Starting phenix.real_space_refine on Thu Mar 21 05:27:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/03_2024/6ahu_9627_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/03_2024/6ahu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/03_2024/6ahu_9627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/03_2024/6ahu_9627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/03_2024/6ahu_9627_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahu_9627/03_2024/6ahu_9627_neut.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 640": "NH1" <-> "NH2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B ARG 831": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B ARG 1008": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 15.60, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 13.12 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 10.23 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: 12.82 Time building geometry restraints manager: 13.96 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: 99.47 - 106.41: 3038 106.41 - 113.35: 17367 113.35 - 120.30: 11609 120.30 - 127.24: 10681 127.24 - 134.18: 1058 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=" 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 angle pdb=" C THR E 106 " pdb=" N ILE E 107 " pdb=" CA ILE E 107 " ideal model delta sigma weight residual 120.53 127.69 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" CA LEU H 92 " pdb=" CB LEU H 92 " pdb=" CG LEU H 92 " ideal model delta sigma weight residual 116.30 132.91 -16.61 3.50e+00 8.16e-02 2.25e+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: 4970 0.089 - 0.178: 298 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 2.440 nonbonded pdb=" O TRP H 86 " pdb=" OG1 THR H 90 " model vdw 2.291 2.440 nonbonded pdb=" O ILE B 493 " pdb=" NH2 ARG G 25 " model vdw 2.294 2.520 nonbonded pdb=" O2' A A 32 " pdb=" O VAL G 39 " model vdw 2.301 2.440 nonbonded pdb=" O2' A T 58 " pdb=" OP2 A T 60 " model vdw 2.322 2.440 ... (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 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: 0.900 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: 5.370 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 90.590 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30847 Z= 0.202 Angle : 0.770 16.606 43753 Z= 0.422 Chirality : 0.041 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.002 TRP B 708 HIS 0.007 0.001 HIS K 22 PHE 0.029 0.002 PHE L 260 TYR 0.025 0.001 TYR G 70 ARG 0.008 0.000 ARG D 207 *********************** 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 fitting. rotamer outliers: 2 poor density : 925 time to evaluate : 2.387 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 261 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6655 (mm-30) REVERT: B 340 LEU cc_start: 0.8062 (tp) cc_final: 0.7813 (tt) REVERT: C 30 ILE cc_start: 0.7827 (mt) cc_final: 0.7011 (pt) REVERT: C 180 LEU cc_start: 0.8922 (tp) cc_final: 0.8624 (mt) REVERT: C 207 TRP cc_start: 0.2453 (t-100) cc_final: 0.1657 (t-100) REVERT: D 140 ILE cc_start: 0.7379 (pp) cc_final: 0.7048 (pp) REVERT: D 180 LEU cc_start: 0.7683 (mt) cc_final: 0.7474 (mt) REVERT: D 205 SER cc_start: 0.8550 (p) cc_final: 0.8047 (p) REVERT: F 6 LYS cc_start: 0.6821 (mttt) cc_final: 0.6562 (mmtm) REVERT: F 80 CYS cc_start: 0.7764 (t) cc_final: 0.7220 (t) REVERT: G 83 ASN cc_start: 0.7478 (t0) cc_final: 0.7221 (t0) REVERT: G 109 ASP cc_start: 0.8263 (m-30) cc_final: 0.7771 (t70) REVERT: I 224 ASN cc_start: 0.8147 (m-40) cc_final: 0.7858 (m-40) REVERT: J 100 TYR cc_start: 0.6060 (m-10) cc_final: 0.5856 (m-10) REVERT: J 155 VAL cc_start: 0.8589 (t) cc_final: 0.8083 (m) REVERT: K 6 LYS cc_start: 0.5527 (tttt) cc_final: 0.5313 (mptt) REVERT: K 39 CYS cc_start: 0.6215 (t) cc_final: 0.5600 (t) REVERT: K 40 TYR cc_start: 0.7817 (t80) cc_final: 0.7370 (t80) REVERT: K 47 LYS cc_start: 0.8324 (tttt) cc_final: 0.7968 (ttpp) REVERT: K 73 LEU cc_start: 0.7640 (pp) cc_final: 0.7228 (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: 0.8188 (tp) outliers start: 2 outliers final: 0 residues processed: 927 average time/residue: 0.5173 time to fit residues: 718.6318 Evaluate side-chains 441 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 119 optimal weight: 0.2980 chunk 232 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 172 optimal weight: 0.0670 chunk 268 optimal weight: 7.9990 overall best weight: 1.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 802 HIS B 958 HIS ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS E 75 GLN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 148 GLN ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN I 27 HIS I 88 ASN I 143 ASN ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 224 ASN J 27 HIS J 143 ASN J 231 HIS ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS L 29 HIS L 36 HIS L 39 ASN L 203 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS L 337 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30847 Z= 0.241 Angle : 0.710 14.925 43753 Z= 0.357 Chirality : 0.041 0.314 5283 Planarity : 0.006 0.064 4022 Dihedral : 21.066 155.950 9381 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.36 % Favored : 89.57 % Rotamer: Outliers : 3.88 % Allowed : 13.10 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.14), residues: 2559 helix: -2.85 (0.13), residues: 796 sheet: -1.45 (0.22), residues: 509 loop : -3.15 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 708 HIS 0.008 0.001 HIS B 958 PHE 0.021 0.002 PHE B 704 TYR 0.023 0.002 TYR L 339 ARG 0.032 0.001 ARG C 194 *********************** 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 560 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 472 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7799 (t) REVERT: B 720 GLN cc_start: 0.7687 (mm-40) cc_final: 0.6940 (pp30) REVERT: C 30 ILE cc_start: 0.7878 (mt) cc_final: 0.7463 (tp) REVERT: C 42 HIS cc_start: 0.8167 (t70) cc_final: 0.7654 (t70) REVERT: C 180 LEU cc_start: 0.8867 (tp) cc_final: 0.8516 (mp) REVERT: D 82 ARG cc_start: 0.6701 (mmm160) cc_final: 0.6252 (mmt-90) REVERT: D 85 ARG cc_start: 0.5308 (ttp-110) cc_final: 0.4841 (ttp-170) REVERT: D 135 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7841 (pp) REVERT: D 180 LEU cc_start: 0.8003 (mt) cc_final: 0.7794 (mt) REVERT: E 86 TYR cc_start: 0.5982 (t80) cc_final: 0.5691 (t80) REVERT: E 140 LYS cc_start: 0.8198 (mttt) cc_final: 0.7646 (mtmm) REVERT: F 59 GLN cc_start: 0.3272 (OUTLIER) cc_final: 0.2478 (pt0) REVERT: F 79 THR cc_start: 0.7894 (p) cc_final: 0.7682 (t) REVERT: F 91 LEU cc_start: 0.6513 (tp) cc_final: 0.6261 (tp) REVERT: G 45 PHE cc_start: 0.8175 (t80) cc_final: 0.7843 (t80) REVERT: G 53 GLN cc_start: 0.8322 (tp40) cc_final: 0.8008 (tp40) REVERT: G 83 ASN cc_start: 0.8416 (t0) cc_final: 0.7895 (t0) REVERT: G 87 GLN cc_start: 0.8231 (tp40) cc_final: 0.7952 (mm-40) REVERT: G 109 ASP cc_start: 0.8079 (m-30) cc_final: 0.7609 (t70) REVERT: G 116 ASP cc_start: 0.5991 (m-30) cc_final: 0.5702 (m-30) REVERT: H 84 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7926 (mttp) REVERT: I 113 PHE cc_start: 0.8374 (t80) cc_final: 0.8070 (t80) REVERT: I 224 ASN cc_start: 0.8554 (m110) cc_final: 0.8324 (m-40) REVERT: J 77 LEU cc_start: 0.8533 (tp) cc_final: 0.8308 (tp) REVERT: J 78 THR cc_start: 0.7820 (m) cc_final: 0.7490 (p) REVERT: J 155 VAL cc_start: 0.8732 (t) cc_final: 0.8460 (m) REVERT: J 165 MET cc_start: 0.6662 (mmt) cc_final: 0.6345 (mmt) REVERT: J 192 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6364 (tm-30) REVERT: K 47 LYS cc_start: 0.8803 (tttt) cc_final: 0.8396 (ttpp) REVERT: K 68 LEU cc_start: 0.6559 (pp) cc_final: 0.6049 (pp) REVERT: L 52 LEU cc_start: 0.6866 (tp) cc_final: 0.6498 (tp) outliers start: 88 outliers final: 56 residues processed: 535 average time/residue: 0.4241 time to fit residues: 352.1131 Evaluate side-chains 435 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 376 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 978 CYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 132 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 163 HIS 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 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 88 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 84 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER 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 179 ILE Chi-restraints excluded: chain I residue 223 THR 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 180 CYS Chi-restraints excluded: chain J residue 221 VAL 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 28 ASP Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 223 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 239 optimal weight: 0.1980 chunk 267 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN B 392 ASN ** B 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 HIS ** B 969 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** C 118 ASN C 146 HIS E 59 ASN E 75 GLN G 35 ASN ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS I 65 GLN I 175 ASN I 184 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN J 224 ASN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS L 39 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS L 327 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30847 Z= 0.157 Angle : 0.616 14.793 43753 Z= 0.308 Chirality : 0.038 0.293 5283 Planarity : 0.005 0.069 4022 Dihedral : 20.979 158.093 9381 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.89 % Favored : 90.07 % Rotamer: Outliers : 3.84 % Allowed : 15.70 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.15), residues: 2559 helix: -1.80 (0.16), residues: 791 sheet: -1.28 (0.22), residues: 516 loop : -3.04 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 708 HIS 0.013 0.001 HIS L 13 PHE 0.022 0.001 PHE F 28 TYR 0.017 0.001 TYR F 151 ARG 0.009 0.000 ARG F 39 *********************** 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 510 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 423 time to evaluate : 2.845 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: B 114 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: B 120 LYS cc_start: 0.7757 (ptmm) cc_final: 0.7128 (tptp) REVERT: B 204 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7772 (t) REVERT: B 331 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6486 (pp) REVERT: B 427 MET cc_start: 0.6335 (tpt) cc_final: 0.6080 (tpt) REVERT: B 720 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7013 (pp30) REVERT: C 41 MET cc_start: 0.5186 (mtt) cc_final: 0.4962 (mtt) REVERT: C 131 LEU cc_start: 0.7307 (tp) cc_final: 0.7065 (tp) REVERT: C 180 LEU cc_start: 0.8884 (tp) cc_final: 0.8529 (mp) REVERT: D 85 ARG cc_start: 0.5372 (ttp-110) cc_final: 0.4885 (ttp-170) REVERT: D 135 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7907 (pp) REVERT: D 180 LEU cc_start: 0.7934 (mt) cc_final: 0.7665 (mt) REVERT: E 64 ILE cc_start: 0.8826 (mm) cc_final: 0.8571 (mm) REVERT: E 86 TYR cc_start: 0.5984 (t80) cc_final: 0.5692 (t80) REVERT: E 140 LYS cc_start: 0.8066 (mttt) cc_final: 0.7705 (mtmm) REVERT: F 91 LEU cc_start: 0.6730 (tp) cc_final: 0.6443 (tp) REVERT: G 45 PHE cc_start: 0.8028 (t80) cc_final: 0.7620 (t80) REVERT: G 53 GLN cc_start: 0.8414 (tp40) cc_final: 0.8084 (tp40) REVERT: G 83 ASN cc_start: 0.8345 (t0) cc_final: 0.7682 (t0) REVERT: G 109 ASP cc_start: 0.7949 (m-30) cc_final: 0.7581 (t70) REVERT: G 116 ASP cc_start: 0.5940 (m-30) cc_final: 0.5654 (m-30) REVERT: G 132 ILE cc_start: 0.9041 (mm) cc_final: 0.8762 (mm) REVERT: I 113 PHE cc_start: 0.8238 (t80) cc_final: 0.8027 (t80) REVERT: J 77 LEU cc_start: 0.8503 (tp) cc_final: 0.8240 (tp) REVERT: J 155 VAL cc_start: 0.8792 (t) cc_final: 0.8540 (m) REVERT: J 165 MET cc_start: 0.6664 (mmt) cc_final: 0.6250 (mmt) REVERT: J 177 MET cc_start: 0.7483 (mmm) cc_final: 0.7270 (mmm) REVERT: J 192 GLU cc_start: 0.6597 (tm-30) cc_final: 0.6340 (tm-30) REVERT: K 47 LYS cc_start: 0.8565 (tttt) cc_final: 0.8213 (ttpp) outliers start: 87 outliers final: 51 residues processed: 483 average time/residue: 0.4040 time to fit residues: 307.4269 Evaluate side-chains 419 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 364 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 392 ASN 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 857 VAL Chi-restraints excluded: chain B residue 958 HIS 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 163 HIS Chi-restraints excluded: chain D residue 165 PHE 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 F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU 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 206 LEU Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 58 LYS Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 166 SER 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 359 ASP Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN B 392 ASN B 538 GLN B 565 ASN B 958 HIS ** B 969 GLN ** 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 146 HIS ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 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** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30847 Z= 0.193 Angle : 0.621 15.708 43753 Z= 0.309 Chirality : 0.038 0.307 5283 Planarity : 0.005 0.072 4022 Dihedral : 20.949 157.302 9381 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.10 % Favored : 88.86 % Rotamer: Outliers : 4.32 % Allowed : 16.18 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.15), residues: 2559 helix: -1.29 (0.17), residues: 818 sheet: -1.12 (0.22), residues: 517 loop : -2.92 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 708 HIS 0.013 0.001 HIS L 29 PHE 0.021 0.002 PHE F 28 TYR 0.022 0.002 TYR K 40 ARG 0.011 0.001 ARG D 82 *********************** 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 485 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 387 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 LYS cc_start: 0.7875 (ptmm) cc_final: 0.7249 (tptp) REVERT: B 139 MET cc_start: 0.6652 (ppp) cc_final: 0.5482 (ppp) REVERT: B 234 CYS cc_start: 0.7451 (m) cc_final: 0.7140 (m) REVERT: B 720 GLN cc_start: 0.7650 (mm-40) cc_final: 0.6970 (pp30) REVERT: C 131 LEU cc_start: 0.7334 (tp) cc_final: 0.7089 (tp) REVERT: C 180 LEU cc_start: 0.8833 (tp) cc_final: 0.8509 (mt) REVERT: C 203 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7787 (pp) REVERT: D 82 ARG cc_start: 0.6923 (mmm160) cc_final: 0.6556 (mmt180) REVERT: D 135 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7896 (pp) REVERT: D 180 LEU cc_start: 0.8015 (mt) cc_final: 0.7783 (mt) REVERT: E 140 LYS cc_start: 0.8138 (mttt) cc_final: 0.7798 (mtmm) REVERT: F 91 LEU cc_start: 0.6622 (tp) cc_final: 0.6377 (tp) REVERT: G 45 PHE cc_start: 0.7987 (t80) cc_final: 0.7615 (t80) REVERT: G 53 GLN cc_start: 0.8346 (tp40) cc_final: 0.7998 (tp40) REVERT: G 83 ASN cc_start: 0.8425 (t0) cc_final: 0.7731 (t0) REVERT: G 116 ASP cc_start: 0.5850 (m-30) cc_final: 0.5474 (m-30) REVERT: I 113 PHE cc_start: 0.8496 (t80) cc_final: 0.8248 (t80) REVERT: J 77 LEU cc_start: 0.8682 (tp) cc_final: 0.8445 (tp) REVERT: J 78 THR cc_start: 0.8046 (m) cc_final: 0.7749 (p) REVERT: J 165 MET cc_start: 0.6902 (mmt) cc_final: 0.6537 (mmt) REVERT: K 16 PHE cc_start: 0.8483 (t80) cc_final: 0.8230 (t80) REVERT: K 38 TYR cc_start: 0.7782 (m-80) cc_final: 0.7516 (m-80) REVERT: K 47 LYS cc_start: 0.8590 (tttt) cc_final: 0.8227 (ttpp) REVERT: K 68 LEU cc_start: 0.7370 (pp) cc_final: 0.6698 (pp) REVERT: K 87 TRP cc_start: 0.6737 (OUTLIER) cc_final: 0.6091 (m-10) outliers start: 98 outliers final: 64 residues processed: 455 average time/residue: 0.4124 time to fit residues: 297.3514 Evaluate side-chains 405 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 338 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 312 TRP Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 868 SER Chi-restraints excluded: chain B residue 958 HIS Chi-restraints excluded: chain B residue 963 LEU 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 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 181 ASN 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 F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 50 MET 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 56 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER 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 223 THR Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU 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 K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 58 LYS Chi-restraints excluded: chain K residue 87 TRP Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 186 THR 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 320 SER Chi-restraints excluded: chain L residue 359 ASP 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 238 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 HIS B 891 HIS B 958 HIS B 969 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS D 136 HIS E 75 GLN ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN K 19 GLN K 22 HIS ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 58 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30847 Z= 0.243 Angle : 0.658 16.583 43753 Z= 0.330 Chirality : 0.040 0.315 5283 Planarity : 0.005 0.074 4022 Dihedral : 20.995 153.389 9381 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.57 % Favored : 88.39 % Rotamer: Outliers : 5.29 % Allowed : 16.89 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.16), residues: 2559 helix: -0.95 (0.18), residues: 820 sheet: -1.19 (0.22), residues: 524 loop : -2.87 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 708 HIS 0.043 0.002 HIS B 958 PHE 0.022 0.002 PHE B 310 TYR 0.020 0.002 TYR K 40 ARG 0.007 0.001 ARG L 28 *********************** 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 513 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 393 time to evaluate : 2.623 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 118 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7349 (tpp) REVERT: B 120 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7410 (tptp) REVERT: B 139 MET cc_start: 0.6921 (ppp) cc_final: 0.5917 (ppp) REVERT: B 310 PHE cc_start: 0.5259 (t80) cc_final: 0.4964 (t80) REVERT: B 312 TRP cc_start: 0.7159 (OUTLIER) cc_final: 0.6841 (m100) REVERT: B 434 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8043 (mt) REVERT: B 507 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (pp) REVERT: B 654 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8536 (ttmt) REVERT: C 131 LEU cc_start: 0.7846 (tp) cc_final: 0.7457 (tp) REVERT: C 180 LEU cc_start: 0.8831 (tp) cc_final: 0.8510 (mt) REVERT: C 203 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7939 (pp) REVERT: D 135 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8040 (pp) REVERT: D 160 GLU cc_start: 0.6773 (tm-30) cc_final: 0.5944 (tm-30) REVERT: D 180 LEU cc_start: 0.8152 (mt) cc_final: 0.7937 (mt) REVERT: E 140 LYS cc_start: 0.8326 (mttt) cc_final: 0.8059 (mtmm) REVERT: F 80 CYS cc_start: 0.8806 (t) cc_final: 0.8385 (t) REVERT: G 53 GLN cc_start: 0.8586 (tp40) cc_final: 0.8288 (tp40) REVERT: G 83 ASN cc_start: 0.8508 (t0) cc_final: 0.8006 (t0) REVERT: G 116 ASP cc_start: 0.6078 (m-30) cc_final: 0.5652 (m-30) REVERT: I 110 GLU cc_start: 0.6395 (mp0) cc_final: 0.6136 (mp0) REVERT: I 175 ASN cc_start: 0.7984 (m110) cc_final: 0.7742 (m110) REVERT: J 77 LEU cc_start: 0.8841 (tp) cc_final: 0.8519 (tp) REVERT: J 165 MET cc_start: 0.7441 (mmt) cc_final: 0.6833 (mmt) REVERT: K 47 LYS cc_start: 0.8616 (tttt) cc_final: 0.8231 (ttpp) REVERT: K 87 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: L 194 MET cc_start: 0.7728 (mmm) cc_final: 0.7505 (mpp) outliers start: 120 outliers final: 78 residues processed: 475 average time/residue: 0.4196 time to fit residues: 314.4039 Evaluate side-chains 421 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 335 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 868 SER Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 SER 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 163 HIS Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 181 ASN 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 F residue 38 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 50 MET Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 88 LEU 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 74 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER 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 68 SER Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU 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 154 LEU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 180 CYS 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 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 87 TRP Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 147 SER Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 186 THR 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 359 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 0.3980 chunk 286 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 0.0000 chunk 150 optimal weight: 0.9980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30847 Z= 0.164 Angle : 0.625 15.846 43753 Z= 0.308 Chirality : 0.039 0.327 5283 Planarity : 0.005 0.102 4022 Dihedral : 20.978 156.764 9381 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.71 % Favored : 89.21 % Rotamer: Outliers : 4.23 % Allowed : 19.22 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.16), residues: 2559 helix: -0.74 (0.18), residues: 833 sheet: -1.03 (0.22), residues: 528 loop : -2.84 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 201 HIS 0.011 0.001 HIS G 72 PHE 0.019 0.001 PHE B 310 TYR 0.025 0.002 TYR G 38 ARG 0.012 0.001 ARG L 6 *********************** 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 472 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 376 time to evaluate : 2.997 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 120 LYS cc_start: 0.8150 (ptmm) cc_final: 0.7497 (tptp) REVERT: B 139 MET cc_start: 0.6930 (ppp) cc_final: 0.5840 (ppp) REVERT: B 434 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7950 (mt) REVERT: B 507 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7512 (pp) REVERT: B 552 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6914 (t80) REVERT: C 131 LEU cc_start: 0.7806 (tp) cc_final: 0.7446 (tp) REVERT: C 180 LEU cc_start: 0.8833 (tp) cc_final: 0.8517 (mt) REVERT: C 185 ASN cc_start: 0.1576 (m-40) cc_final: 0.0297 (p0) REVERT: C 227 GLN cc_start: 0.6868 (pm20) cc_final: 0.6631 (pm20) REVERT: D 85 ARG cc_start: 0.5027 (ttp-110) cc_final: 0.4584 (ttm110) REVERT: D 135 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8002 (pp) REVERT: D 160 GLU cc_start: 0.6393 (tm-30) cc_final: 0.6130 (tm-30) REVERT: D 180 LEU cc_start: 0.7976 (mt) cc_final: 0.7750 (mt) REVERT: D 206 GLU cc_start: 0.7812 (mp0) cc_final: 0.7547 (pm20) REVERT: E 125 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7412 (tp) REVERT: E 136 GLU cc_start: 0.8690 (tp30) cc_final: 0.8433 (tp30) REVERT: E 140 LYS cc_start: 0.8272 (mttt) cc_final: 0.8033 (mtmm) REVERT: F 80 CYS cc_start: 0.8799 (t) cc_final: 0.8392 (t) REVERT: G 45 PHE cc_start: 0.8224 (t80) cc_final: 0.7473 (t80) REVERT: G 53 GLN cc_start: 0.8551 (tp40) cc_final: 0.8233 (tp40) REVERT: G 83 ASN cc_start: 0.8582 (t0) cc_final: 0.8072 (t0) REVERT: G 116 ASP cc_start: 0.6055 (m-30) cc_final: 0.5744 (m-30) REVERT: I 113 PHE cc_start: 0.8519 (t80) cc_final: 0.8299 (t80) REVERT: J 77 LEU cc_start: 0.8718 (tp) cc_final: 0.8495 (tp) REVERT: J 165 MET cc_start: 0.7415 (mmt) cc_final: 0.6811 (mmt) REVERT: K 38 TYR cc_start: 0.8148 (m-80) cc_final: 0.7464 (m-80) REVERT: K 47 LYS cc_start: 0.8359 (tttt) cc_final: 0.8014 (tttp) REVERT: K 87 TRP cc_start: 0.7268 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: L 194 MET cc_start: 0.7809 (mmm) cc_final: 0.7515 (mpp) REVERT: L 236 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.7139 (mtp85) outliers start: 96 outliers final: 65 residues processed: 442 average time/residue: 0.4082 time to fit residues: 286.0625 Evaluate side-chains 404 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 333 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 413 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 868 SER Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 135 LEU 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 181 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 125 LEU 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 50 MET Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER 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 41 PHE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 87 TRP Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 29 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 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 359 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 285 optimal weight: 0.1980 chunk 178 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 HIS ** B 602 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 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN E 75 GLN F 37 HIS ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30847 Z= 0.161 Angle : 0.621 15.948 43753 Z= 0.306 Chirality : 0.038 0.362 5283 Planarity : 0.005 0.083 4022 Dihedral : 20.947 159.439 9381 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.82 % Favored : 89.14 % Rotamer: Outliers : 3.92 % Allowed : 20.19 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2559 helix: -0.57 (0.18), residues: 828 sheet: -1.02 (0.22), residues: 534 loop : -2.73 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 708 HIS 0.020 0.001 HIS L 29 PHE 0.019 0.001 PHE J 41 TYR 0.026 0.002 TYR F 99 ARG 0.007 0.000 ARG D 82 *********************** 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 454 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 365 time to evaluate : 2.696 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 120 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7528 (tptp) REVERT: B 139 MET cc_start: 0.6939 (ppp) cc_final: 0.5820 (ppp) REVERT: B 144 MET cc_start: 0.4699 (tmm) cc_final: 0.4355 (tmm) REVERT: B 336 LYS cc_start: 0.8467 (tppt) cc_final: 0.8218 (tppt) REVERT: B 434 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7918 (mt) REVERT: B 552 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.6899 (t80) REVERT: B 692 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7929 (ptt90) REVERT: C 131 LEU cc_start: 0.7817 (tp) cc_final: 0.7443 (tp) REVERT: C 180 LEU cc_start: 0.8833 (tp) cc_final: 0.8524 (mt) REVERT: C 185 ASN cc_start: 0.1514 (m-40) cc_final: 0.0284 (p0) REVERT: C 203 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7932 (pp) REVERT: C 227 GLN cc_start: 0.6919 (pm20) cc_final: 0.6676 (pm20) REVERT: D 135 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8004 (pp) REVERT: D 160 GLU cc_start: 0.6341 (tm-30) cc_final: 0.5985 (tm-30) REVERT: D 206 GLU cc_start: 0.7840 (mp0) cc_final: 0.7424 (pm20) REVERT: F 80 CYS cc_start: 0.8697 (t) cc_final: 0.8315 (t) REVERT: G 45 PHE cc_start: 0.8202 (t80) cc_final: 0.7455 (t80) REVERT: G 53 GLN cc_start: 0.8553 (tp40) cc_final: 0.8212 (tp40) REVERT: G 70 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.5120 (p90) REVERT: G 83 ASN cc_start: 0.8512 (t0) cc_final: 0.8054 (t0) REVERT: G 116 ASP cc_start: 0.6032 (m-30) cc_final: 0.5740 (m-30) REVERT: I 113 PHE cc_start: 0.8535 (t80) cc_final: 0.8252 (t80) REVERT: J 77 LEU cc_start: 0.8697 (tp) cc_final: 0.8495 (tp) REVERT: J 165 MET cc_start: 0.7496 (mmt) cc_final: 0.6928 (mmt) REVERT: J 192 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6236 (tm-30) REVERT: K 87 TRP cc_start: 0.7280 (OUTLIER) cc_final: 0.6487 (m-10) REVERT: L 13 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.5808 (m-70) REVERT: L 106 THR cc_start: 0.9467 (m) cc_final: 0.9244 (m) REVERT: L 194 MET cc_start: 0.7786 (mmm) cc_final: 0.7544 (mpp) REVERT: L 236 ARG cc_start: 0.7378 (ttp-110) cc_final: 0.7146 (mtp85) outliers start: 89 outliers final: 66 residues processed: 426 average time/residue: 0.4061 time to fit residues: 274.4416 Evaluate side-chains 408 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 334 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 413 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 868 SER 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 135 CYS Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 144 THR 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 135 LEU 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 181 ASN Chi-restraints excluded: chain D residue 183 VAL 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 39 ARG Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 50 MET 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 H residue 62 ASP 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 197 ILE Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU 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 172 SER Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 87 TRP 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 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 359 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 170 optimal weight: 0.2980 chunk 85 optimal weight: 0.0570 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.0030 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 HIS ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 146 HIS ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30847 Z= 0.152 Angle : 0.610 15.736 43753 Z= 0.299 Chirality : 0.038 0.325 5283 Planarity : 0.005 0.074 4022 Dihedral : 20.908 164.876 9381 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.90 % Favored : 89.02 % Rotamer: Outliers : 3.53 % Allowed : 20.81 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2559 helix: -0.43 (0.18), residues: 830 sheet: -0.94 (0.22), residues: 537 loop : -2.69 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 201 HIS 0.005 0.001 HIS L 13 PHE 0.013 0.001 PHE F 28 TYR 0.024 0.001 TYR K 40 ARG 0.006 0.000 ARG D 82 *********************** 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 441 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 361 time to evaluate : 2.738 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: B 120 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7537 (tptp) REVERT: B 139 MET cc_start: 0.6930 (ppp) cc_final: 0.5779 (ppp) REVERT: B 336 LYS cc_start: 0.8462 (tppt) cc_final: 0.8243 (tppt) REVERT: B 429 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7566 (ptm) REVERT: B 552 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6906 (t80) REVERT: B 692 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7854 (ptt90) REVERT: B 842 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7311 (tpt90) REVERT: C 131 LEU cc_start: 0.7678 (tp) cc_final: 0.7303 (tp) REVERT: C 203 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7764 (pp) REVERT: C 227 GLN cc_start: 0.6902 (pm20) cc_final: 0.6660 (pm20) REVERT: D 82 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6511 (ptp90) REVERT: D 135 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7987 (pp) REVERT: D 160 GLU cc_start: 0.6221 (tm-30) cc_final: 0.5839 (tm-30) REVERT: D 206 GLU cc_start: 0.7835 (mp0) cc_final: 0.7619 (pm20) REVERT: E 136 GLU cc_start: 0.8457 (tp30) cc_final: 0.8171 (tp30) REVERT: E 140 LYS cc_start: 0.8203 (mttt) cc_final: 0.7807 (mtmm) REVERT: F 80 CYS cc_start: 0.8585 (t) cc_final: 0.8246 (t) REVERT: G 45 PHE cc_start: 0.8212 (t80) cc_final: 0.7495 (t80) REVERT: G 53 GLN cc_start: 0.8542 (tp40) cc_final: 0.8246 (tp40) REVERT: G 70 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5078 (p90) REVERT: G 83 ASN cc_start: 0.8513 (t0) cc_final: 0.8068 (t0) REVERT: G 116 ASP cc_start: 0.5627 (m-30) cc_final: 0.5294 (m-30) REVERT: I 113 PHE cc_start: 0.8516 (t80) cc_final: 0.8289 (t80) REVERT: J 165 MET cc_start: 0.7486 (mmt) cc_final: 0.6915 (mmt) REVERT: K 87 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: L 13 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.5648 (m-70) REVERT: L 106 THR cc_start: 0.9463 (m) cc_final: 0.9225 (m) REVERT: L 194 MET cc_start: 0.7862 (mmm) cc_final: 0.7573 (mpp) REVERT: L 236 ARG cc_start: 0.7348 (ttp-110) cc_final: 0.7137 (mtp85) outliers start: 80 outliers final: 54 residues processed: 418 average time/residue: 0.3909 time to fit residues: 261.5390 Evaluate side-chains 400 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 338 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 868 SER Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 146 HIS 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 163 HIS Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL 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 39 ARG Chi-restraints excluded: chain F residue 40 VAL 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 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 197 ILE Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 87 TRP Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 29 HIS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 247 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 359 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 HIS ** B 602 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** C 108 HIS E 75 GLN ** H 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30847 Z= 0.176 Angle : 0.638 16.107 43753 Z= 0.313 Chirality : 0.038 0.344 5283 Planarity : 0.005 0.074 4022 Dihedral : 20.907 165.930 9381 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.02 % Favored : 88.94 % Rotamer: Outliers : 3.00 % Allowed : 21.91 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2559 helix: -0.40 (0.18), residues: 831 sheet: -0.93 (0.22), residues: 545 loop : -2.67 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 201 HIS 0.005 0.001 HIS C 146 PHE 0.023 0.001 PHE I 4 TYR 0.026 0.002 TYR F 99 ARG 0.013 0.001 ARG H 76 *********************** 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 423 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 355 time to evaluate : 2.480 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: B 139 MET cc_start: 0.6955 (ppp) cc_final: 0.6537 (ppp) REVERT: B 144 MET cc_start: 0.4654 (tmm) cc_final: 0.4397 (tmm) REVERT: B 201 TRP cc_start: 0.7124 (t60) cc_final: 0.6824 (t-100) REVERT: B 336 LYS cc_start: 0.8461 (tppt) cc_final: 0.8260 (tppt) REVERT: B 429 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7486 (ptm) REVERT: B 552 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6853 (t80) REVERT: B 692 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7953 (ptt90) REVERT: C 41 MET cc_start: 0.6556 (mpp) cc_final: 0.5691 (mpt) REVERT: C 133 LEU cc_start: 0.8530 (mt) cc_final: 0.8293 (mm) REVERT: C 180 LEU cc_start: 0.8807 (tt) cc_final: 0.8590 (pp) REVERT: C 203 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7775 (pp) REVERT: C 227 GLN cc_start: 0.6830 (pm20) cc_final: 0.6579 (pm20) REVERT: D 82 ARG cc_start: 0.7402 (mmm160) cc_final: 0.6508 (ptp90) REVERT: D 135 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8020 (pp) REVERT: D 160 GLU cc_start: 0.6368 (tm-30) cc_final: 0.5937 (tm-30) REVERT: E 136 GLU cc_start: 0.8549 (tp30) cc_final: 0.8285 (tp30) REVERT: E 140 LYS cc_start: 0.8183 (mttt) cc_final: 0.7778 (mtmm) REVERT: F 80 CYS cc_start: 0.8653 (t) cc_final: 0.8284 (t) REVERT: G 45 PHE cc_start: 0.8215 (t80) cc_final: 0.7478 (t80) REVERT: G 53 GLN cc_start: 0.8575 (tp40) cc_final: 0.8286 (tp40) REVERT: G 70 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.5053 (p90) REVERT: G 83 ASN cc_start: 0.8621 (t0) cc_final: 0.8140 (t0) REVERT: G 116 ASP cc_start: 0.5482 (m-30) cc_final: 0.5141 (m-30) REVERT: J 165 MET cc_start: 0.7520 (mmt) cc_final: 0.7000 (mmt) REVERT: J 192 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6304 (tm-30) REVERT: K 87 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6365 (m-10) REVERT: L 13 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.5597 (m-70) REVERT: L 106 THR cc_start: 0.9459 (m) cc_final: 0.9231 (m) REVERT: L 194 MET cc_start: 0.7906 (mmm) cc_final: 0.7604 (mpp) REVERT: L 227 LEU cc_start: 0.8638 (tp) cc_final: 0.8426 (tp) REVERT: L 236 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7180 (mtp85) outliers start: 68 outliers final: 54 residues processed: 404 average time/residue: 0.3977 time to fit residues: 254.4789 Evaluate side-chains 396 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 334 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 413 TRP Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 857 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 144 THR 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 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 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 103 VAL 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 137 ILE Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER 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 J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 206 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 K residue 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 87 TRP 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 310 VAL Chi-restraints excluded: chain L residue 359 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.0020 chunk 281 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 195 optimal weight: 0.0870 chunk 294 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 591 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN B 969 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 146 HIS ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN J 175 ASN ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30847 Z= 0.281 Angle : 0.714 16.268 43753 Z= 0.353 Chirality : 0.041 0.360 5283 Planarity : 0.006 0.075 4022 Dihedral : 21.003 157.687 9381 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.27 % Favored : 87.65 % Rotamer: Outliers : 3.40 % Allowed : 21.78 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2559 helix: -0.39 (0.18), residues: 818 sheet: -1.16 (0.22), residues: 554 loop : -2.74 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 201 HIS 0.010 0.001 HIS E 102 PHE 0.035 0.002 PHE I 113 TYR 0.025 0.002 TYR F 99 ARG 0.009 0.001 ARG K 78 ********************** 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 429 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 352 time to evaluate : 2.720 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: B 144 MET cc_start: 0.4707 (tmm) cc_final: 0.4411 (tmm) REVERT: B 249 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7302 (p90) REVERT: B 552 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.6797 (t80) REVERT: B 692 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8086 (ptt90) REVERT: C 131 LEU cc_start: 0.7671 (tp) cc_final: 0.7243 (tp) REVERT: C 180 LEU cc_start: 0.8852 (tt) cc_final: 0.8631 (pp) REVERT: C 185 ASN cc_start: 0.1074 (m-40) cc_final: 0.0119 (p0) REVERT: C 203 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7915 (pt) REVERT: D 82 ARG cc_start: 0.7490 (mmm160) cc_final: 0.6644 (mtm-85) REVERT: D 135 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8153 (pp) REVERT: D 160 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6149 (tm-30) REVERT: E 136 GLU cc_start: 0.8719 (tp30) cc_final: 0.8472 (tp30) REVERT: E 140 LYS cc_start: 0.8319 (mttt) cc_final: 0.7904 (mtmm) REVERT: F 80 CYS cc_start: 0.8782 (t) cc_final: 0.8409 (t) REVERT: G 45 PHE cc_start: 0.7961 (t80) cc_final: 0.7322 (t80) REVERT: G 46 LYS cc_start: 0.8450 (tttt) cc_final: 0.8016 (tttt) REVERT: G 70 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.5049 (p90) REVERT: G 83 ASN cc_start: 0.8619 (t0) cc_final: 0.8116 (t0) REVERT: I 43 GLU cc_start: 0.7087 (tp30) cc_final: 0.6444 (pm20) REVERT: I 202 ASP cc_start: 0.7673 (t70) cc_final: 0.7457 (t70) REVERT: J 156 TYR cc_start: 0.7932 (p90) cc_final: 0.7731 (p90) REVERT: J 165 MET cc_start: 0.7622 (mmt) cc_final: 0.7131 (mmt) REVERT: J 192 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6749 (tm-30) REVERT: K 87 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: L 13 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.5927 (m-70) outliers start: 77 outliers final: 62 residues processed: 407 average time/residue: 0.4315 time to fit residues: 279.5119 Evaluate side-chains 406 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 336 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 MET Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 413 TRP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 868 SER 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 144 THR 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 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 164 ILE Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 103 VAL 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 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 H residue 17 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 86 TRP Chi-restraints excluded: chain H residue 88 SER 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 197 ILE Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 206 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 K residue 28 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 87 TRP Chi-restraints excluded: chain L residue 13 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 359 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 1.9990 chunk 250 optimal weight: 0.0010 chunk 71 optimal weight: 5.9990 chunk 216 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 235 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 591 HIS ** B 602 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** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 111 GLN ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.131797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.104433 restraints weight = 80622.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.106593 restraints weight = 46475.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.106849 restraints weight = 32707.845| |-----------------------------------------------------------------------------| 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30847 Z= 0.168 Angle : 0.660 15.853 43753 Z= 0.323 Chirality : 0.039 0.354 5283 Planarity : 0.005 0.074 4022 Dihedral : 20.993 165.336 9381 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.55 % Favored : 89.41 % Rotamer: Outliers : 2.95 % Allowed : 22.57 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2559 helix: -0.34 (0.18), residues: 834 sheet: -0.94 (0.23), residues: 533 loop : -2.67 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 201 HIS 0.004 0.001 HIS L 75 PHE 0.033 0.002 PHE I 113 TYR 0.025 0.002 TYR K 40 ARG 0.007 0.001 ARG L 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6301.43 seconds wall clock time: 114 minutes 35.82 seconds (6875.82 seconds total)