_final: 0.6956 (t-170) REVERT: B1 1301 ASP cc_start: 0.8076 (t0) cc_final: 0.7661 (m-30) REVERT: B2 456 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6773 (mmm-85) REVERT: B2 619 MET cc_start: 0.5008 (tmm) cc_final: 0.4607 (mtp) REVERT: B3 230 GLU cc_start: 0.8651 (pm20) cc_final: 0.8321 (pm20) REVERT: B3 331 ASP cc_start: 0.8227 (m-30) cc_final: 0.7574 (m-30) REVERT: B3 447 MET cc_start: 0.6106 (mmm) cc_final: 0.5765 (tmm) REVERT: B3 701 LEU cc_start: 0.7605 (mp) cc_final: 0.6875 (tt) REVERT: B3 770 LEU cc_start: 0.7796 (pt) cc_final: 0.7539 (mp) REVERT: B3 1064 ASP cc_start: 0.8232 (m-30) cc_final: 0.7976 (m-30) REVERT: B4 1 MET cc_start: 0.4863 (tmm) cc_final: 0.4258 (ttm) REVERT: B4 30 TRP cc_start: 0.7116 (t-100) cc_final: 0.6217 (t-100) REVERT: B4 59 VAL cc_start: 0.9374 (p) cc_final: 0.9169 (t) REVERT: B4 76 MET cc_start: 0.6753 (mmt) cc_final: 0.5855 (mtm) REVERT: B5 25 ASP cc_start: 0.8227 (m-30) cc_final: 0.7961 (m-30) REVERT: B5 59 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8041 (mm-30) REVERT: A2 53 SER cc_start: 0.8518 (m) cc_final: 0.8162 (p) outliers start: 3 outliers final: 1 residues processed: 464 average time/residue: 0.1847 time to fit residues: 130.5356 Evaluate side-chains 293 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B3 residue 667 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 550 HIS B2 534 GLN B3 93 GLN B3 138 GLN B3 526 HIS B3 636 GLN B3 805 ASN B5 13 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.177606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107424 restraints weight = 34010.675| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.46 r_work: 0.3200 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25177 Z= 0.162 Angle : 0.650 12.904 34360 Z= 0.325 Chirality : 0.044 0.297 3870 Planarity : 0.005 0.053 4220 Dihedral : 14.720 179.744 4202 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.92 % Allowed : 22.66 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: -0.06 (0.15), residues: 2881 helix: 1.08 (0.16), residues: 1054 sheet: 0.51 (0.23), residues: 491 loop : -1.17 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGB1 614 TYR 0.020 0.001 TYRB3 989 PHE 0.013 0.001 PHEB31024 TRP 0.011 0.001 TRPB31032 HIS 0.007 0.001 HISB1 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (25165) covalent geometry : angle 0.64296 / 0.32 (34342) hydrogen bonds : bond 0.06999 / 6.31 ( 998) hydrogen bonds : angle 5.27952 / 5.39 ( 2829) metal coordination : bond 0.00377 / 0.31 ( 12) metal coordination : angle 4.20632 / 7.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8378 (m-30) cc_final: 0.8136 (m-30) REVERT: A 805 LYS cc_start: 0.7077 (pttp) cc_final: 0.6745 (ptpt) REVERT: B1 613 MET cc_start: 0.8259 (mtt) cc_final: 0.7973 (mtt) REVERT: B1 776 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7992 (tp30) REVERT: B1 790 LYS cc_start: 0.8490 (tptt) cc_final: 0.7831 (ttmt) REVERT: B1 816 LYS cc_start: 0.8271 (pptt) cc_final: 0.8003 (ptmm) REVERT: B1 830 TYR cc_start: 0.6882 (t80) cc_final: 0.6648 (t80) REVERT: B1 876 MET cc_start: 0.8528 (tpp) cc_final: 0.8018 (mmt) REVERT: B1 903 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: B1 1301 ASP cc_start: 0.8199 (t0) cc_final: 0.7756 (m-30) REVERT: B2 452 LYS cc_start: 0.4211 (OUTLIER) cc_final: 0.3700 (tppt) REVERT: B2 456 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6509 (mmm-85) REVERT: B2 683 TYR cc_start: 0.5310 (m-80) cc_final: 0.5050 (m-80) REVERT: B3 114 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7858 (ttm170) REVERT: B3 331 ASP cc_start: 0.8196 (m-30) cc_final: 0.7648 (m-30) REVERT: B3 447 MET cc_start: 0.6133 (mmm) cc_final: 0.5559 (tpp) REVERT: B3 690 ARG cc_start: 0.8127 (ttt-90) cc_final: 0.7492 (tpp80) REVERT: B3 701 LEU cc_start: 0.7642 (mp) cc_final: 0.6586 (tt) REVERT: B3 723 TYR cc_start: 0.7633 (p90) cc_final: 0.7425 (p90) REVERT: B3 770 LEU cc_start: 0.7836 (pt) cc_final: 0.7383 (mp) REVERT: B3 1064 ASP cc_start: 0.8263 (m-30) cc_final: 0.8051 (m-30) REVERT: B4 1 MET cc_start: 0.4610 (tmm) cc_final: 0.4005 (ttm) REVERT: B4 16 TYR cc_start: 0.7074 (t80) cc_final: 0.6862 (t80) REVERT: B4 30 TRP cc_start: 0.6798 (t-100) cc_final: 0.6076 (t-100) REVERT: B4 74 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8702 (mmm) REVERT: B4 76 MET cc_start: 0.6784 (mmt) cc_final: 0.5547 (mtm) REVERT: B5 25 ASP cc_start: 0.8634 (m-30) cc_final: 0.8366 (m-30) REVERT: A2 53 SER cc_start: 0.7937 (m) cc_final: 0.7428 (p) REVERT: A3 385 LEU cc_start: 0.8763 (tp) cc_final: 0.8470 (tp) REVERT: A3 469 GLU cc_start: 0.7601 (tt0) cc_final: 0.7393 (tt0) outliers start: 73 outliers final: 28 residues processed: 361 average time/residue: 0.1670 time to fit residues: 93.5915 Evaluate side-chains 314 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 600 LEU Chi-restraints excluded: chain B1 residue 735 ILE Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 835 ASP Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B3 residue 114 ARG Chi-restraints excluded: chain B3 residue 250 ILE Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 435 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 805 ASN Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1146 MET Chi-restraints excluded: chain B3 residue 1206 LYS Chi-restraints excluded: chain B3 residue 1213 THR Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 74 MET Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain B6 residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B11209 ASN B2 534 GLN ** B3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B31073 ASN B5 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.174741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103336 restraints weight = 34037.666| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.53 r_work: 0.3135 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25177 Z= 0.216 Angle : 0.673 12.526 34360 Z= 0.332 Chirality : 0.046 0.329 3870 Planarity : 0.005 0.049 4220 Dihedral : 14.530 179.709 4200 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.40 % Allowed : 22.50 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: -0.16 (0.15), residues: 2881 helix: 1.14 (0.16), residues: 1056 sheet: 0.24 (0.23), residues: 511 loop : -1.29 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGB1 517 TYR 0.025 0.002 TYRB3 736 PHE 0.014 0.002 PHEB31024 TRP 0.024 0.002 TRPB1 732 HIS 0.006 0.001 HISB2 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (25165) covalent geometry : angle 0.66166 / 0.33 (34342) hydrogen bonds : bond 0.06159 / 5.57 ( 998) hydrogen bonds : angle 4.94882 / 5.02 ( 2829) metal coordination : bond 0.00982 / 0.93 ( 12) metal coordination : angle 5.49104 / 9.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8310 (m-30) cc_final: 0.7931 (m-30) REVERT: A 805 LYS cc_start: 0.7103 (pttp) cc_final: 0.6813 (ptpt) REVERT: A 814 MET cc_start: 0.2655 (ttt) cc_final: 0.2085 (ptt) REVERT: B1 609 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6093 (mpp) REVERT: B1 613 MET cc_start: 0.8233 (mtt) cc_final: 0.7879 (mtt) REVERT: B1 614 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7314 (mtt180) REVERT: B1 776 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7777 (tp30) REVERT: B1 816 LYS cc_start: 0.8105 (pptt) cc_final: 0.7791 (ptmm) REVERT: B1 830 TYR cc_start: 0.6754 (t80) cc_final: 0.6454 (t80) REVERT: B1 831 ARG cc_start: 0.7890 (tpp-160) cc_final: 0.7642 (tpm170) REVERT: B1 867 MET cc_start: 0.7565 (ttm) cc_final: 0.7133 (ttm) REVERT: B1 903 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8565 (t0) cc_final: 0.8287 (t0) REVERT: B1 1301 ASP cc_start: 0.8145 (t0) cc_final: 0.7720 (m-30) REVERT: B2 452 LYS cc_start: 0.4348 (OUTLIER) cc_final: 0.3898 (tppt) REVERT: B2 456 ARG cc_start: 0.7107 (ttm110) cc_final: 0.6562 (mmm-85) REVERT: B2 460 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7088 (p90) REVERT: B2 524 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8374 (mp) REVERT: B2 683 TYR cc_start: 0.5397 (m-80) cc_final: 0.5119 (m-80) REVERT: B3 114 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7991 (ttm170) REVERT: B3 235 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B3 294 LYS cc_start: 0.8251 (pttt) cc_final: 0.7292 (ptpt) REVERT: B3 331 ASP cc_start: 0.8179 (m-30) cc_final: 0.7596 (m-30) REVERT: B3 447 MET cc_start: 0.6046 (mmm) cc_final: 0.5747 (tpp) REVERT: B3 690 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7543 (tpp80) REVERT: B3 701 LEU cc_start: 0.7635 (mp) cc_final: 0.6707 (tt) REVERT: B3 770 LEU cc_start: 0.7718 (pt) cc_final: 0.7236 (mp) REVERT: B4 1 MET cc_start: 0.4752 (tmm) cc_final: 0.4307 (ttm) REVERT: B4 9 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8377 (ttm170) REVERT: B4 11 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8114 (tp40) REVERT: B4 30 TRP cc_start: 0.6840 (t-100) cc_final: 0.6201 (t-100) REVERT: B4 64 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6416 (tm-30) REVERT: B4 76 MET cc_start: 0.6715 (mmt) cc_final: 0.5384 (mtm) REVERT: B4 85 ARG cc_start: 0.7343 (ptt-90) cc_final: 0.7117 (ptt-90) REVERT: B5 25 ASP cc_start: 0.8559 (m-30) cc_final: 0.8193 (m-30) REVERT: A2 53 SER cc_start: 0.8033 (m) cc_final: 0.7539 (p) REVERT: A3 385 LEU cc_start: 0.8763 (tp) cc_final: 0.8407 (tp) REVERT: A3 397 TYR cc_start: 0.8148 (t80) cc_final: 0.7853 (t80) outliers start: 85 outliers final: 51 residues processed: 353 average time/residue: 0.1635 time to fit residues: 91.1962 Evaluate side-chains 331 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 600 LEU Chi-restraints excluded: chain B1 residue 609 MET Chi-restraints excluded: chain B1 residue 627 THR Chi-restraints excluded: chain B1 residue 731 LEU Chi-restraints excluded: chain B1 residue 735 ILE Chi-restraints excluded: chain B1 residue 806 ILE Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 835 ASP Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 961 VAL Chi-restraints excluded: chain B1 residue 989 VAL Chi-restraints excluded: chain B1 residue 997 LEU Chi-restraints excluded: chain B1 residue 1004 ILE Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1118 ILE Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1239 VAL Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 452 LYS Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 524 LEU Chi-restraints excluded: chain B2 residue 564 ILE Chi-restraints excluded: chain B3 residue 33 SER Chi-restraints excluded: chain B3 residue 114 ARG Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 404 LEU Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 614 VAL Chi-restraints excluded: chain B3 residue 633 LEU Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 673 VAL Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 754 ILE Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 1034 THR Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1146 MET Chi-restraints excluded: chain B3 residue 1213 THR Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B6 residue 101 MET Chi-restraints excluded: chain A2 residue 59 CYS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Chi-restraints excluded: chain A3 residue 457 SER Chi-restraints excluded: chain A3 residue 475 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 284 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 267 optimal weight: 0.1980 chunk 31 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 124 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11209 ASN B2 534 GLN B31073 ASN B5 8 HIS B5 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121577 restraints weight = 34190.812| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.06 r_work: 0.3193 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25177 Z= 0.108 Angle : 0.589 12.356 34360 Z= 0.286 Chirality : 0.043 0.398 3870 Planarity : 0.004 0.050 4220 Dihedral : 14.250 179.895 4200 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.60 % Allowed : 23.78 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 0.11 (0.16), residues: 2881 helix: 1.44 (0.16), residues: 1068 sheet: 0.21 (0.22), residues: 527 loop : -1.17 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGB3 463 TYR 0.019 0.001 TYRB3 520 PHE 0.012 0.001 PHEB31024 TRP 0.015 0.001 TRPA3 387 HIS 0.003 0.001 HISB3 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (25165) covalent geometry : angle 0.58146 / 0.29 (34342) hydrogen bonds : bond 0.04281 / 3.83 ( 998) hydrogen bonds : angle 4.57500 / 4.68 ( 2829) metal coordination : bond 0.00467 / 0.35 ( 12) metal coordination : angle 4.16876 / 6.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 292 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8358 (m-30) cc_final: 0.7836 (m-30) REVERT: A 805 LYS cc_start: 0.7159 (pttp) cc_final: 0.6850 (ptpt) REVERT: A 814 MET cc_start: 0.2751 (ttt) cc_final: 0.2310 (ptt) REVERT: B1 613 MET cc_start: 0.8230 (mtt) cc_final: 0.7880 (mtt) REVERT: B1 614 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7285 (mtt180) REVERT: B1 776 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7714 (tp30) REVERT: B1 796 CYS cc_start: 0.6604 (m) cc_final: 0.6161 (m) REVERT: B1 816 LYS cc_start: 0.8232 (pptt) cc_final: 0.7958 (ptmm) REVERT: B1 830 TYR cc_start: 0.6729 (t80) cc_final: 0.6476 (t80) REVERT: B1 867 MET cc_start: 0.7399 (ttm) cc_final: 0.7019 (ttm) REVERT: B1 903 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: B1 980 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6912 (tp30) REVERT: B1 1002 ASN cc_start: 0.8509 (t0) cc_final: 0.8265 (t0) REVERT: B1 1301 ASP cc_start: 0.8080 (t0) cc_final: 0.7648 (m-30) REVERT: B2 619 MET cc_start: 0.4334 (mtp) cc_final: 0.3676 (tpt) REVERT: B2 636 MET cc_start: 0.8447 (mtm) cc_final: 0.8216 (mtm) REVERT: B2 683 TYR cc_start: 0.5360 (m-80) cc_final: 0.5121 (m-80) REVERT: B3 213 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B3 235 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B3 294 LYS cc_start: 0.8204 (pttt) cc_final: 0.7181 (ptpt) REVERT: B3 447 MET cc_start: 0.5985 (mmm) cc_final: 0.5750 (tpp) REVERT: B3 690 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7681 (tpp80) REVERT: B3 701 LEU cc_start: 0.7568 (mp) cc_final: 0.6698 (tt) REVERT: B3 770 LEU cc_start: 0.7820 (pt) cc_final: 0.7270 (mp) REVERT: B4 1 MET cc_start: 0.4568 (tmm) cc_final: 0.4013 (ttm) REVERT: B4 9 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8366 (ttm170) REVERT: B4 11 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7985 (tp40) REVERT: B4 16 TYR cc_start: 0.6607 (t80) cc_final: 0.6182 (t80) REVERT: B4 30 TRP cc_start: 0.6684 (t-100) cc_final: 0.6109 (t-100) REVERT: B4 64 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6323 (tm-30) REVERT: B4 76 MET cc_start: 0.6608 (mmt) cc_final: 0.5160 (mtm) REVERT: B5 25 ASP cc_start: 0.8537 (m-30) cc_final: 0.8144 (m-30) REVERT: A2 53 SER cc_start: 0.7876 (m) cc_final: 0.7394 (p) REVERT: A3 385 LEU cc_start: 0.8732 (tp) cc_final: 0.8364 (tp) REVERT: A3 463 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8106 (ttmt) outliers start: 65 outliers final: 33 residues processed: 338 average time/residue: 0.1769 time to fit residues: 93.4847 Evaluate side-chains 309 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 735 ILE Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 1004 ILE Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 673 VAL Chi-restraints excluded: chain B3 residue 762 LEU Chi-restraints excluded: chain B3 residue 764 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1146 MET Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Chi-restraints excluded: chain A3 residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 205 optimal weight: 10.0000 chunk 101 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 248 optimal weight: 0.3980 chunk 121 optimal weight: 0.5980 chunk 277 optimal weight: 0.9990 chunk 117 optimal weight: 0.0870 chunk 194 optimal weight: 0.0980 chunk 31 optimal weight: 7.9990 chunk 256 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B11209 ASN B5 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.179158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111820 restraints weight = 34239.247| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.71 r_work: 0.3224 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25177 Z= 0.100 Angle : 0.565 11.951 34360 Z= 0.273 Chirality : 0.042 0.337 3870 Planarity : 0.004 0.049 4220 Dihedral : 13.904 179.637 4200 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.28 % Allowed : 24.38 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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 (0.16), residues: 2881 helix: 1.65 (0.16), residues: 1065 sheet: 0.29 (0.22), residues: 527 loop : -1.08 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGB3 275 TYR 0.023 0.001 TYRB3 723 PHE 0.020 0.001 PHEB3 702 TRP 0.017 0.001 TRPB3 460 HIS 0.003 0.000 HISB1 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (25165) covalent geometry : angle 0.55891 / 0.27 (34342) hydrogen bonds : bond 0.03621 / 3.21 ( 998) hydrogen bonds : angle 4.34938 / 4.48 ( 2829) metal coordination : bond 0.00364 / 0.27 ( 12) metal coordination : angle 3.52567 / 5.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8506 (m-30) cc_final: 0.8018 (m-30) REVERT: A 805 LYS cc_start: 0.7181 (pttp) cc_final: 0.6958 (ptpt) REVERT: A 814 MET cc_start: 0.2646 (ttt) cc_final: 0.2382 (ptt) REVERT: B1 613 MET cc_start: 0.8127 (mtt) cc_final: 0.7745 (mtt) REVERT: B1 614 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7274 (mtt180) REVERT: B1 776 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7755 (tp30) REVERT: B1 790 LYS cc_start: 0.8355 (tptt) cc_final: 0.7657 (ttmt) REVERT: B1 796 CYS cc_start: 0.6638 (m) cc_final: 0.6204 (m) REVERT: B1 816 LYS cc_start: 0.8120 (pptt) cc_final: 0.7901 (ptmm) REVERT: B1 830 TYR cc_start: 0.6623 (t80) cc_final: 0.6402 (t80) REVERT: B1 903 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8557 (t0) cc_final: 0.8322 (t0) REVERT: B2 524 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8331 (mp) REVERT: B2 619 MET cc_start: 0.4322 (mtp) cc_final: 0.3696 (tpt) REVERT: B2 683 TYR cc_start: 0.5394 (m-80) cc_final: 0.5165 (m-80) REVERT: B3 199 GLU cc_start: 0.8381 (tt0) cc_final: 0.8048 (tp30) REVERT: B3 213 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8659 (tp) REVERT: B3 235 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8552 (pp) REVERT: B3 294 LYS cc_start: 0.8199 (pttt) cc_final: 0.7229 (ptpt) REVERT: B3 690 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7648 (tpp80) REVERT: B3 701 LEU cc_start: 0.7266 (mp) cc_final: 0.6315 (tt) REVERT: B3 770 LEU cc_start: 0.7695 (pt) cc_final: 0.7116 (mp) REVERT: B4 1 MET cc_start: 0.4563 (tmm) cc_final: 0.3940 (ttm) REVERT: B4 9 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8445 (ttm170) REVERT: B4 11 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7959 (tp40) REVERT: B4 30 TRP cc_start: 0.6689 (t-100) cc_final: 0.6146 (t-100) REVERT: B4 64 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6308 (tm-30) REVERT: B4 76 MET cc_start: 0.6721 (mmt) cc_final: 0.5232 (mtm) REVERT: B5 25 ASP cc_start: 0.8358 (m-30) cc_final: 0.7991 (m-30) REVERT: A2 53 SER cc_start: 0.7953 (m) cc_final: 0.7537 (p) REVERT: A3 385 LEU cc_start: 0.8663 (tp) cc_final: 0.8277 (tp) REVERT: A3 463 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8179 (ttmt) outliers start: 57 outliers final: 31 residues processed: 331 average time/residue: 0.1716 time to fit residues: 89.1372 Evaluate side-chains 315 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B2 residue 454 LEU Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 524 LEU Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 88 VAL Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 399 ASP Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 508 CYS Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Chi-restraints excluded: chain A3 residue 464 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 221 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 202 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 692 HIS B11209 ASN B3 28 GLN B5 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.178108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111169 restraints weight = 34249.965| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.81 r_work: 0.3194 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25177 Z= 0.110 Angle : 0.577 11.714 34360 Z= 0.277 Chirality : 0.043 0.428 3870 Planarity : 0.004 0.050 4220 Dihedral : 13.742 179.908 4200 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.76 % Allowed : 24.30 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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 (0.16), residues: 2881 helix: 1.64 (0.16), residues: 1071 sheet: 0.30 (0.22), residues: 532 loop : -1.07 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGB3 275 TYR 0.017 0.001 TYRB3 989 PHE 0.020 0.001 PHEB3 702 TRP 0.014 0.001 TRPB3 460 HIS 0.003 0.001 HISB3 998 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (25165) covalent geometry : angle 0.56981 / 0.28 (34342) hydrogen bonds : bond 0.03742 / 3.34 ( 998) hydrogen bonds : angle 4.28949 / 4.42 ( 2829) metal coordination : bond 0.00423 / 0.32 ( 12) metal coordination : angle 3.89214 / 6.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8474 (m-30) cc_final: 0.7941 (m-30) REVERT: A 814 MET cc_start: 0.2662 (ttt) cc_final: 0.2402 (ptt) REVERT: B1 613 MET cc_start: 0.8278 (mtt) cc_final: 0.7828 (mtt) REVERT: B1 776 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7792 (tp30) REVERT: B1 796 CYS cc_start: 0.6657 (m) cc_final: 0.6231 (m) REVERT: B1 816 LYS cc_start: 0.8136 (pptt) cc_final: 0.7910 (ptmm) REVERT: B1 830 TYR cc_start: 0.6529 (t80) cc_final: 0.6284 (t80) REVERT: B1 867 MET cc_start: 0.7492 (ttm) cc_final: 0.6897 (ttm) REVERT: B1 903 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8549 (t0) cc_final: 0.8320 (t0) REVERT: B1 1075 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6925 (mtp180) REVERT: B1 1133 MET cc_start: 0.8175 (mtm) cc_final: 0.7846 (mtp) REVERT: B2 619 MET cc_start: 0.4435 (mtp) cc_final: 0.3720 (tpt) REVERT: B2 683 TYR cc_start: 0.5473 (m-80) cc_final: 0.5234 (m-80) REVERT: B3 199 GLU cc_start: 0.8388 (tt0) cc_final: 0.8052 (tp30) REVERT: B3 213 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8628 (tp) REVERT: B3 235 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8540 (pp) REVERT: B3 294 LYS cc_start: 0.8209 (pttt) cc_final: 0.7238 (ptpt) REVERT: B3 316 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7491 (mt-10) REVERT: B3 690 ARG cc_start: 0.8124 (ttt-90) cc_final: 0.7673 (tpp80) REVERT: B3 701 LEU cc_start: 0.7427 (mp) cc_final: 0.6408 (tt) REVERT: B3 721 LEU cc_start: 0.7721 (tt) cc_final: 0.7217 (tp) REVERT: B3 770 LEU cc_start: 0.7660 (pt) cc_final: 0.7089 (mp) REVERT: B4 1 MET cc_start: 0.4595 (tmm) cc_final: 0.3994 (ttm) REVERT: B4 9 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8476 (ttm170) REVERT: B4 11 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7983 (tp40) REVERT: B4 16 TYR cc_start: 0.6638 (t80) cc_final: 0.6166 (t80) REVERT: B4 30 TRP cc_start: 0.6721 (t-100) cc_final: 0.6131 (t-100) REVERT: B4 64 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6322 (tm-30) REVERT: B4 76 MET cc_start: 0.6758 (mmt) cc_final: 0.5296 (mtm) REVERT: B5 25 ASP cc_start: 0.8410 (m-30) cc_final: 0.8037 (m-30) REVERT: A2 53 SER cc_start: 0.7923 (m) cc_final: 0.7517 (p) REVERT: A3 385 LEU cc_start: 0.8691 (tp) cc_final: 0.8115 (tp) REVERT: A3 463 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8124 (ttmt) outliers start: 69 outliers final: 38 residues processed: 334 average time/residue: 0.1631 time to fit residues: 85.7434 Evaluate side-chains 320 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 989 VAL Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1160 GLU Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 88 VAL Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 614 VAL Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1146 MET Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain A3 residue 383 LEU Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Chi-restraints excluded: chain A3 residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 236 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 234 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 692 HIS B11209 ASN B3 28 GLN B5 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107951 restraints weight = 34270.307| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.72 r_work: 0.3161 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25177 Z= 0.152 Angle : 0.614 11.520 34360 Z= 0.296 Chirality : 0.044 0.340 3870 Planarity : 0.004 0.048 4220 Dihedral : 13.614 179.090 4200 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 2.96 % Allowed : 24.46 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 0.21 (0.16), residues: 2881 helix: 1.53 (0.16), residues: 1073 sheet: 0.23 (0.22), residues: 539 loop : -1.13 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGB3 275 TYR 0.022 0.001 TYRB3 989 PHE 0.020 0.001 PHEB3 702 TRP 0.013 0.001 TRPB3 460 HIS 0.004 0.001 HISB11184 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (25165) covalent geometry : angle 0.60515 / 0.29 (34342) hydrogen bonds : bond 0.04284 / 3.83 ( 998) hydrogen bonds : angle 4.39862 / 4.49 ( 2829) metal coordination : bond 0.00497 / 0.40 ( 12) metal coordination : angle 4.60874 / 7.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 275 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8484 (m-30) cc_final: 0.7928 (m-30) REVERT: B1 518 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: B1 613 MET cc_start: 0.8223 (mtt) cc_final: 0.7734 (mtt) REVERT: B1 776 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7833 (tp30) REVERT: B1 796 CYS cc_start: 0.6612 (m) cc_final: 0.6158 (m) REVERT: B1 816 LYS cc_start: 0.8151 (pptt) cc_final: 0.7936 (ptmm) REVERT: B1 830 TYR cc_start: 0.6551 (t80) cc_final: 0.6306 (t80) REVERT: B1 867 MET cc_start: 0.7496 (ttm) cc_final: 0.6919 (ttm) REVERT: B1 903 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8596 (t0) cc_final: 0.8376 (t0) REVERT: B1 1075 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7082 (mtp180) REVERT: B1 1133 MET cc_start: 0.8187 (mtm) cc_final: 0.7880 (mtp) REVERT: B2 457 MET cc_start: 0.8444 (mmm) cc_final: 0.8067 (mpp) REVERT: B2 619 MET cc_start: 0.4469 (mtp) cc_final: 0.3742 (tpt) REVERT: B3 199 GLU cc_start: 0.8411 (tt0) cc_final: 0.8029 (tp30) REVERT: B3 213 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B3 235 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B3 294 LYS cc_start: 0.8211 (pttt) cc_final: 0.7245 (ptpt) REVERT: B3 316 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7445 (mt-10) REVERT: B3 331 ASP cc_start: 0.8078 (m-30) cc_final: 0.7526 (m-30) REVERT: B3 370 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B3 590 MET cc_start: 0.6498 (mpp) cc_final: 0.6152 (pmm) REVERT: B3 690 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7756 (tpp80) REVERT: B3 701 LEU cc_start: 0.7451 (mp) cc_final: 0.6374 (tt) REVERT: B3 721 LEU cc_start: 0.7762 (tt) cc_final: 0.7304 (tp) REVERT: B3 770 LEU cc_start: 0.7679 (pt) cc_final: 0.7137 (mp) REVERT: B4 1 MET cc_start: 0.4575 (tmm) cc_final: 0.3959 (ttm) REVERT: B4 9 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8508 (ttm170) REVERT: B4 11 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8083 (tp40) REVERT: B4 16 TYR cc_start: 0.6638 (t80) cc_final: 0.6113 (t80) REVERT: B4 30 TRP cc_start: 0.6783 (t-100) cc_final: 0.6176 (t-100) REVERT: B4 64 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6327 (tm-30) REVERT: B4 76 MET cc_start: 0.6730 (mmt) cc_final: 0.5196 (mtm) REVERT: B5 25 ASP cc_start: 0.8525 (m-30) cc_final: 0.8175 (m-30) REVERT: B6 21 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5482 (pt) REVERT: A2 53 SER cc_start: 0.7957 (m) cc_final: 0.7516 (p) outliers start: 74 outliers final: 47 residues processed: 330 average time/residue: 0.1630 time to fit residues: 84.6884 Evaluate side-chains 321 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain B1 residue 518 GLN Chi-restraints excluded: chain B1 residue 582 LEU Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 627 THR Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 989 VAL Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1160 GLU Chi-restraints excluded: chain B1 residue 1174 GLU Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 614 VAL Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 675 LEU Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 994 GLN Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1135 HIS Chi-restraints excluded: chain B3 residue 1146 MET Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 44 MET Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain B6 residue 21 LEU Chi-restraints excluded: chain A3 residue 383 LEU Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Chi-restraints excluded: chain A3 residue 464 LEU Chi-restraints excluded: chain A3 residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 59 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 195 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 692 HIS B11209 ASN B3 666 ASN B3 881 GLN B5 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105356 restraints weight = 33918.174| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.45 r_work: 0.3168 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25177 Z= 0.148 Angle : 0.615 13.688 34360 Z= 0.296 Chirality : 0.044 0.334 3870 Planarity : 0.004 0.063 4220 Dihedral : 13.520 178.922 4200 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 2.44 % Allowed : 25.30 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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 (0.16), residues: 2881 helix: 1.55 (0.16), residues: 1058 sheet: 0.16 (0.22), residues: 539 loop : -1.15 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 810 TYR 0.021 0.001 TYRB3 989 PHE 0.019 0.001 PHEB3 702 TRP 0.014 0.001 TRPB3 460 HIS 0.003 0.001 HISB11184 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (25165) covalent geometry : angle 0.60550 / 0.30 (34342) hydrogen bonds : bond 0.04309 / 3.87 ( 998) hydrogen bonds : angle 4.39014 / 4.52 ( 2829) metal coordination : bond 0.00486 / 0.39 ( 12) metal coordination : angle 4.69382 / 7.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8562 (m-30) cc_final: 0.8005 (m-30) REVERT: A 814 MET cc_start: 0.3585 (ptt) cc_final: 0.2555 (ppp) REVERT: B1 518 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: B1 613 MET cc_start: 0.8288 (mtt) cc_final: 0.7824 (mtt) REVERT: B1 776 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7914 (tp30) REVERT: B1 796 CYS cc_start: 0.6870 (m) cc_final: 0.6440 (m) REVERT: B1 816 LYS cc_start: 0.8202 (pptt) cc_final: 0.7976 (ptmm) REVERT: B1 830 TYR cc_start: 0.6570 (t80) cc_final: 0.6306 (t80) REVERT: B1 856 ASP cc_start: 0.8055 (m-30) cc_final: 0.7447 (m-30) REVERT: B1 867 MET cc_start: 0.7516 (ttm) cc_final: 0.6845 (ttm) REVERT: B1 903 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8651 (t0) cc_final: 0.8439 (t0) REVERT: B1 1133 MET cc_start: 0.8381 (mtm) cc_final: 0.8037 (mtp) REVERT: B2 457 MET cc_start: 0.8531 (mmm) cc_final: 0.8181 (mtt) REVERT: B2 566 ILE cc_start: 0.7484 (tp) cc_final: 0.7064 (tp) REVERT: B2 619 MET cc_start: 0.4357 (mtp) cc_final: 0.3637 (tpt) REVERT: B3 199 GLU cc_start: 0.8441 (tt0) cc_final: 0.8067 (tp30) REVERT: B3 213 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8740 (tp) REVERT: B3 235 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8489 (pp) REVERT: B3 294 LYS cc_start: 0.8142 (pttt) cc_final: 0.7173 (ptpt) REVERT: B3 316 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7603 (mt-10) REVERT: B3 690 ARG cc_start: 0.8247 (ttt-90) cc_final: 0.7860 (tpp80) REVERT: B3 701 LEU cc_start: 0.7520 (mp) cc_final: 0.6480 (tt) REVERT: B3 721 LEU cc_start: 0.7974 (tt) cc_final: 0.7539 (tp) REVERT: B3 770 LEU cc_start: 0.7640 (pt) cc_final: 0.7120 (mp) REVERT: B4 1 MET cc_start: 0.4549 (tmm) cc_final: 0.3976 (ttm) REVERT: B4 9 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8575 (ttm170) REVERT: B4 11 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8236 (tp40) REVERT: B4 16 TYR cc_start: 0.6821 (t80) cc_final: 0.6291 (t80) REVERT: B4 30 TRP cc_start: 0.6757 (t-100) cc_final: 0.6093 (t-100) REVERT: B4 60 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7937 (mp0) REVERT: B4 64 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6420 (tm-30) REVERT: B4 65 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B4 76 MET cc_start: 0.6659 (mmt) cc_final: 0.5344 (mtm) REVERT: B5 25 ASP cc_start: 0.8714 (m-30) cc_final: 0.8469 (m-30) REVERT: B6 21 LEU cc_start: 0.5750 (OUTLIER) cc_final: 0.5474 (pt) REVERT: A2 53 SER cc_start: 0.8012 (m) cc_final: 0.7541 (p) REVERT: A3 385 LEU cc_start: 0.8735 (tp) cc_final: 0.8456 (tp) outliers start: 61 outliers final: 43 residues processed: 312 average time/residue: 0.1651 time to fit residues: 81.2611 Evaluate side-chains 310 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain B1 residue 424 ILE Chi-restraints excluded: chain B1 residue 518 GLN Chi-restraints excluded: chain B1 residue 623 TYR Chi-restraints excluded: chain B1 residue 690 ILE Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 989 VAL Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1122 THR Chi-restraints excluded: chain B1 residue 1160 GLU Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B1 residue 1296 ILE Chi-restraints excluded: chain B2 residue 460 PHE Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 614 VAL Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 943 THR Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1146 MET Chi-restraints excluded: chain B4 residue 7 SER Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B5 residue 19 ILE Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain B6 residue 21 LEU Chi-restraints excluded: chain A3 residue 383 LEU Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 135 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 278 optimal weight: 0.0000 chunk 111 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 258 optimal weight: 3.9990 chunk 245 optimal weight: 0.0980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 692 HIS B5 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110811 restraints weight = 34222.420| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.70 r_work: 0.3195 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25177 Z= 0.105 Angle : 0.594 12.100 34360 Z= 0.284 Chirality : 0.042 0.348 3870 Planarity : 0.004 0.056 4220 Dihedral : 13.413 179.893 4200 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 2.04 % Allowed : 25.70 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 0.35 (0.16), residues: 2881 helix: 1.72 (0.17), residues: 1046 sheet: 0.24 (0.22), residues: 535 loop : -1.02 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 804 TYR 0.026 0.001 TYRB1 898 PHE 0.019 0.001 PHEB1 526 TRP 0.025 0.001 TRPB1 732 HIS 0.003 0.000 HISB5 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (25165) covalent geometry : angle 0.58733 / 0.28 (34342) hydrogen bonds : bond 0.03616 / 3.22 ( 998) hydrogen bonds : angle 4.26028 / 4.37 ( 2829) metal coordination : bond 0.00391 / 0.30 ( 12) metal coordination : angle 3.89193 / 6.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8527 (m-30) cc_final: 0.7903 (m-30) REVERT: A 814 MET cc_start: 0.3674 (ptt) cc_final: 0.2721 (ppp) REVERT: B1 518 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: B1 613 MET cc_start: 0.8151 (mtt) cc_final: 0.7698 (mtt) REVERT: B1 776 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7776 (tp30) REVERT: B1 796 CYS cc_start: 0.6587 (m) cc_final: 0.6179 (m) REVERT: B1 816 LYS cc_start: 0.8113 (pptt) cc_final: 0.7897 (ptmm) REVERT: B1 830 TYR cc_start: 0.6369 (t80) cc_final: 0.6021 (t80) REVERT: B1 903 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8529 (t0) cc_final: 0.8313 (t0) REVERT: B1 1133 MET cc_start: 0.8132 (mtm) cc_final: 0.7728 (mtp) REVERT: B2 566 ILE cc_start: 0.7576 (tp) cc_final: 0.7131 (tp) REVERT: B2 619 MET cc_start: 0.4403 (mtp) cc_final: 0.3643 (tpt) REVERT: B2 636 MET cc_start: 0.8458 (mtp) cc_final: 0.8204 (mtm) REVERT: B3 199 GLU cc_start: 0.8396 (tt0) cc_final: 0.8031 (tp30) REVERT: B3 213 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8677 (tp) REVERT: B3 235 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8481 (pp) REVERT: B3 294 LYS cc_start: 0.8102 (pttt) cc_final: 0.7180 (ptpt) REVERT: B3 518 GLN cc_start: 0.4716 (tm-30) cc_final: 0.4441 (tm-30) REVERT: B3 690 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.7739 (tpp80) REVERT: B3 701 LEU cc_start: 0.7362 (mp) cc_final: 0.6347 (tt) REVERT: B3 721 LEU cc_start: 0.7709 (tt) cc_final: 0.7268 (tp) REVERT: B3 770 LEU cc_start: 0.7563 (pt) cc_final: 0.7017 (mp) REVERT: B4 1 MET cc_start: 0.4625 (tmm) cc_final: 0.3748 (ttm) REVERT: B4 9 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8520 (ttm170) REVERT: B4 11 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8112 (tp40) REVERT: B4 16 TYR cc_start: 0.6699 (t80) cc_final: 0.6164 (t80) REVERT: B4 30 TRP cc_start: 0.6671 (t-100) cc_final: 0.6059 (t-100) REVERT: B4 60 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7968 (mt-10) REVERT: B4 64 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6324 (tm-30) REVERT: B4 65 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7384 (mm-30) REVERT: B4 76 MET cc_start: 0.6635 (mmt) cc_final: 0.5307 (mtm) REVERT: B5 25 ASP cc_start: 0.8456 (m-30) cc_final: 0.8197 (m-30) REVERT: A2 53 SER cc_start: 0.7978 (m) cc_final: 0.7523 (p) REVERT: A3 385 LEU cc_start: 0.8674 (tp) cc_final: 0.8175 (tp) outliers start: 51 outliers final: 37 residues processed: 305 average time/residue: 0.1788 time to fit residues: 85.5844 Evaluate side-chains 302 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain B1 residue 424 ILE Chi-restraints excluded: chain B1 residue 518 GLN Chi-restraints excluded: chain B1 residue 690 ILE Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 980 GLU Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1107 GLN Chi-restraints excluded: chain B1 residue 1160 GLU Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 614 VAL Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B3 residue 1208 LEU Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B5 residue 44 MET Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain A3 residue 383 LEU Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 453 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 126 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 243 optimal weight: 0.0570 chunk 255 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 270 optimal weight: 3.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 692 HIS ** B3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.175532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105740 restraints weight = 33156.449| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.37 r_work: 0.3172 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25177 Z= 0.141 Angle : 0.620 11.665 34360 Z= 0.297 Chirality : 0.044 0.331 3870 Planarity : 0.004 0.050 4220 Dihedral : 13.415 179.630 4200 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 2.12 % Allowed : 25.50 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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: 0.26 (0.16), residues: 2881 helix: 1.66 (0.17), residues: 1047 sheet: 0.24 (0.22), residues: 534 loop : -1.11 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGB3 275 TYR 0.020 0.001 TYRB3 989 PHE 0.019 0.001 PHEB1 526 TRP 0.014 0.001 TRPB3 460 HIS 0.003 0.001 HISB2 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (25165) covalent geometry : angle 0.61132 / 0.30 (34342) hydrogen bonds : bond 0.04167 / 3.73 ( 998) hydrogen bonds : angle 4.29972 / 4.41 ( 2829) metal coordination : bond 0.00507 / 0.41 ( 12) metal coordination : angle 4.61123 / 7.64 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 97 ASP cc_start: 0.8560 (m-30) cc_final: 0.7957 (m-30) REVERT: H 103 LYS cc_start: 0.7711 (tptp) cc_final: 0.7477 (tptp) REVERT: A 805 LYS cc_start: 0.7252 (pttt) cc_final: 0.6741 (pptt) REVERT: A 814 MET cc_start: 0.3892 (ptt) cc_final: 0.2958 (ppp) REVERT: B1 518 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: B1 613 MET cc_start: 0.8281 (mtt) cc_final: 0.7820 (mtt) REVERT: B1 776 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7883 (tp30) REVERT: B1 796 CYS cc_start: 0.6837 (m) cc_final: 0.6406 (m) REVERT: B1 816 LYS cc_start: 0.8189 (pptt) cc_final: 0.7960 (ptmm) REVERT: B1 830 TYR cc_start: 0.6477 (t80) cc_final: 0.6072 (t80) REVERT: B1 856 ASP cc_start: 0.8088 (m-30) cc_final: 0.7637 (m-30) REVERT: B1 903 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: B1 1002 ASN cc_start: 0.8616 (t0) cc_final: 0.8409 (t0) REVERT: B1 1075 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7411 (mtp180) REVERT: B2 566 ILE cc_start: 0.7524 (tp) cc_final: 0.7121 (tp) REVERT: B2 619 MET cc_start: 0.4338 (mtp) cc_final: 0.3612 (tpt) REVERT: B2 636 MET cc_start: 0.8445 (mtp) cc_final: 0.8240 (mtm) REVERT: B3 199 GLU cc_start: 0.8414 (tt0) cc_final: 0.8055 (tp30) REVERT: B3 213 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8739 (tp) REVERT: B3 235 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8490 (pp) REVERT: B3 294 LYS cc_start: 0.8125 (pttt) cc_final: 0.7177 (ptpt) REVERT: B3 316 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7582 (mt-10) REVERT: B3 331 ASP cc_start: 0.8182 (m-30) cc_final: 0.7654 (m-30) REVERT: B3 518 GLN cc_start: 0.4726 (tm-30) cc_final: 0.4451 (tm-30) REVERT: B3 690 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7843 (tpp80) REVERT: B3 701 LEU cc_start: 0.7459 (mp) cc_final: 0.6436 (tt) REVERT: B3 721 LEU cc_start: 0.7935 (tt) cc_final: 0.7454 (tp) REVERT: B3 770 LEU cc_start: 0.7607 (pt) cc_final: 0.7087 (mp) REVERT: B4 1 MET cc_start: 0.4515 (tmm) cc_final: 0.3687 (ttm) REVERT: B4 9 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8527 (ttm170) REVERT: B4 11 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8246 (tp40) REVERT: B4 16 TYR cc_start: 0.6903 (t80) cc_final: 0.6338 (t80) REVERT: B4 30 TRP cc_start: 0.6713 (t-100) cc_final: 0.6079 (t-100) REVERT: B4 64 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6410 (tm-30) REVERT: B4 65 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B4 76 MET cc_start: 0.6725 (mmt) cc_final: 0.5393 (mtm) REVERT: B5 25 ASP cc_start: 0.8702 (m-30) cc_final: 0.8417 (m-30) REVERT: B5 35 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: A2 53 SER cc_start: 0.8004 (m) cc_final: 0.7523 (p) REVERT: A3 385 LEU cc_start: 0.8716 (tp) cc_final: 0.8229 (tp) outliers start: 53 outliers final: 39 residues processed: 307 average time/residue: 0.1741 time to fit residues: 84.4191 Evaluate side-chains 306 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain B1 residue 518 GLN Chi-restraints excluded: chain B1 residue 575 LEU Chi-restraints excluded: chain B1 residue 690 ILE Chi-restraints excluded: chain B1 residue 817 HIS Chi-restraints excluded: chain B1 residue 903 GLN Chi-restraints excluded: chain B1 residue 1010 THR Chi-restraints excluded: chain B1 residue 1017 LEU Chi-restraints excluded: chain B1 residue 1069 HIS Chi-restraints excluded: chain B1 residue 1075 ARG Chi-restraints excluded: chain B1 residue 1152 SER Chi-restraints excluded: chain B1 residue 1160 GLU Chi-restraints excluded: chain B1 residue 1166 ILE Chi-restraints excluded: chain B1 residue 1174 GLU Chi-restraints excluded: chain B1 residue 1293 ASN Chi-restraints excluded: chain B2 residue 583 LYS Chi-restraints excluded: chain B2 residue 587 HIS Chi-restraints excluded: chain B3 residue 213 LEU Chi-restraints excluded: chain B3 residue 220 VAL Chi-restraints excluded: chain B3 residue 235 LEU Chi-restraints excluded: chain B3 residue 374 SER Chi-restraints excluded: chain B3 residue 412 ILE Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 530 ASP Chi-restraints excluded: chain B3 residue 614 VAL Chi-restraints excluded: chain B3 residue 667 ILE Chi-restraints excluded: chain B3 residue 784 THR Chi-restraints excluded: chain B3 residue 823 MET Chi-restraints excluded: chain B3 residue 845 GLU Chi-restraints excluded: chain B3 residue 869 MET Chi-restraints excluded: chain B3 residue 915 LEU Chi-restraints excluded: chain B3 residue 920 VAL Chi-restraints excluded: chain B3 residue 968 ARG Chi-restraints excluded: chain B3 residue 1003 SER Chi-restraints excluded: chain B3 residue 1102 LEU Chi-restraints excluded: chain B4 residue 50 THR Chi-restraints excluded: chain B4 residue 53 HIS Chi-restraints excluded: chain B5 residue 35 GLN Chi-restraints excluded: chain B5 residue 44 MET Chi-restraints excluded: chain B5 residue 48 ASP Chi-restraints excluded: chain A3 residue 383 LEU Chi-restraints excluded: chain A3 residue 425 HIS Chi-restraints excluded: chain A3 residue 438 LEU Chi-restraints excluded: chain A3 residue 440 ILE Chi-restraints excluded: chain A3 residue 453 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 243 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 692 HIS B11209 ASN B5 13 HIS B5 23 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.176814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109839 restraints weight = 34188.855| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.82 r_work: 0.3168 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25177 Z= 0.114 Angle : 0.604 12.191 34360 Z= 0.289 Chirality : 0.043 0.348 3870 Planarity : 0.004 0.051 4220 Dihedral : 13.378 179.561 4200 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 2.04 % Allowed : 25.70 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % 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 (0.16), residues: 2881 helix: 1.76 (0.17), residues: 1041 sheet: 0.27 (0.22), residues: 534 loop : -1.08 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGB3 275 TYR 0.019 0.001 TYRB3 989 PHE 0.019 0.001 PHEB1 526 TRP 0.017 0.001 TRPB3 460 HIS 0.003 0.001 HISB3 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (25165) covalent geometry : angle 0.59661 / 0.29 (34342) hydrogen bonds : bond 0.03794 / 3.39 ( 998) hydrogen bonds : angle 4.27037 / 4.36 ( 2829) metal coordination : bond 0.00436 / 0.34 ( 12) metal coordination : angle 4.23845 / 6.91 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.66 seconds wall clock time: 122 minutes 5.26 seconds (7325.26 seconds total)