Starting phenix.real_space_refine on Mon Sep 14 07:41:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ahu_9627/09_2026/6ahu_9627_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ahu_9627/09_2026/6ahu_9627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ahu_9627/09_2026/6ahu_9627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ahu_9627/09_2026/6ahu_9627.map" model { file = "/net/cci-nas-00/data/ceres_data/6ahu_9627/09_2026/6ahu_9627_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ahu_9627/09_2026/6ahu_9627_neut.cif" } resolution = 3.66 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= 0.000 sd= 0.008 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 1 6.06 5 P 413 5.49 5 S 112 5.16 5 C 17011 2.51 5 N 5269 2.21 5 O 6580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29386 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 7295 Classifications: {'RNA': 341} Modifications used: {'rna2p_pur': 28, 'rna2p_pyr': 20, 'rna3p_pur': 152, 'rna3p_pyr': 141} Link IDs: {'rna2p': 48, 'rna3p': 292} Chain: "B" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6142 Classifications: {'peptide': 774} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 723} Chain breaks: 4 Chain: "C" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1448 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1197 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 10, 'TRANS': 118} Chain breaks: 2 Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1021 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1824 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "J" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1905 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "K" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 979 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2939 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 341} Chain: "T" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1535 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 61} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24659 SG CYS K 92 68.808 76.740 55.775 1.00101.00 S Time building chain proxies: 5.76, per 1000 atoms: 0.20 Number of scatterers: 29386 At special positions: 0 Unit cell: (146.52, 129.36, 200.64, 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 1 29.99 S 112 16.00 P 413 15.00 O 6580 8.00 N 5269 7.00 C 17011 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: 2.13 Conformation dependent library (CDL) restraints added in 863.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 92 " 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 23 sheets defined 36.5% alpha, 16.9% beta 85 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'B' and resid 100 through 127 removed outlier: 3.766A pdb=" N THR B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.949A pdb=" N ARG B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.106A pdb=" N ARG B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.771A pdb=" N GLU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 204 through 211 removed outlier: 4.105A pdb=" N LYS B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 211 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 4.074A pdb=" N TYR B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.916A pdb=" N CYS B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.590A pdb=" N LEU B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.717A pdb=" N THR B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 4.141A pdb=" N VAL B 455 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 456' Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.576A pdb=" N ILE B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.612A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS B 481 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 removed outlier: 3.655A pdb=" N VAL B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 542 " --> pdb=" O GLN B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.594A pdb=" N TRP B 554 " --> pdb=" O SER B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 555 through 565 removed outlier: 3.509A pdb=" N CYS B 559 " --> pdb=" O ASN B 555 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.642A pdb=" N MET B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Proline residue: B 633 - end of helix removed outlier: 3.922A pdb=" N TYR B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 4.299A pdb=" N SER B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 653 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 removed outlier: 3.603A pdb=" N LEU B 680 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 682 " --> pdb=" O LYS B 678 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 removed outlier: 3.878A pdb=" N THR B 712 " --> pdb=" O TRP B 708 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 716 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL B 719 " --> pdb=" O TRP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 820 removed outlier: 3.543A pdb=" N ALA B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 818 " --> pdb=" O GLN B 814 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS B 819 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 removed outlier: 3.767A pdb=" N CYS B 845 " --> pdb=" O THR B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 889 removed outlier: 4.014A pdb=" N PHE B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 884 " --> pdb=" O LYS B 880 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 886 " --> pdb=" O ASP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 905 through 920 removed outlier: 3.918A pdb=" N LEU B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 910 " --> pdb=" O SER B 906 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 920 " --> pdb=" O LYS B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 957 removed outlier: 4.012A pdb=" N VAL B 955 " --> pdb=" O PRO B 951 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 951 through 957' Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.623A pdb=" N MET B 993 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 996 " --> pdb=" O ASP B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.662A pdb=" N GLN C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.549A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.641A pdb=" N ARG C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.649A pdb=" N GLN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.576A pdb=" N LEU C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.854A pdb=" N GLN D 94 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 112 removed outlier: 3.775A pdb=" N ARG D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.622A pdb=" N LEU E 22 " --> pdb=" O PRO E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 41 removed outlier: 3.613A pdb=" N ARG E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 73 through 81 removed outlier: 4.293A pdb=" N VAL E 77 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 3.572A pdb=" N LEU E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 124 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.524A pdb=" N GLU E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.219A pdb=" N PHE F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP F 30 " --> pdb=" O GLY F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 59 removed outlier: 3.769A pdb=" N ALA F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 75 Processing helix chain 'F' and resid 76 through 86 removed outlier: 3.776A pdb=" N LEU F 84 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 77 through 93 removed outlier: 3.625A pdb=" N ILE G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN G 83 " --> pdb=" O ASN G 79 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 52 removed outlier: 3.605A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 58 removed outlier: 3.824A pdb=" N ALA H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 89 removed outlier: 3.717A pdb=" N TRP H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'I' and resid 14 through 29 removed outlier: 3.586A pdb=" N LEU I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 83 through 91 removed outlier: 3.658A pdb=" N CYS I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN I 88 " --> pdb=" O PRO I 84 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL I 89 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 91' Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.980A pdb=" N ARG I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.712A pdb=" N ILE I 115 " --> pdb=" O LYS I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.692A pdb=" N ILE I 142 " --> pdb=" O LYS I 138 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP I 147 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 181 removed outlier: 4.104A pdb=" N TYR I 168 " --> pdb=" O THR I 164 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR I 169 " --> pdb=" O MET I 165 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 173 " --> pdb=" O THR I 169 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU I 174 " --> pdb=" O ILE I 170 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS I 181 " --> pdb=" O MET I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 210 removed outlier: 3.660A pdb=" N LEU I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 237 removed outlier: 3.578A pdb=" N SER I 222 " --> pdb=" O LYS I 218 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN I 224 " --> pdb=" O ALA I 220 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N CYS I 225 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA I 228 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU I 229 " --> pdb=" O CYS I 225 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG I 235 " --> pdb=" O HIS I 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 3.634A pdb=" N GLY J 20 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU J 28 " --> pdb=" O THR J 24 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 removed outlier: 3.638A pdb=" N CYS J 87 " --> pdb=" O ASP J 83 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN J 88 " --> pdb=" O PRO J 84 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 109 through 119 removed outlier: 3.555A pdb=" N HIS J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 149 removed outlier: 3.675A pdb=" N VAL J 144 " --> pdb=" O PRO J 140 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA J 145 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP J 147 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 178 removed outlier: 3.961A pdb=" N TYR J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 170 " --> pdb=" O ARG J 166 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 172 " --> pdb=" O TYR J 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 210 removed outlier: 3.646A pdb=" N ALA J 204 " --> pdb=" O PRO J 200 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN J 205 " --> pdb=" O TYR J 201 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 237 removed outlier: 3.758A pdb=" N ALA J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL J 221 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER J 222 " --> pdb=" O LYS J 218 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN J 224 " --> pdb=" O ALA J 220 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS J 225 " --> pdb=" O VAL J 221 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU J 233 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 28 removed outlier: 4.214A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE K 11 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG K 13 " --> pdb=" O GLU K 9 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN K 15 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS K 22 " --> pdb=" O TYR K 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN K 27 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 49 Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.738A pdb=" N LEU K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'L' and resid 30 through 35 Processing helix chain 'L' and resid 53 through 61 removed outlier: 3.558A pdb=" N MET L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.693A pdb=" N GLU L 125 " --> pdb=" O LYS L 121 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY L 128 " --> pdb=" O TYR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 154 Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.527A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU L 171 " --> pdb=" O TRP L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 197 removed outlier: 3.945A pdb=" N TYR L 196 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 249 removed outlier: 3.606A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP L 242 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY L 245 " --> pdb=" O PHE L 241 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA L 246 " --> pdb=" O ASP L 242 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 247 " --> pdb=" O TRP L 243 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE L 248 " --> pdb=" O LEU L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.641A pdb=" N ILE L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 303 removed outlier: 4.467A pdb=" N GLU L 303 " --> pdb=" O TYR L 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 300 through 303' Processing sheet with id=AA1, first strand: chain 'B' and resid 212 through 215 removed outlier: 4.264A pdb=" N ARG B 225 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 215 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 223 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 243 through 244 removed outlier: 3.524A pdb=" N LEU B 507 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 448 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 252 through 256 removed outlier: 3.558A pdb=" N TRP B 413 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 289 through 294 removed outlier: 3.788A pdb=" N THR B 309 " --> pdb=" O TRP B 330 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 330 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 311 " --> pdb=" O TRP B 328 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP B 328 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS B 313 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 326 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.259A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B1006 " --> pdb=" O CYS B 876 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 875 " --> pdb=" O LEU B 964 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR B 962 " --> pdb=" O VAL B 877 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.259A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 861 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 980 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP B 971 " --> pdb=" O GLU B 980 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 115 removed outlier: 4.036A pdb=" N GLN C 112 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE C 182 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 131 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL C 156 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 174 through 178 removed outlier: 3.929A pdb=" N ILE D 177 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE D 165 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 140 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU D 187 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 142 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 185 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 144 " --> pdb=" O VAL D 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 55 through 59 removed outlier: 6.919A pdb=" N VAL E 55 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG E 68 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR E 57 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 59 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE E 64 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 9 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 10 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU E 101 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU E 12 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASN E 99 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'F' and resid 34 through 35 removed outlier: 6.637A pdb=" N GLY F 34 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 38 removed outlier: 6.482A pdb=" N ASN G 35 " --> pdb=" O TYR G 70 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N HIS G 72 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE G 37 " --> pdb=" O HIS G 72 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE G 69 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 103 through 109 removed outlier: 3.510A pdb=" N SER G 103 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA G 129 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 109 " --> pdb=" O ARG G 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 9 through 14 removed outlier: 3.622A pdb=" N GLU H 9 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS L 19 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 11 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU L 14 " --> pdb=" O VAL L 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL L 16 " --> pdb=" O MET L 353 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR L 349 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP L 348 " --> pdb=" O PHE L 344 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TRP L 309 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE L 44 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS L 279 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE L 46 " --> pdb=" O TYR L 277 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.643A pdb=" N ILE H 77 " --> pdb=" O HIS H 20 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN H 106 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS H 25 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL H 104 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU H 27 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE H 102 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.741A pdb=" N ALA I 34 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL I 33 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ARG I 76 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 35 " --> pdb=" O ARG I 76 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR I 78 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL I 39 " --> pdb=" O ILE I 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.741A pdb=" N ALA I 34 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL I 33 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ARG I 76 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 35 " --> pdb=" O ARG I 76 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR I 78 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N VAL I 102 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR I 75 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ALA I 104 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU I 77 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE I 106 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 79 " --> pdb=" O PHE I 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 34 through 35 removed outlier: 5.934A pdb=" N ILE J 35 " --> pdb=" O ARG J 76 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR J 78 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL J 39 " --> pdb=" O ILE J 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 34 through 35 removed outlier: 5.934A pdb=" N ILE J 35 " --> pdb=" O ARG J 76 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR J 78 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR J 75 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ALA J 104 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU J 77 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE J 106 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE J 79 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL J 103 " --> pdb=" O LEU J 124 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N CYS J 126 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL J 105 " --> pdb=" O CYS J 126 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL J 125 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL J 155 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 188 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 76 through 81 removed outlier: 3.659A pdb=" N THR K 76 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 131 through 133 removed outlier: 4.085A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER L 91 " --> pdb=" O HIS L 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA L 182 " --> pdb=" O TYR L 93 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU L 95 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE L 177 " --> pdb=" O ASN L 71 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN L 201 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 322 through 323 610 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 215 hydrogen bonds 386 hydrogen bond angles 0 basepair planarities 85 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7978 1.34 - 1.46: 9164 1.46 - 1.58: 12734 1.58 - 1.70: 824 1.70 - 1.83: 147 Bond restraints: 30847 Sorted by residual: bond pdb=" C VAL B 659 " pdb=" N PRO B 660 " ideal model delta sigma weight residual 1.334 1.404 -0.070 2.34e-02 1.83e+03 8.91e+00 bond pdb=" C ASP B 406 " pdb=" N PRO B 407 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.63e+00 bond pdb=" C LYS D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C ALA B 832 " pdb=" N PRO B 833 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.92e+00 bond pdb=" C ASN H 15 " pdb=" N PRO H 16 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.20e-03 1.49e+04 4.47e+00 ... (remaining 30842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 43366 3.32 - 6.64: 323 6.64 - 9.96: 59 9.96 - 13.28: 4 13.28 - 16.61: 1 Bond angle restraints: 43753 Sorted by residual: angle pdb=" C LEU K 69 " pdb=" N VAL K 70 " pdb=" CA VAL K 70 " ideal model delta sigma weight residual 120.24 124.86 -4.62 6.30e-01 2.52e+00 5.38e+01 angle pdb=" C ARG G 23 " pdb=" N LYS G 24 " pdb=" CA LYS G 24 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C3' U A 126 " pdb=" O3' U A 126 " pdb=" P U A 127 " ideal model delta sigma weight residual 119.70 126.55 -6.85 1.20e+00 6.94e-01 3.26e+01 angle pdb=" C3' G A 74 " pdb=" O3' G A 74 " pdb=" P G A 75 " ideal model delta sigma weight residual 119.70 126.17 -6.47 1.20e+00 6.94e-01 2.90e+01 angle pdb=" C ARG G 25 " pdb=" N LEU G 26 " pdb=" CA LEU G 26 " ideal model delta sigma weight residual 120.58 127.45 -6.87 1.32e+00 5.74e-01 2.71e+01 ... (remaining 43748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.64: 17992 30.64 - 61.27: 960 61.27 - 91.91: 437 91.91 - 122.55: 7 122.55 - 153.19: 2 Dihedral angle restraints: 19398 sinusoidal: 11847 harmonic: 7551 Sorted by residual: dihedral pdb=" CA GLU D 171 " pdb=" C GLU D 171 " pdb=" N ASP D 172 " pdb=" CA ASP D 172 " ideal model delta harmonic sigma weight residual 180.00 -134.69 -45.31 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA PRO B 463 " pdb=" C PRO B 463 " pdb=" N HIS B 464 " pdb=" CA HIS B 464 " ideal model delta harmonic sigma weight residual 180.00 -135.69 -44.31 0 5.00e+00 4.00e-02 7.85e+01 dihedral pdb=" CA LYS D 170 " pdb=" C LYS D 170 " pdb=" N GLU D 171 " pdb=" CA GLU D 171 " ideal model delta harmonic sigma weight residual -180.00 -141.70 -38.30 0 5.00e+00 4.00e-02 5.87e+01 ... (remaining 19395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4610 0.089 - 0.178: 658 0.178 - 0.266: 12 0.266 - 0.355: 2 0.355 - 0.444: 1 Chirality restraints: 5283 Sorted by residual: chirality pdb=" CB ILE B 499 " pdb=" CA ILE B 499 " pdb=" CG1 ILE B 499 " pdb=" CG2 ILE B 499 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C3' G A 261 " pdb=" C4' G A 261 " pdb=" O3' G A 261 " pdb=" C2' G A 261 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C3' C A 326 " pdb=" C4' C A 326 " pdb=" O3' C A 326 " pdb=" C2' C A 326 " both_signs ideal model delta sigma weight residual False -2.48 -2.18 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 5280 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 463 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C PRO B 463 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO B 463 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS B 464 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 30 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO G 31 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 31 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 31 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 170 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C LYS D 170 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS D 170 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU D 171 " -0.015 2.00e-02 2.50e+03 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 7234 2.81 - 3.33: 23352 3.33 - 3.85: 50440 3.85 - 4.38: 58503 4.38 - 4.90: 88564 Nonbonded interactions: 228093 Sorted by model distance: nonbonded pdb=" OH TYR J 30 " pdb=" O ARG J 198 " model vdw 2.284 3.040 nonbonded pdb=" O TRP H 86 " pdb=" OG1 THR H 90 " model vdw 2.291 3.040 nonbonded pdb=" O ILE B 493 " pdb=" NH2 ARG G 25 " model vdw 2.294 3.120 nonbonded pdb=" O2' A A 32 " pdb=" O VAL G 39 " model vdw 2.301 3.040 nonbonded pdb=" O2' A T 58 " pdb=" OP2 A T 60 " model vdw 2.322 3.040 ... (remaining 228088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 237) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 : 0.004 0.321 30848 Z= 0.203 Angle : 0.860 16.606 43753 Z= 0.571 Chirality : 0.055 0.444 5283 Planarity : 0.006 0.066 4022 Dihedral : 18.211 153.187 14494 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.85 % Favored : 89.92 % Rotamer: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.16 % 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: -5.26 (0.12), residues: 2559 helix: -4.73 (0.06), residues: 738 sheet: -1.92 (0.21), residues: 512 loop : -3.42 (0.13), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 207 TYR 0.025 0.001 TYR G 70 PHE 0.029 0.002 PHE L 260 TRP 0.043 0.002 TRP B 708 HIS 0.007 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.19 (30847) covalent geometry : angle 0.86027 / 0.57 (43753) hydrogen bonds : bond 0.31565 / 33.97 ( 823) hydrogen bonds : angle 10.99392 / 13.56 ( 2108) metal coordination : bond 0.32098 / 16.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 925 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6648 (mm-30) REVERT: B 263 LEU cc_start: 0.7682 (mt) cc_final: 0.7478 (mt) REVERT: B 340 LEU cc_start: 0.8062 (tp) cc_final: 0.7808 (tt) REVERT: B 720 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7180 (pp30) REVERT: C 30 ILE cc_start: 0.7827 (mt) cc_final: 0.7014 (pt) REVERT: C 180 LEU cc_start: 0.8922 (tp) cc_final: 0.8627 (mt) REVERT: C 207 TRP cc_start: 0.2453 (t-100) cc_final: 0.1666 (t-100) REVERT: D 140 ILE cc_start: 0.7379 (pp) cc_final: 0.7051 (pp) REVERT: D 180 LEU cc_start: 0.7683 (mt) cc_final: 0.7475 (mt) REVERT: D 205 SER cc_start: 0.8550 (p) cc_final: 0.8033 (p) REVERT: F 6 LYS cc_start: 0.6821 (mttt) cc_final: 0.6556 (mmtm) REVERT: F 80 CYS cc_start: 0.7764 (t) cc_final: 0.7226 (t) REVERT: G 83 ASN cc_start: 0.7478 (t0) cc_final: 0.7233 (t0) REVERT: G 109 ASP cc_start: 0.8263 (m-30) cc_final: 0.7776 (t70) REVERT: I 224 ASN cc_start: 0.8147 (m-40) cc_final: 0.7862 (m-40) REVERT: J 100 TYR cc_start: 0.6060 (m-10) cc_final: 0.5852 (m-10) REVERT: J 155 VAL cc_start: 0.8589 (t) cc_final: 0.8084 (m) REVERT: K 6 LYS cc_start: 0.5527 (tttt) cc_final: 0.5308 (mptt) REVERT: K 39 CYS cc_start: 0.6215 (t) cc_final: 0.5601 (t) REVERT: K 40 TYR cc_start: 0.7817 (t80) cc_final: 0.7385 (t80) REVERT: K 73 LEU cc_start: 0.7640 (pp) cc_final: 0.7220 (mm) REVERT: L 126 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7299 (mt-10) REVERT: L 147 SER cc_start: 0.7072 (t) cc_final: 0.6560 (t) REVERT: L 244 LEU cc_start: 0.8398 (tp) cc_final: 0.8183 (tp) outliers start: 2 outliers final: 0 residues processed: 927 average time/residue: 0.2235 time to fit residues: 310.3680 Evaluate side-chains 442 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.0770 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 187 ASN B 332 HIS B 392 ASN B 565 ASN B 710 GLN B 802 HIS B 958 HIS ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 136 HIS E 6 HIS E 99 ASN F 148 GLN H 39 GLN I 27 HIS I 65 GLN I 88 ASN I 184 ASN J 27 HIS J 143 ASN J 231 HIS K 19 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS L 29 HIS L 36 HIS L 75 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.143002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.119040 restraints weight = 81685.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.121382 restraints weight = 46691.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.122157 restraints weight = 31429.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.122371 restraints weight = 27134.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.122474 restraints weight = 26643.503| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 30848 Z= 0.160 Angle : 0.714 15.640 43753 Z= 0.368 Chirality : 0.042 0.258 5283 Planarity : 0.007 0.081 4022 Dihedral : 20.970 156.500 9381 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.73 % Favored : 90.19 % Rotamer: Outliers : 3.79 % Allowed : 13.14 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -4.13 (0.13), residues: 2559 helix: -2.90 (0.13), residues: 774 sheet: -1.49 (0.21), residues: 504 loop : -3.19 (0.14), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 133 TYR 0.031 0.002 TYR C 29 PHE 0.028 0.002 PHE B 310 TRP 0.027 0.002 TRP B 708 HIS 0.010 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (30847) covalent geometry : angle 0.71353 / 0.37 (43753) hydrogen bonds : bond 0.07888 / 8.48 ( 823) hydrogen bonds : angle 6.40271 / 7.94 ( 2108) metal coordination : bond 0.01194 / 0.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 485 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7775 (mtt90) REVERT: B 720 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7181 (pp30) REVERT: C 131 LEU cc_start: 0.7288 (tp) cc_final: 0.7020 (tp) REVERT: C 163 ARG cc_start: 0.5356 (mmm-85) cc_final: 0.4776 (mmm-85) REVERT: C 180 LEU cc_start: 0.8852 (tp) cc_final: 0.8558 (mp) REVERT: D 79 ARG cc_start: 0.5187 (mmt180) cc_final: 0.4865 (mmm160) REVERT: D 85 ARG cc_start: 0.5177 (ttp-110) cc_final: 0.4759 (ttp-170) REVERT: D 104 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7747 (mp0) REVERT: D 135 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (pp) REVERT: D 159 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6410 (mt0) REVERT: D 180 LEU cc_start: 0.7850 (mt) cc_final: 0.7642 (mt) REVERT: E 140 LYS cc_start: 0.8299 (mttt) cc_final: 0.7956 (mmtm) REVERT: F 4 PHE cc_start: 0.7176 (m-80) cc_final: 0.6954 (m-80) REVERT: F 59 GLN cc_start: 0.3046 (OUTLIER) cc_final: 0.2660 (pt0) REVERT: G 83 ASN cc_start: 0.8242 (t0) cc_final: 0.7547 (t0) REVERT: G 109 ASP cc_start: 0.8054 (m-30) cc_final: 0.7537 (t0) REVERT: H 20 HIS cc_start: 0.6734 (m-70) cc_final: 0.6459 (m170) REVERT: H 82 LEU cc_start: 0.8904 (tp) cc_final: 0.8671 (tp) REVERT: H 84 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7828 (mttp) REVERT: I 76 ARG cc_start: 0.6745 (ttp-170) cc_final: 0.6437 (ttt180) REVERT: I 202 ASP cc_start: 0.7865 (t70) cc_final: 0.7610 (t70) REVERT: J 155 VAL cc_start: 0.8705 (t) cc_final: 0.8276 (m) REVERT: J 165 MET cc_start: 0.6700 (mmt) cc_final: 0.6352 (tpt) REVERT: K 40 TYR cc_start: 0.7988 (t80) cc_final: 0.7746 (t80) REVERT: K 68 LEU cc_start: 0.6969 (pp) cc_final: 0.6444 (pp) REVERT: K 73 LEU cc_start: 0.7833 (pp) cc_final: 0.7148 (tt) REVERT: L 325 GLU cc_start: 0.6973 (pp20) cc_final: 0.6768 (pp20) outliers start: 86 outliers final: 48 residues processed: 538 average time/residue: 0.1976 time to fit residues: 165.9882 Evaluate side-chains 442 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 391 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 246 LYS Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 71 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 348 GLN B 958 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 118 ASN D 94 GLN D 108 GLN E 99 ASN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS I 143 ASN I 175 ASN I 184 ASN J 27 HIS ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 HIS L 206 GLN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.131690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104080 restraints weight = 81147.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107137 restraints weight = 47224.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107845 restraints weight = 28246.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.108203 restraints weight = 25586.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108358 restraints weight = 25133.875| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 30848 Z= 0.279 Angle : 0.827 17.444 43753 Z= 0.424 Chirality : 0.047 0.224 5283 Planarity : 0.007 0.072 4022 Dihedral : 21.076 153.978 9381 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.88 % Favored : 88.08 % Rotamer: Outliers : 5.69 % Allowed : 13.93 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -3.43 (0.15), residues: 2559 helix: -1.83 (0.16), residues: 796 sheet: -1.36 (0.21), residues: 513 loop : -3.02 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG K 100 TYR 0.036 0.003 TYR F 151 PHE 0.032 0.003 PHE K 16 TRP 0.041 0.003 TRP B 708 HIS 0.030 0.003 HIS L 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.28 (30847) covalent geometry : angle 0.82651 / 0.42 (43753) hydrogen bonds : bond 0.07017 / 7.62 ( 823) hydrogen bonds : angle 5.86079 / 7.41 ( 2108) metal coordination : bond 0.01082 / 0.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 423 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 LYS cc_start: 0.8046 (ptmm) cc_final: 0.7483 (tptp) REVERT: B 139 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6651 (ppp) REVERT: B 429 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8012 (ptm) REVERT: B 654 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8733 (mtpt) REVERT: C 163 ARG cc_start: 0.6861 (mmm-85) cc_final: 0.6122 (mmm-85) REVERT: C 180 LEU cc_start: 0.9031 (tp) cc_final: 0.8573 (mt) REVERT: D 135 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8035 (pp) REVERT: D 206 GLU cc_start: 0.7931 (mp0) cc_final: 0.7385 (mp0) REVERT: E 136 GLU cc_start: 0.8578 (pp20) cc_final: 0.8348 (tp30) REVERT: E 140 LYS cc_start: 0.8241 (mttt) cc_final: 0.7735 (mtmm) REVERT: F 4 PHE cc_start: 0.7267 (m-80) cc_final: 0.6978 (m-80) REVERT: F 59 GLN cc_start: 0.4195 (OUTLIER) cc_final: 0.3819 (pp30) REVERT: G 83 ASN cc_start: 0.8572 (t0) cc_final: 0.8016 (t0) REVERT: G 109 ASP cc_start: 0.8202 (m-30) cc_final: 0.7627 (t70) REVERT: H 50 ASP cc_start: 0.8039 (m-30) cc_final: 0.7661 (m-30) REVERT: I 87 CYS cc_start: 0.6940 (p) cc_final: 0.6536 (p) REVERT: I 230 LEU cc_start: 0.7757 (tp) cc_final: 0.7449 (tp) REVERT: J 165 MET cc_start: 0.7289 (mmt) cc_final: 0.6918 (mmt) REVERT: J 192 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6519 (tm-30) REVERT: K 38 TYR cc_start: 0.8390 (m-10) cc_final: 0.8042 (m-80) REVERT: L 62 ASN cc_start: 0.8097 (m-40) cc_final: 0.7891 (m-40) outliers start: 129 outliers final: 69 residues processed: 509 average time/residue: 0.1908 time to fit residues: 153.7809 Evaluate side-chains 415 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 341 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 27 HIS Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 243 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 HIS ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN J 184 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 327 ASN L 337 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.134018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.107046 restraints weight = 79664.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.109049 restraints weight = 45647.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.109506 restraints weight = 31984.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.110488 restraints weight = 27913.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.110432 restraints weight = 25594.701| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30848 Z= 0.134 Angle : 0.668 15.015 43753 Z= 0.341 Chirality : 0.040 0.200 5283 Planarity : 0.005 0.072 4022 Dihedral : 21.054 156.155 9381 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 3.79 % Allowed : 17.46 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -3.18 (0.15), residues: 2559 helix: -1.41 (0.17), residues: 802 sheet: -1.26 (0.22), residues: 512 loop : -3.01 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 100 TYR 0.018 0.002 TYR G 70 PHE 0.021 0.002 PHE I 41 TRP 0.027 0.002 TRP B 708 HIS 0.011 0.001 HIS E 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (30847) covalent geometry : angle 0.66789 / 0.34 (43753) hydrogen bonds : bond 0.05479 / 6.00 ( 823) hydrogen bonds : angle 5.51005 / 6.93 ( 2108) metal coordination : bond 0.00099 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 380 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6671 (ppp) REVERT: B 235 TYR cc_start: 0.7759 (t80) cc_final: 0.7522 (t80) REVERT: B 247 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7283 (pp) REVERT: B 427 MET cc_start: 0.6416 (tpt) cc_final: 0.6127 (tpt) REVERT: B 429 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7873 (ptm) REVERT: C 180 LEU cc_start: 0.8910 (tp) cc_final: 0.8557 (mp) REVERT: D 135 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7989 (pp) REVERT: D 206 GLU cc_start: 0.7992 (mp0) cc_final: 0.7315 (mp0) REVERT: E 136 GLU cc_start: 0.8655 (pp20) cc_final: 0.8262 (tp30) REVERT: F 4 PHE cc_start: 0.7286 (m-80) cc_final: 0.6905 (m-80) REVERT: G 83 ASN cc_start: 0.8519 (t0) cc_final: 0.8038 (t0) REVERT: G 109 ASP cc_start: 0.7762 (m-30) cc_final: 0.7509 (t70) REVERT: H 50 ASP cc_start: 0.7820 (m-30) cc_final: 0.7512 (m-30) REVERT: I 45 LYS cc_start: 0.6953 (mmmt) cc_final: 0.6638 (tptt) REVERT: J 165 MET cc_start: 0.7405 (mmt) cc_final: 0.6957 (mmt) REVERT: J 192 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6556 (tm-30) REVERT: L 62 ASN cc_start: 0.7811 (m-40) cc_final: 0.7605 (m-40) outliers start: 86 outliers final: 54 residues processed: 438 average time/residue: 0.1810 time to fit residues: 127.0176 Evaluate side-chains 406 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 348 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 978 CYS Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 203 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 241 optimal weight: 0.3980 chunk 269 optimal weight: 1.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 138 HIS B 205 HIS ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN ** B 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.130299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.102496 restraints weight = 80238.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.104586 restraints weight = 49512.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105095 restraints weight = 32637.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.105791 restraints weight = 28770.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.106012 restraints weight = 27284.369| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 30848 Z= 0.204 Angle : 0.691 16.653 43753 Z= 0.358 Chirality : 0.042 0.212 5283 Planarity : 0.006 0.072 4022 Dihedral : 21.074 153.186 9381 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.84 % Favored : 88.12 % Rotamer: Outliers : 4.59 % Allowed : 17.72 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -3.04 (0.16), residues: 2559 helix: -1.16 (0.17), residues: 823 sheet: -1.30 (0.22), residues: 507 loop : -2.98 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 154 TYR 0.029 0.002 TYR F 99 PHE 0.029 0.002 PHE B 310 TRP 0.030 0.002 TRP B 708 HIS 0.010 0.002 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (30847) covalent geometry : angle 0.69051 / 0.36 (43753) hydrogen bonds : bond 0.05771 / 6.41 ( 823) hydrogen bonds : angle 5.39845 / 6.80 ( 2108) metal coordination : bond 0.00228 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 364 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7625 (p90) REVERT: B 427 MET cc_start: 0.6741 (tpt) cc_final: 0.6541 (tpt) REVERT: B 434 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8307 (mt) REVERT: C 180 LEU cc_start: 0.8997 (tp) cc_final: 0.8599 (mp) REVERT: C 203 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7609 (pp) REVERT: D 135 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8122 (pp) REVERT: D 206 GLU cc_start: 0.8015 (mp0) cc_final: 0.7292 (mp0) REVERT: E 136 GLU cc_start: 0.8596 (pp20) cc_final: 0.8378 (tm-30) REVERT: F 4 PHE cc_start: 0.7442 (m-80) cc_final: 0.7091 (m-80) REVERT: F 99 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6202 (t80) REVERT: G 45 PHE cc_start: 0.7990 (t80) cc_final: 0.7560 (t80) REVERT: G 52 CYS cc_start: 0.8164 (m) cc_final: 0.7781 (m) REVERT: G 83 ASN cc_start: 0.8426 (t0) cc_final: 0.7826 (t0) REVERT: G 109 ASP cc_start: 0.7890 (m-30) cc_final: 0.7535 (t0) REVERT: H 50 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: I 175 ASN cc_start: 0.8240 (m110) cc_final: 0.7923 (m110) REVERT: I 196 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7208 (mp0) REVERT: J 165 MET cc_start: 0.7685 (mmt) cc_final: 0.7081 (mmt) REVERT: J 192 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6651 (tm-30) REVERT: K 18 TYR cc_start: 0.7620 (t80) cc_final: 0.7353 (t80) REVERT: L 62 ASN cc_start: 0.8001 (m-40) cc_final: 0.7788 (m-40) REVERT: L 351 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8304 (tp) outliers start: 104 outliers final: 69 residues processed: 436 average time/residue: 0.1852 time to fit residues: 128.4943 Evaluate side-chains 400 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 324 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 250 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 247 optimal weight: 0.5980 chunk 268 optimal weight: 3.9990 chunk 279 optimal weight: 0.0030 chunk 48 optimal weight: 0.3980 chunk 202 optimal weight: 30.0000 chunk 122 optimal weight: 0.0470 chunk 293 optimal weight: 50.0000 overall best weight: 0.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN J 184 ASN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS L 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.132851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.104797 restraints weight = 79419.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.107975 restraints weight = 45979.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.108356 restraints weight = 28144.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.108705 restraints weight = 25904.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108832 restraints weight = 25356.950| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30848 Z= 0.119 Angle : 0.645 15.685 43753 Z= 0.327 Chirality : 0.039 0.205 5283 Planarity : 0.005 0.079 4022 Dihedral : 21.066 155.609 9381 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 3.75 % Allowed : 19.58 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.84 (0.16), residues: 2559 helix: -0.95 (0.17), residues: 821 sheet: -1.18 (0.22), residues: 522 loop : -2.91 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 137 TYR 0.028 0.002 TYR F 99 PHE 0.018 0.002 PHE B 310 TRP 0.025 0.001 TRP B 708 HIS 0.022 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (30847) covalent geometry : angle 0.64487 / 0.33 (43753) hydrogen bonds : bond 0.05006 / 5.59 ( 823) hydrogen bonds : angle 5.22577 / 6.63 ( 2108) metal coordination : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 373 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 429 MET cc_start: 0.8255 (ptm) cc_final: 0.7958 (ptm) REVERT: B 575 MET cc_start: 0.7802 (mtt) cc_final: 0.7546 (mtt) REVERT: B 992 ASP cc_start: 0.7808 (m-30) cc_final: 0.7601 (m-30) REVERT: C 180 LEU cc_start: 0.8931 (tp) cc_final: 0.8569 (mp) REVERT: C 185 ASN cc_start: 0.2019 (m-40) cc_final: 0.0627 (p0) REVERT: C 203 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7682 (pp) REVERT: D 79 ARG cc_start: 0.6040 (mmt180) cc_final: 0.5546 (mmm160) REVERT: D 86 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5653 (tt) REVERT: D 135 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8073 (pp) REVERT: D 160 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6530 (tm-30) REVERT: D 203 ARG cc_start: 0.6457 (ttm110) cc_final: 0.5767 (ttm110) REVERT: D 206 GLU cc_start: 0.7826 (mp0) cc_final: 0.7079 (mp0) REVERT: E 136 GLU cc_start: 0.8674 (pp20) cc_final: 0.8345 (tp30) REVERT: E 140 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7394 (mtmm) REVERT: F 4 PHE cc_start: 0.7384 (m-80) cc_final: 0.7052 (m-80) REVERT: F 99 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.6106 (t80) REVERT: G 45 PHE cc_start: 0.7792 (t80) cc_final: 0.7362 (t80) REVERT: G 52 CYS cc_start: 0.7970 (m) cc_final: 0.7627 (m) REVERT: G 70 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.5541 (p90) REVERT: G 83 ASN cc_start: 0.8416 (t0) cc_final: 0.8015 (t0) REVERT: G 109 ASP cc_start: 0.7746 (m-30) cc_final: 0.7532 (t70) REVERT: H 50 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: H 103 ARG cc_start: 0.6624 (mpt-90) cc_final: 0.6367 (mtt90) REVERT: H 106 GLN cc_start: 0.8287 (tt0) cc_final: 0.7911 (tt0) REVERT: I 45 LYS cc_start: 0.6984 (mmmt) cc_final: 0.6768 (mmmt) REVERT: I 196 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7067 (mp0) REVERT: J 165 MET cc_start: 0.7530 (mmt) cc_final: 0.6972 (mmt) REVERT: J 192 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6608 (tm-30) REVERT: K 30 GLU cc_start: 0.7548 (mp0) cc_final: 0.7323 (pm20) REVERT: K 38 TYR cc_start: 0.7899 (m-80) cc_final: 0.7416 (m-80) REVERT: L 62 ASN cc_start: 0.7790 (m-40) cc_final: 0.7568 (m-40) REVERT: L 236 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.7154 (mtp85) outliers start: 85 outliers final: 56 residues processed: 435 average time/residue: 0.1822 time to fit residues: 126.5525 Evaluate side-chains 397 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 335 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 163 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 184 ASN Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 114 optimal weight: 0.0770 chunk 106 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 21 optimal weight: 40.0000 chunk 55 optimal weight: 0.0000 chunk 143 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN B 720 GLN C 42 HIS ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.131121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.103110 restraints weight = 80397.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105801 restraints weight = 48062.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.106049 restraints weight = 30358.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106390 restraints weight = 28864.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.106679 restraints weight = 26756.651| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30848 Z= 0.152 Angle : 0.646 16.996 43753 Z= 0.331 Chirality : 0.040 0.307 5283 Planarity : 0.005 0.074 4022 Dihedral : 21.043 154.804 9381 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.49 % Favored : 88.47 % Rotamer: Outliers : 4.45 % Allowed : 19.49 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.78 (0.16), residues: 2559 helix: -0.87 (0.18), residues: 837 sheet: -1.15 (0.22), residues: 524 loop : -2.93 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 100 TYR 0.027 0.002 TYR F 99 PHE 0.025 0.002 PHE I 4 TRP 0.025 0.002 TRP B 708 HIS 0.005 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (30847) covalent geometry : angle 0.64643 / 0.33 (43753) hydrogen bonds : bond 0.05131 / 5.80 ( 823) hydrogen bonds : angle 5.13726 / 6.49 ( 2108) metal coordination : bond 0.00123 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 345 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.4112 (OUTLIER) cc_final: 0.3597 (tmm) REVERT: B 552 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6807 (t80) REVERT: B 575 MET cc_start: 0.7863 (mtt) cc_final: 0.7565 (mtt) REVERT: B 678 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7750 (ttmm) REVERT: B 992 ASP cc_start: 0.7884 (m-30) cc_final: 0.7664 (m-30) REVERT: C 41 MET cc_start: 0.6450 (mpp) cc_final: 0.6223 (mpp) REVERT: C 180 LEU cc_start: 0.8928 (tp) cc_final: 0.8561 (mp) REVERT: C 185 ASN cc_start: 0.2042 (m-40) cc_final: 0.0680 (p0) REVERT: C 203 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7736 (pp) REVERT: C 227 GLN cc_start: 0.6799 (pm20) cc_final: 0.6535 (pm20) REVERT: D 79 ARG cc_start: 0.5864 (mmt180) cc_final: 0.5406 (mmm160) REVERT: D 86 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5537 (tt) REVERT: D 135 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8076 (pp) REVERT: D 160 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6835 (tm-30) REVERT: D 206 GLU cc_start: 0.7916 (mp0) cc_final: 0.7575 (mp0) REVERT: E 136 GLU cc_start: 0.8629 (pp20) cc_final: 0.8228 (tp30) REVERT: F 4 PHE cc_start: 0.7402 (m-80) cc_final: 0.7131 (m-80) REVERT: F 99 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6145 (t80) REVERT: G 45 PHE cc_start: 0.7690 (t80) cc_final: 0.7442 (t80) REVERT: G 52 CYS cc_start: 0.8011 (m) cc_final: 0.7671 (m) REVERT: G 70 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.5533 (p90) REVERT: G 83 ASN cc_start: 0.8468 (t0) cc_final: 0.7414 (t0) REVERT: G 109 ASP cc_start: 0.7774 (m-30) cc_final: 0.7544 (t70) REVERT: H 50 ASP cc_start: 0.7733 (m-30) cc_final: 0.7379 (m-30) REVERT: H 54 GLU cc_start: 0.6432 (pt0) cc_final: 0.5642 (pt0) REVERT: H 106 GLN cc_start: 0.8359 (tt0) cc_final: 0.8025 (tt0) REVERT: I 153 GLU cc_start: 0.8061 (tp30) cc_final: 0.7725 (tp30) REVERT: I 166 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6989 (tpp80) REVERT: I 196 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6974 (mp0) REVERT: J 165 MET cc_start: 0.7612 (mmt) cc_final: 0.7022 (mmt) REVERT: K 38 TYR cc_start: 0.8143 (m-80) cc_final: 0.7745 (m-80) REVERT: K 40 TYR cc_start: 0.7895 (t80) cc_final: 0.7649 (t80) outliers start: 101 outliers final: 73 residues processed: 415 average time/residue: 0.1811 time to fit residues: 120.1417 Evaluate side-chains 403 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 322 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 163 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 171 GLU Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 137 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 197 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS C 58 GLN C 108 HIS ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.100352 restraints weight = 80438.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.102605 restraints weight = 47070.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.102830 restraints weight = 32758.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.103283 restraints weight = 30610.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.103326 restraints weight = 28004.418| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30848 Z= 0.206 Angle : 0.709 16.421 43753 Z= 0.362 Chirality : 0.043 0.375 5283 Planarity : 0.006 0.090 4022 Dihedral : 21.090 152.513 9381 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 4.63 % Allowed : 19.75 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.79 (0.16), residues: 2559 helix: -0.83 (0.17), residues: 850 sheet: -1.21 (0.22), residues: 514 loop : -2.95 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 95 TYR 0.027 0.002 TYR F 99 PHE 0.020 0.002 PHE I 4 TRP 0.026 0.002 TRP B 708 HIS 0.031 0.002 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (30847) covalent geometry : angle 0.70936 / 0.36 (43753) hydrogen bonds : bond 0.05501 / 6.18 ( 823) hydrogen bonds : angle 5.21504 / 6.59 ( 2108) metal coordination : bond 0.00131 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 354 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.4507 (tmm) cc_final: 0.4046 (tmm) REVERT: B 244 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8538 (pt) REVERT: B 249 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7921 (p90) REVERT: B 312 TRP cc_start: 0.7449 (OUTLIER) cc_final: 0.7147 (m100) REVERT: B 552 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 678 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7876 (ttmm) REVERT: C 180 LEU cc_start: 0.8921 (tp) cc_final: 0.8535 (mp) REVERT: C 185 ASN cc_start: 0.2115 (m-40) cc_final: 0.0710 (p0) REVERT: C 203 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7737 (pp) REVERT: D 86 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5559 (tt) REVERT: D 135 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8085 (pp) REVERT: D 160 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 206 GLU cc_start: 0.8051 (mp0) cc_final: 0.7482 (mp0) REVERT: F 4 PHE cc_start: 0.7562 (m-80) cc_final: 0.7305 (m-80) REVERT: G 45 PHE cc_start: 0.8095 (t80) cc_final: 0.7325 (t80) REVERT: G 52 CYS cc_start: 0.8115 (m) cc_final: 0.7748 (m) REVERT: G 70 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5423 (p90) REVERT: G 83 ASN cc_start: 0.8506 (t0) cc_final: 0.7641 (t0) REVERT: G 109 ASP cc_start: 0.7779 (m-30) cc_final: 0.7463 (t0) REVERT: H 50 ASP cc_start: 0.7754 (m-30) cc_final: 0.7354 (m-30) REVERT: I 166 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7241 (tpp80) REVERT: I 196 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7069 (mp0) REVERT: J 165 MET cc_start: 0.7860 (mmt) cc_final: 0.7288 (mmt) REVERT: K 38 TYR cc_start: 0.8261 (m-80) cc_final: 0.7860 (m-80) REVERT: K 113 ARG cc_start: 0.6158 (ttt180) cc_final: 0.5940 (ttt-90) REVERT: L 236 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7303 (mtp85) outliers start: 105 outliers final: 81 residues processed: 424 average time/residue: 0.1839 time to fit residues: 125.1835 Evaluate side-chains 427 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 337 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 163 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 209 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 50.0000 chunk 159 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 HIS ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS I 65 GLN ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.130095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101916 restraints weight = 79839.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104322 restraints weight = 47543.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.104687 restraints weight = 31604.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105051 restraints weight = 29655.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.105099 restraints weight = 28104.673| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30848 Z= 0.138 Angle : 0.666 16.629 43753 Z= 0.340 Chirality : 0.040 0.202 5283 Planarity : 0.005 0.073 4022 Dihedral : 21.095 153.773 9381 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 4.19 % Allowed : 20.81 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % 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: -2.70 (0.16), residues: 2559 helix: -0.73 (0.17), residues: 846 sheet: -1.19 (0.22), residues: 510 loop : -2.90 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 5 TYR 0.026 0.002 TYR F 99 PHE 0.025 0.002 PHE I 4 TRP 0.024 0.002 TRP B 708 HIS 0.014 0.001 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30847) covalent geometry : angle 0.66562 / 0.34 (43753) hydrogen bonds : bond 0.05035 / 5.68 ( 823) hydrogen bonds : angle 5.12907 / 6.50 ( 2108) metal coordination : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 346 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.3907 (tmm) REVERT: B 249 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7531 (p90) REVERT: B 552 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6723 (t80) REVERT: C 180 LEU cc_start: 0.8847 (tp) cc_final: 0.8539 (mp) REVERT: C 185 ASN cc_start: 0.1918 (m-40) cc_final: 0.0761 (p0) REVERT: C 203 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7707 (pp) REVERT: C 227 GLN cc_start: 0.6971 (pm20) cc_final: 0.6627 (pm20) REVERT: D 86 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5498 (tt) REVERT: D 135 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8043 (pp) REVERT: D 160 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 206 GLU cc_start: 0.8039 (mp0) cc_final: 0.7580 (mp0) REVERT: E 140 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7666 (mtmm) REVERT: F 4 PHE cc_start: 0.7522 (m-80) cc_final: 0.7292 (m-80) REVERT: F 80 CYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8364 (t) REVERT: G 45 PHE cc_start: 0.8087 (t80) cc_final: 0.7253 (t80) REVERT: G 52 CYS cc_start: 0.8074 (m) cc_final: 0.7702 (m) REVERT: G 70 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.5453 (p90) REVERT: G 83 ASN cc_start: 0.8464 (t0) cc_final: 0.7828 (t0) REVERT: G 109 ASP cc_start: 0.7751 (m-30) cc_final: 0.7525 (t70) REVERT: H 50 ASP cc_start: 0.7670 (m-30) cc_final: 0.7253 (m-30) REVERT: I 166 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7032 (tpp80) REVERT: I 196 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6965 (mp0) REVERT: J 77 LEU cc_start: 0.9006 (tp) cc_final: 0.8518 (tp) REVERT: J 165 MET cc_start: 0.7893 (mmt) cc_final: 0.7349 (mmt) REVERT: J 178 GLN cc_start: 0.7420 (pt0) cc_final: 0.7186 (pt0) REVERT: J 192 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6713 (tm-30) REVERT: K 38 TYR cc_start: 0.8168 (m-80) cc_final: 0.7735 (m-80) REVERT: L 194 MET cc_start: 0.8002 (mmm) cc_final: 0.7705 (mpp) REVERT: L 236 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.7291 (mtp85) outliers start: 95 outliers final: 73 residues processed: 405 average time/residue: 0.1782 time to fit residues: 115.5286 Evaluate side-chains 412 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 330 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 413 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 163 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 184 ASN Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 246 LYS Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 0.0370 chunk 29 optimal weight: 30.0000 chunk 235 optimal weight: 0.4980 chunk 245 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.130075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101968 restraints weight = 79601.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104541 restraints weight = 46431.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104533 restraints weight = 31418.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.104777 restraints weight = 30225.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.105944 restraints weight = 28095.681| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.335 30848 Z= 0.182 Angle : 0.774 59.198 43753 Z= 0.420 Chirality : 0.041 0.507 5283 Planarity : 0.006 0.132 4022 Dihedral : 21.099 153.850 9381 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 3.88 % Allowed : 21.47 % Favored : 74.65 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.70 (0.16), residues: 2559 helix: -0.74 (0.17), residues: 847 sheet: -1.18 (0.22), residues: 510 loop : -2.90 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 574 TYR 0.028 0.002 TYR F 99 PHE 0.027 0.002 PHE I 4 TRP 0.024 0.002 TRP B 708 HIS 0.209 0.003 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (30847) covalent geometry : angle 0.77415 / 0.42 (43753) hydrogen bonds : bond 0.05022 / 5.67 ( 823) hydrogen bonds : angle 5.13041 / 6.50 ( 2108) metal coordination : bond 0.00038 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 328 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.4385 (OUTLIER) cc_final: 0.3870 (tmm) REVERT: B 249 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7553 (p90) REVERT: B 552 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6735 (t80) REVERT: C 42 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8440 (t-170) REVERT: C 180 LEU cc_start: 0.8904 (tp) cc_final: 0.8552 (mp) REVERT: C 185 ASN cc_start: 0.2010 (m-40) cc_final: 0.0819 (p0) REVERT: C 203 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7744 (pp) REVERT: C 227 GLN cc_start: 0.6971 (pm20) cc_final: 0.6640 (pm20) REVERT: D 135 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8059 (pp) REVERT: D 160 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7152 (tm-30) REVERT: D 206 GLU cc_start: 0.8122 (mp0) cc_final: 0.7575 (mp0) REVERT: E 140 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7720 (mtmm) REVERT: F 4 PHE cc_start: 0.7560 (m-80) cc_final: 0.7317 (m-80) REVERT: F 80 CYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8425 (t) REVERT: G 45 PHE cc_start: 0.8126 (t80) cc_final: 0.7276 (t80) REVERT: G 52 CYS cc_start: 0.8164 (m) cc_final: 0.7774 (m) REVERT: G 70 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.5421 (p90) REVERT: G 83 ASN cc_start: 0.8606 (t0) cc_final: 0.7946 (t0) REVERT: G 109 ASP cc_start: 0.7806 (m-30) cc_final: 0.7509 (t70) REVERT: H 50 ASP cc_start: 0.7736 (m-30) cc_final: 0.7297 (m-30) REVERT: I 166 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7097 (tpp80) REVERT: I 196 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6982 (mp0) REVERT: J 77 LEU cc_start: 0.8883 (tp) cc_final: 0.8645 (tp) REVERT: J 165 MET cc_start: 0.7957 (mmt) cc_final: 0.7391 (mmt) REVERT: J 178 GLN cc_start: 0.7503 (pt0) cc_final: 0.7247 (pt0) REVERT: J 192 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6766 (tm-30) REVERT: K 38 TYR cc_start: 0.8246 (m-80) cc_final: 0.7813 (m-80) REVERT: L 194 MET cc_start: 0.8023 (mmm) cc_final: 0.7696 (mpp) REVERT: L 236 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.7300 (mtp85) outliers start: 88 outliers final: 75 residues processed: 384 average time/residue: 0.1784 time to fit residues: 109.3048 Evaluate side-chains 411 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 327 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 413 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 163 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 184 ASN Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 246 LYS Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 212 SER Chi-restraints excluded: chain L residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 104 optimal weight: 0.0570 chunk 5 optimal weight: 50.0000 chunk 290 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 61 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 chunk 258 optimal weight: 0.0570 chunk 271 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.130048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.101949 restraints weight = 80441.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.104046 restraints weight = 46130.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104325 restraints weight = 32768.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.104755 restraints weight = 30172.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104863 restraints weight = 28416.017| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.335 30848 Z= 0.183 Angle : 0.746 47.155 43753 Z= 0.399 Chirality : 0.041 0.467 5283 Planarity : 0.006 0.132 4022 Dihedral : 21.099 153.850 9381 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 3.70 % Allowed : 21.56 % Favored : 74.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % 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: -2.70 (0.16), residues: 2559 helix: -0.74 (0.17), residues: 847 sheet: -1.18 (0.22), residues: 510 loop : -2.90 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 574 TYR 0.028 0.002 TYR F 99 PHE 0.027 0.002 PHE I 4 TRP 0.024 0.002 TRP B 708 HIS 0.209 0.003 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (30847) covalent geometry : angle 0.74587 / 0.40 (43753) hydrogen bonds : bond 0.05022 / 5.67 ( 823) hydrogen bonds : angle 5.13041 / 6.50 ( 2108) metal coordination : bond 0.00038 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5015.04 seconds wall clock time: 87 minutes 33.59 seconds (5253.59 seconds total)