Starting phenix.real_space_refine on Wed Mar 20 15:45:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/03_2024/6ahr_9626_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/03_2024/6ahr_9626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/03_2024/6ahr_9626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/03_2024/6ahr_9626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/03_2024/6ahr_9626_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ahr_9626/03_2024/6ahr_9626_neut.pdb" } resolution = 3.92 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= 0.006 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 341 5.49 5 S 112 5.16 5 C 16326 2.51 5 N 4995 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27851 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 7295 Classifications: {'RNA': 341} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 19, 'rna3p_pur': 153, 'rna3p_pyr': 142} Link IDs: {'rna2p': 46, 'rna3p': 294} 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: "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 24422 SG CYS K 62 59.158 83.678 50.866 1.00111.85 S ATOM 24659 SG CYS K 92 57.012 80.753 51.196 1.00115.22 S Time building chain proxies: 14.58, per 1000 atoms: 0.52 Number of scatterers: 27851 At special positions: 0 Unit cell: (143.88, 134.64, 198, 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 341 15.00 O 6076 8.00 N 4995 7.00 C 16326 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: 12.31 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 92 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 62 " 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: 94 helices and 22 sheets defined 40.2% alpha, 17.9% beta 86 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 10.74 Creating SS restraints... Processing helix chain 'B' and resid 100 through 127 removed outlier: 3.642A pdb=" N ALA B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 4.061A pdb=" N ARG B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.818A pdb=" N MET B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 145' Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.029A pdb=" N ARG B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 4.117A pdb=" N ILE B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.806A pdb=" N ARG B 211 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.721A pdb=" N TYR B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 removed outlier: 4.024A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 4.519A pdb=" N LYS B 287 " --> pdb=" O CYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 4.301A pdb=" N GLU B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.692A pdb=" N HIS B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.881A pdb=" N ASP B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 473 through 493 removed outlier: 4.327A pdb=" N VAL B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 542 removed outlier: 3.665A pdb=" N VAL B 536 " --> pdb=" O ASP B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.590A pdb=" N ARG B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 579 " --> pdb=" O MET B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 638 Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 643 through 654 removed outlier: 3.549A pdb=" N LYS B 654 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 687 Processing helix chain 'B' and resid 707 through 722 removed outlier: 4.097A pdb=" N GLN B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 820 removed outlier: 3.568A pdb=" N TRP B 818 " --> pdb=" O GLN B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 852 removed outlier: 3.526A pdb=" N CYS B 845 " --> pdb=" O THR B 841 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 848 " --> pdb=" O ALA B 844 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 849 " --> pdb=" O CYS B 845 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 850 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.640A pdb=" N ASP B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 920 removed outlier: 3.995A pdb=" N LYS B 907 " --> pdb=" O PRO B 903 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 920 " --> pdb=" O LYS B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 957 removed outlier: 4.361A pdb=" N ARG B 954 " --> pdb=" O GLY B 950 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 955 " --> pdb=" O PRO B 951 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 950 through 957' Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.542A pdb=" N LEU B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 992 " --> pdb=" O THR B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 removed outlier: 3.612A pdb=" N GLN C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 removed outlier: 3.586A pdb=" N GLU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.565A pdb=" N ARG C 110 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 111 " --> pdb=" O HIS C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.434A pdb=" N ARG C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 4.435A pdb=" N LEU C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.603A pdb=" N ARG C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 200 No H-bonds generated for 'chain 'C' and resid 198 through 200' Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.872A pdb=" N GLN D 93 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.956A 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 115 removed outlier: 4.078A pdb=" N HIS D 103 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 204 through 210 removed outlier: 3.951A pdb=" N SER D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 106 through 130 removed outlier: 4.040A pdb=" N LEU E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASN E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 148 removed outlier: 4.074A pdb=" N ALA E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.024A pdb=" N PHE F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 59 removed outlier: 4.071A pdb=" N ARG F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 75 through 88 removed outlier: 3.768A pdb=" N ALA F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.512A pdb=" N SER G 28 " --> pdb=" O ARG G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 57 removed outlier: 3.879A pdb=" N GLN G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 93 removed outlier: 3.945A pdb=" N ALA G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE G 93 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 52 removed outlier: 3.618A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 50 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 91 Processing helix chain 'H' and resid 112 through 117 removed outlier: 3.960A pdb=" N ASN H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.584A pdb=" N ILE I 142 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 180 Processing helix chain 'I' and resid 201 through 211 removed outlier: 3.944A pdb=" N ASN I 205 " --> pdb=" O TYR I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 237 removed outlier: 4.593A pdb=" N ARG I 226 " --> pdb=" O SER I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 Processing helix chain 'J' and resid 83 through 93 Processing helix chain 'J' and resid 109 through 119 Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.694A pdb=" N ILE J 142 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 180 Processing helix chain 'J' and resid 202 through 211 removed outlier: 3.635A pdb=" N PHE J 210 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 237 removed outlier: 4.257A pdb=" N ARG J 226 " --> pdb=" O SER J 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 28 removed outlier: 3.727A pdb=" N GLN K 12 " --> pdb=" O ARG K 8 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG K 13 " --> pdb=" O GLU K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 49 Processing helix chain 'K' and resid 54 through 61 Processing helix chain 'K' and resid 69 through 74 removed outlier: 4.160A pdb=" N LEU K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 106 No H-bonds generated for 'chain 'K' and resid 104 through 106' Processing helix chain 'K' and resid 107 through 113 Processing helix chain 'K' and resid 114 through 121 removed outlier: 4.412A pdb=" N LEU K 118 " --> pdb=" O PRO K 114 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY K 119 " --> pdb=" O GLU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 7 Processing helix chain 'L' and resid 28 through 35 Processing helix chain 'L' and resid 53 through 61 removed outlier: 3.509A pdb=" N LEU L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 79 through 86 Processing helix chain 'L' and resid 120 through 128 removed outlier: 3.509A pdb=" N GLY L 128 " --> pdb=" O TYR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.748A pdb=" N LEU L 155 " --> pdb=" O MET L 151 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN L 156 " --> pdb=" O GLU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.503A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 197 removed outlier: 3.816A pdb=" N TYR L 196 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 248 Processing helix chain 'L' and resid 286 through 300 Processing helix chain 'L' and resid 301 through 303 No H-bonds generated for 'chain 'L' and resid 301 through 303' Processing sheet with id=AA1, first strand: chain 'B' and resid 212 through 216 removed outlier: 7.039A pdb=" N HIS B 213 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 448 through 449 removed outlier: 4.174A pdb=" N LYS B 448 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 595 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 290 through 295 removed outlier: 3.558A pdb=" N GLY B 306 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 313 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 326 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 257 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.440A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY B 979 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 978 " --> pdb=" O SER B 973 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.440A pdb=" N CYS B 804 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N TRP B 858 " --> pdb=" O CYS B 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 965 " --> pdb=" O ILE B 875 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 982 " --> pdb=" O THR B 968 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 978 " --> pdb=" O SER B 973 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 115 removed outlier: 3.804A pdb=" N LEU C 131 " --> pdb=" O PHE C 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 174 through 178 removed outlier: 6.052A pdb=" N ILE D 139 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 187 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 183 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 192 " --> pdb=" O THR J 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 55 through 58 removed outlier: 6.726A pdb=" N VAL E 55 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG E 68 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR E 8 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS E 102 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU E 10 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 100 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 2 through 7 removed outlier: 6.836A pdb=" N MET F 38 " --> pdb=" O CYS F 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 18 through 21 removed outlier: 3.828A pdb=" N GLU G 19 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL G 108 " --> pdb=" O GLU G 19 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N THR G 21 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU G 106 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN G 35 " --> pdb=" O TYR G 70 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N HIS G 72 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE G 37 " --> pdb=" O HIS G 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.993A pdb=" N GLU H 9 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS L 19 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU L 14 " --> pdb=" O VAL L 355 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER L 270 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL L 272 " --> pdb=" O GLN L 218 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN L 218 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA L 274 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 61 through 67 removed outlier: 6.050A pdb=" N ILE H 63 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG H 76 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR H 65 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE H 74 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 72 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS H 25 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL H 104 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU H 27 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE H 102 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.858A pdb=" N LEU I 7 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA I 34 " --> pdb=" O LEU I 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 38 through 39 removed outlier: 6.643A pdb=" N VAL I 39 " --> pdb=" O ILE I 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 152 through 156 Processing sheet with id=AB8, first strand: chain 'J' and resid 6 through 9 removed outlier: 4.167A pdb=" N LEU J 7 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 34 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL J 33 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 38 through 39 removed outlier: 6.650A pdb=" N VAL J 39 " --> pdb=" O ILE J 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AC2, first strand: chain 'K' and resid 76 through 81 Processing sheet with id=AC3, first strand: chain 'L' and resid 132 through 136 removed outlier: 6.482A pdb=" N ILE L 145 " --> pdb=" O PRO L 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL L 107 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA L 94 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE L 179 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS L 70 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU L 181 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N PHE L 68 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N TRP L 183 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N TYR L 66 " --> pdb=" O TRP L 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 322 through 323 857 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 232 hydrogen bonds 444 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 12.56 Time building geometry restraints manager: 13.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6657 1.34 - 1.46: 7548 1.46 - 1.58: 14099 1.58 - 1.70: 681 1.70 - 1.82: 147 Bond restraints: 29132 Sorted by residual: bond pdb=" C CYS B 706 " pdb=" N PRO B 707 " ideal model delta sigma weight residual 1.332 1.384 -0.052 8.20e-03 1.49e+04 4.06e+01 bond pdb=" C ILE B 632 " pdb=" N PRO B 633 " ideal model delta sigma weight residual 1.336 1.409 -0.074 1.23e-02 6.61e+03 3.58e+01 bond pdb=" C VAL K 70 " pdb=" N PRO K 71 " ideal model delta sigma weight residual 1.337 1.392 -0.055 9.80e-03 1.04e+04 3.19e+01 bond pdb=" C VAL C 161 " pdb=" N PRO C 162 " ideal model delta sigma weight residual 1.336 1.385 -0.049 9.80e-03 1.04e+04 2.53e+01 bond pdb=" C SER I 157 " pdb=" N PRO I 158 " ideal model delta sigma weight residual 1.332 1.366 -0.034 8.20e-03 1.49e+04 1.74e+01 ... (remaining 29127 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.93: 2737 106.93 - 113.80: 16851 113.80 - 120.68: 11696 120.68 - 127.56: 8971 127.56 - 134.43: 827 Bond angle restraints: 41082 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 120.33 125.87 -5.54 8.00e-01 1.56e+00 4.80e+01 angle pdb=" C ARG G 23 " pdb=" N LYS G 24 " pdb=" CA LYS G 24 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C LEU C 174 " pdb=" N LYS C 175 " pdb=" CA LYS C 175 " ideal model delta sigma weight residual 120.82 128.50 -7.68 1.47e+00 4.63e-01 2.73e+01 angle pdb=" C CYS I 180 " pdb=" N LYS I 181 " pdb=" CA LYS I 181 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG D 95 " pdb=" N TYR D 96 " pdb=" CA TYR D 96 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 ... (remaining 41077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 17189 35.58 - 71.16: 943 71.16 - 106.74: 132 106.74 - 142.32: 1 142.32 - 177.91: 6 Dihedral angle restraints: 18271 sinusoidal: 10720 harmonic: 7551 Sorted by residual: dihedral pdb=" C4' G A 12 " pdb=" C3' G A 12 " pdb=" C2' G A 12 " pdb=" C1' G A 12 " ideal model delta sinusoidal sigma weight residual -35.00 36.14 -71.14 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' U A 80 " pdb=" C3' U A 80 " pdb=" C2' U A 80 " pdb=" C1' U A 80 " ideal model delta sinusoidal sigma weight residual -35.00 36.14 -71.14 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" O4' U A 80 " pdb=" C2' U A 80 " pdb=" C1' U A 80 " pdb=" C3' U A 80 " ideal model delta sinusoidal sigma weight residual -35.00 32.68 -67.68 1 8.00e+00 1.56e-02 9.30e+01 ... (remaining 18268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4381 0.076 - 0.153: 459 0.153 - 0.229: 77 0.229 - 0.306: 4 0.306 - 0.382: 2 Chirality restraints: 4923 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 2.26 0.38 2.00e-01 2.50e+01 3.65e+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 -2.17 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CG LEU D 84 " pdb=" CB LEU D 84 " pdb=" CD1 LEU D 84 " pdb=" CD2 LEU D 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4920 not shown) Planarity restraints: 3950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 148 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO F 149 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO F 149 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 149 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 61 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO J 62 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO J 62 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 62 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR J 60 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C THR J 60 " -0.048 2.00e-02 2.50e+03 pdb=" O THR J 60 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU J 61 " 0.016 2.00e-02 2.50e+03 ... (remaining 3947 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 36 2.37 - 3.01: 12407 3.01 - 3.64: 41032 3.64 - 4.27: 62527 4.27 - 4.90: 96014 Nonbonded interactions: 212016 Sorted by model distance: nonbonded pdb=" O4' G A 73 " pdb=" N6 A A 315 " model vdw 1.742 2.520 nonbonded pdb=" O2' C A 326 " pdb=" O5' U A 327 " model vdw 1.851 2.440 nonbonded pdb=" O2' G A 12 " pdb=" OP1 G A 13 " model vdw 1.873 2.440 nonbonded pdb=" N6 A A 269 " pdb=" N3 A A 315 " model vdw 1.942 2.600 nonbonded pdb=" OP1 C A 328 " pdb=" NH2 ARG L 139 " model vdw 1.959 2.520 ... (remaining 212011 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: 1.270 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: 0.030 Extract box with map and model: 5.370 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 85.930 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29132 Z= 0.255 Angle : 0.956 16.429 41082 Z= 0.547 Chirality : 0.050 0.382 4923 Planarity : 0.007 0.081 3950 Dihedral : 18.562 177.906 13367 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.16 % Favored : 89.57 % Rotamer: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.20 % 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: -4.23 (0.13), residues: 2559 helix: -2.76 (0.12), residues: 885 sheet: -1.14 (0.20), residues: 562 loop : -3.75 (0.15), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 78 HIS 0.008 0.001 HIS K 107 PHE 0.030 0.002 PHE C 43 TYR 0.039 0.002 TYR G 70 ARG 0.005 0.001 ARG J 166 *********************** 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 976 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 973 time to evaluate : 2.600 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: B 238 MET cc_start: 0.7798 (ttt) cc_final: 0.7595 (ttm) REVERT: B 463 PRO cc_start: 0.6120 (Cg_exo) cc_final: 0.5900 (Cg_endo) REVERT: B 522 LYS cc_start: 0.8030 (tttt) cc_final: 0.7727 (pttm) REVERT: B 1001 GLN cc_start: 0.6809 (pm20) cc_final: 0.6604 (pm20) REVERT: D 105 LEU cc_start: 0.8747 (tp) cc_final: 0.8396 (tt) REVERT: D 110 ILE cc_start: 0.7663 (mm) cc_final: 0.7230 (mm) REVERT: D 215 LYS cc_start: 0.3279 (mttt) cc_final: 0.2900 (mttt) REVERT: E 8 TYR cc_start: 0.7483 (m-80) cc_final: 0.7204 (m-80) REVERT: F 79 THR cc_start: 0.7718 (p) cc_final: 0.7481 (p) REVERT: F 94 VAL cc_start: 0.8522 (t) cc_final: 0.6960 (p) REVERT: F 102 VAL cc_start: 0.6926 (t) cc_final: 0.6706 (p) REVERT: G 41 MET cc_start: 0.6529 (tpp) cc_final: 0.6114 (tpp) REVERT: H 80 SER cc_start: 0.8104 (p) cc_final: 0.7698 (m) REVERT: I 81 VAL cc_start: 0.8073 (t) cc_final: 0.7724 (p) REVERT: I 133 LEU cc_start: 0.4466 (tt) cc_final: 0.4218 (mm) REVERT: I 138 LYS cc_start: 0.7889 (tttt) cc_final: 0.7566 (mmpt) REVERT: I 155 VAL cc_start: 0.8163 (t) cc_final: 0.7654 (p) REVERT: I 195 LEU cc_start: 0.7796 (mt) cc_final: 0.7414 (mp) REVERT: I 202 ASP cc_start: 0.5746 (t70) cc_final: 0.5491 (t70) REVERT: I 209 LEU cc_start: 0.7791 (tp) cc_final: 0.7100 (mt) REVERT: J 198 ARG cc_start: 0.4501 (mmt-90) cc_final: 0.4227 (mmp80) REVERT: K 51 LEU cc_start: 0.8456 (mt) cc_final: 0.8185 (pp) REVERT: K 76 THR cc_start: 0.6023 (m) cc_final: 0.5727 (m) REVERT: K 91 THR cc_start: 0.6533 (m) cc_final: 0.6094 (p) REVERT: L 279 CYS cc_start: 0.5239 (t) cc_final: 0.4800 (t) outliers start: 3 outliers final: 2 residues processed: 976 average time/residue: 0.4827 time to fit residues: 681.9387 Evaluate side-chains 470 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 468 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain H residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 0.7980 chunk 219 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 0.3980 chunk 147 optimal weight: 0.0570 chunk 117 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 464 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 ASN B 658 ASN B 802 HIS B 872 HIS ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 42 HIS ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN E 89 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 HIS I 114 HIS I 175 ASN I 224 ASN K 103 ASN K 107 HIS L 34 GLN ** L 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS L 206 GLN ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 223 GLN L 258 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29132 Z= 0.196 Angle : 0.721 15.428 41082 Z= 0.360 Chirality : 0.039 0.195 4923 Planarity : 0.006 0.064 3950 Dihedral : 21.395 175.885 8256 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.59 % Favored : 89.33 % Rotamer: Outliers : 4.98 % Allowed : 15.04 % Favored : 79.98 % 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: -2.99 (0.15), residues: 2559 helix: -0.94 (0.15), residues: 920 sheet: -0.92 (0.21), residues: 555 loop : -3.56 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 631 HIS 0.009 0.001 HIS C 42 PHE 0.023 0.002 PHE L 260 TYR 0.019 0.002 TYR H 19 ARG 0.010 0.001 ARG G 118 *********************** 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 641 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 528 time to evaluate : 2.885 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 114 GLU cc_start: 0.8704 (pt0) cc_final: 0.8314 (tt0) REVERT: B 144 MET cc_start: 0.5138 (ptp) cc_final: 0.4828 (ptp) REVERT: B 214 MET cc_start: 0.7576 (mmm) cc_final: 0.6480 (mmm) REVERT: B 561 SER cc_start: 0.8791 (p) cc_final: 0.8528 (p) REVERT: B 646 GLU cc_start: 0.7504 (tp30) cc_final: 0.7247 (tp30) REVERT: B 957 LEU cc_start: 0.7168 (mt) cc_final: 0.6713 (mp) REVERT: B 966 PHE cc_start: 0.7286 (m-10) cc_final: 0.5872 (p90) REVERT: C 42 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7439 (t-170) REVERT: D 122 GLN cc_start: 0.6891 (tp-100) cc_final: 0.6243 (tp-100) REVERT: E 98 PHE cc_start: 0.6894 (m-80) cc_final: 0.6504 (m-80) REVERT: E 123 LEU cc_start: 0.8306 (mt) cc_final: 0.7970 (tt) REVERT: F 3 ASN cc_start: 0.6712 (p0) cc_final: 0.6246 (t0) REVERT: F 38 MET cc_start: 0.6424 (tpt) cc_final: 0.6101 (tpt) REVERT: G 19 GLU cc_start: 0.5590 (mt-10) cc_final: 0.5004 (mt-10) REVERT: G 125 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7676 (ttm110) REVERT: I 133 LEU cc_start: 0.4284 (tt) cc_final: 0.3982 (mm) REVERT: I 155 VAL cc_start: 0.8387 (t) cc_final: 0.8024 (p) REVERT: J 142 ILE cc_start: 0.7547 (mm) cc_final: 0.7292 (mm) REVERT: J 202 ASP cc_start: 0.7235 (p0) cc_final: 0.6730 (p0) REVERT: J 233 GLU cc_start: 0.8414 (tp30) cc_final: 0.8145 (tp30) REVERT: K 91 THR cc_start: 0.6912 (m) cc_final: 0.6466 (p) REVERT: L 218 GLN cc_start: 0.6251 (OUTLIER) cc_final: 0.6005 (tp-100) REVERT: L 235 CYS cc_start: 0.4762 (m) cc_final: 0.4484 (m) outliers start: 113 outliers final: 61 residues processed: 602 average time/residue: 0.4015 time to fit residues: 374.7694 Evaluate side-chains 466 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 403 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 898 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 7 ASP Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 142 MET Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain L residue 255 ASN Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 260 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 210 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN B 658 ASN B 710 GLN B 891 HIS C 209 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN I 86 HIS I 114 HIS I 119 HIS I 175 ASN J 178 GLN J 224 ASN L 132 HIS ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 258 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29132 Z= 0.177 Angle : 0.674 16.193 41082 Z= 0.332 Chirality : 0.039 0.222 4923 Planarity : 0.005 0.052 3950 Dihedral : 21.149 173.927 8255 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.82 % Favored : 89.14 % Rotamer: Outliers : 4.98 % Allowed : 18.43 % Favored : 76.59 % 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: -2.41 (0.16), residues: 2559 helix: -0.23 (0.16), residues: 920 sheet: -0.82 (0.21), residues: 561 loop : -3.34 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 626 HIS 0.017 0.001 HIS C 42 PHE 0.022 0.002 PHE K 11 TYR 0.019 0.002 TYR E 117 ARG 0.010 0.001 ARG C 154 *********************** 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 567 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 454 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLU cc_start: 0.8730 (pt0) cc_final: 0.8290 (tt0) REVERT: B 144 MET cc_start: 0.5261 (ptp) cc_final: 0.4977 (ptp) REVERT: B 214 MET cc_start: 0.7187 (mmm) cc_final: 0.6643 (mmm) REVERT: B 522 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7189 (tptt) REVERT: B 865 SER cc_start: 0.7745 (p) cc_final: 0.7460 (t) REVERT: B 957 LEU cc_start: 0.6977 (mt) cc_final: 0.6470 (mp) REVERT: B 980 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6295 (mm-30) REVERT: C 154 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6402 (ptt-90) REVERT: D 212 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5642 (t80) REVERT: E 98 PHE cc_start: 0.7351 (m-80) cc_final: 0.7126 (m-80) REVERT: E 123 LEU cc_start: 0.8383 (mt) cc_final: 0.8144 (tp) REVERT: F 3 ASN cc_start: 0.6819 (p0) cc_final: 0.6186 (t0) REVERT: G 125 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7656 (ttm170) REVERT: H 33 VAL cc_start: 0.7352 (OUTLIER) cc_final: 0.7134 (m) REVERT: H 119 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5631 (ttp-170) REVERT: I 133 LEU cc_start: 0.3984 (tt) cc_final: 0.3204 (mt) REVERT: I 223 THR cc_start: 0.8172 (m) cc_final: 0.7914 (p) REVERT: J 142 ILE cc_start: 0.7664 (mm) cc_final: 0.7272 (mm) REVERT: J 169 THR cc_start: 0.8464 (p) cc_final: 0.8194 (t) REVERT: J 233 GLU cc_start: 0.8522 (tp30) cc_final: 0.8279 (tp30) REVERT: K 11 PHE cc_start: 0.7832 (m-80) cc_final: 0.7475 (m-80) REVERT: K 91 THR cc_start: 0.6872 (m) cc_final: 0.6476 (p) REVERT: L 217 LEU cc_start: 0.8349 (tp) cc_final: 0.8084 (tp) outliers start: 113 outliers final: 75 residues processed: 523 average time/residue: 0.3988 time to fit residues: 324.3959 Evaluate side-chains 473 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 394 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 330 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 119 ARG Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 142 MET Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 346 ASN Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 146 HIS ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 27 ASN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS E 111 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN I 114 HIS J 27 HIS ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.7563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 29132 Z= 0.355 Angle : 0.867 16.554 41082 Z= 0.434 Chirality : 0.045 0.258 4923 Planarity : 0.007 0.072 3950 Dihedral : 21.275 176.700 8255 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.61 % Favored : 88.28 % Rotamer: Outliers : 7.14 % Allowed : 18.39 % Favored : 74.47 % 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: -2.53 (0.16), residues: 2559 helix: -0.33 (0.16), residues: 951 sheet: -0.83 (0.22), residues: 537 loop : -3.48 (0.16), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 708 HIS 0.009 0.002 HIS I 119 PHE 0.038 0.003 PHE C 43 TYR 0.034 0.003 TYR H 19 ARG 0.012 0.001 ARG F 100 *********************** 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 654 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 492 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8054 (mtp85) REVERT: B 114 GLU cc_start: 0.8719 (pt0) cc_final: 0.8145 (tt0) REVERT: B 139 MET cc_start: 0.6911 (tmm) cc_final: 0.6640 (tmm) REVERT: B 214 MET cc_start: 0.7812 (mmm) cc_final: 0.7601 (mmm) REVERT: B 241 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7960 (mpp80) REVERT: B 330 TRP cc_start: 0.6869 (OUTLIER) cc_final: 0.6643 (t60) REVERT: B 489 LEU cc_start: 0.9152 (mt) cc_final: 0.8648 (mt) REVERT: B 494 THR cc_start: 0.8369 (p) cc_final: 0.8044 (m) REVERT: B 508 THR cc_start: 0.7978 (m) cc_final: 0.7606 (p) REVERT: B 564 GLU cc_start: 0.7579 (tt0) cc_final: 0.7270 (tm-30) REVERT: B 874 MET cc_start: 0.8049 (mtp) cc_final: 0.7065 (mtp) REVERT: B 980 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6701 (mm-30) REVERT: B 1008 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7826 (ttp80) REVERT: D 122 GLN cc_start: 0.7571 (tp-100) cc_final: 0.6526 (tp-100) REVERT: E 71 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8054 (tptp) REVERT: E 75 GLN cc_start: 0.8032 (pm20) cc_final: 0.7754 (pm20) REVERT: E 123 LEU cc_start: 0.8752 (mt) cc_final: 0.8397 (tp) REVERT: F 41 LYS cc_start: 0.7049 (pttt) cc_final: 0.6809 (tmmt) REVERT: F 54 THR cc_start: 0.9113 (m) cc_final: 0.8894 (p) REVERT: F 84 LEU cc_start: 0.9131 (mm) cc_final: 0.8876 (mm) REVERT: G 38 TYR cc_start: 0.8439 (m-80) cc_final: 0.8102 (m-80) REVERT: G 44 ASP cc_start: 0.7744 (t0) cc_final: 0.7443 (t70) REVERT: G 46 LYS cc_start: 0.8319 (tttt) cc_final: 0.7953 (ttmt) REVERT: G 70 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7792 (p90) REVERT: G 84 ILE cc_start: 0.8935 (pp) cc_final: 0.8547 (pt) REVERT: G 97 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7753 (tp40) REVERT: G 127 ASN cc_start: 0.7923 (m110) cc_final: 0.7344 (m-40) REVERT: H 56 ASP cc_start: 0.7940 (m-30) cc_final: 0.7104 (m-30) REVERT: I 143 ASN cc_start: 0.7757 (m-40) cc_final: 0.7352 (m110) REVERT: I 206 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8815 (tt) REVERT: J 19 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7176 (mmt180) REVERT: J 21 LEU cc_start: 0.9184 (pp) cc_final: 0.8943 (mm) REVERT: J 23 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7540 (mt-10) REVERT: J 40 ASP cc_start: 0.6454 (t70) cc_final: 0.5525 (t70) REVERT: J 165 MET cc_start: 0.7546 (mmt) cc_final: 0.7027 (mmt) REVERT: J 233 GLU cc_start: 0.8860 (tp30) cc_final: 0.8311 (tp30) REVERT: J 237 THR cc_start: 0.8518 (p) cc_final: 0.8196 (p) REVERT: K 47 LYS cc_start: 0.7973 (tttt) cc_final: 0.7314 (tptt) REVERT: K 91 THR cc_start: 0.7996 (m) cc_final: 0.7539 (p) REVERT: L 41 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6223 (ttp-170) REVERT: L 59 LEU cc_start: 0.9049 (tt) cc_final: 0.8811 (pp) REVERT: L 173 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6980 (tppt) REVERT: L 286 LEU cc_start: 0.7715 (mt) cc_final: 0.7287 (mp) REVERT: L 353 MET cc_start: 0.8521 (mtm) cc_final: 0.8052 (mtm) outliers start: 162 outliers final: 97 residues processed: 598 average time/residue: 0.3826 time to fit residues: 359.2474 Evaluate side-chains 500 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 397 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 330 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 119 ARG Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 187 ILE Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 142 MET Chi-restraints excluded: chain L residue 173 LYS Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 254 ASN Chi-restraints excluded: chain L residue 255 ASN Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 4 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS E 41 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN J 27 HIS ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 GLN ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.7697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29132 Z= 0.188 Angle : 0.702 12.429 41082 Z= 0.346 Chirality : 0.040 0.283 4923 Planarity : 0.006 0.132 3950 Dihedral : 21.016 174.424 8255 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.79 % Favored : 89.18 % Rotamer: Outliers : 5.47 % Allowed : 23.10 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.04 % 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: -2.32 (0.16), residues: 2559 helix: -0.02 (0.16), residues: 945 sheet: -0.91 (0.22), residues: 553 loop : -3.38 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 207 HIS 0.013 0.001 HIS B 138 PHE 0.026 0.002 PHE E 53 TYR 0.027 0.002 TYR H 19 ARG 0.007 0.001 ARG K 13 *********************** 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 576 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 452 time to evaluate : 2.803 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: B 111 ARG cc_start: 0.8371 (mtp85) cc_final: 0.8070 (mtp85) REVERT: B 114 GLU cc_start: 0.8667 (pt0) cc_final: 0.8166 (tt0) REVERT: B 139 MET cc_start: 0.6948 (tmm) cc_final: 0.6321 (tmm) REVERT: B 241 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7900 (mpp80) REVERT: B 294 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7772 (mm) REVERT: B 489 LEU cc_start: 0.9141 (mt) cc_final: 0.8731 (mt) REVERT: B 564 GLU cc_start: 0.7622 (tt0) cc_final: 0.7300 (tm-30) REVERT: B 670 MET cc_start: 0.8343 (mpp) cc_final: 0.7682 (mtt) REVERT: B 807 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7652 (ttm110) REVERT: B 874 MET cc_start: 0.8066 (mtp) cc_final: 0.7010 (mtp) REVERT: B 980 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6623 (mm-30) REVERT: E 123 LEU cc_start: 0.8607 (mt) cc_final: 0.8265 (tp) REVERT: F 41 LYS cc_start: 0.6686 (pttt) cc_final: 0.6189 (pttp) REVERT: G 38 TYR cc_start: 0.8344 (m-80) cc_final: 0.7908 (m-80) REVERT: G 52 CYS cc_start: 0.8312 (t) cc_final: 0.7998 (t) REVERT: G 70 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7530 (p90) REVERT: G 84 ILE cc_start: 0.8878 (pp) cc_final: 0.8526 (pt) REVERT: G 97 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7752 (tp40) REVERT: H 52 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7416 (t80) REVERT: H 56 ASP cc_start: 0.7499 (m-30) cc_final: 0.6664 (m-30) REVERT: H 84 LYS cc_start: 0.7544 (mttt) cc_final: 0.7308 (mtmt) REVERT: I 143 ASN cc_start: 0.7870 (m-40) cc_final: 0.7606 (t0) REVERT: J 43 GLU cc_start: 0.6195 (mp0) cc_final: 0.5869 (pm20) REVERT: J 142 ILE cc_start: 0.8995 (mm) cc_final: 0.8705 (mm) REVERT: J 233 GLU cc_start: 0.8898 (tp30) cc_final: 0.8425 (tp30) REVERT: J 239 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.4222 (p90) REVERT: K 47 LYS cc_start: 0.7684 (tttt) cc_final: 0.6849 (tptt) REVERT: K 113 ARG cc_start: 0.7476 (ttp-170) cc_final: 0.7156 (mtp180) REVERT: L 41 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5853 (ttp-170) REVERT: L 88 LYS cc_start: 0.8391 (mttt) cc_final: 0.8048 (mmmm) outliers start: 124 outliers final: 87 residues processed: 534 average time/residue: 0.3885 time to fit residues: 327.8309 Evaluate side-chains 490 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 397 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 119 ARG Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 187 ILE Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 279 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 185 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN J 27 HIS ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 258 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.8669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29132 Z= 0.292 Angle : 0.763 13.363 41082 Z= 0.379 Chirality : 0.042 0.285 4923 Planarity : 0.006 0.075 3950 Dihedral : 21.059 174.452 8255 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.10 % Favored : 88.86 % Rotamer: Outliers : 6.83 % Allowed : 23.94 % Favored : 69.22 % 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: 0.02 (0.17), residues: 953 sheet: -0.96 (0.22), residues: 546 loop : -3.43 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 86 HIS 0.013 0.001 HIS B 138 PHE 0.043 0.002 PHE C 43 TYR 0.044 0.003 TYR J 156 ARG 0.009 0.001 ARG B 692 *********************** 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 592 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 437 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLU cc_start: 0.8759 (pt0) cc_final: 0.8200 (tt0) REVERT: B 139 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6932 (tmm) REVERT: B 241 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7874 (mpp80) REVERT: B 261 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 294 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7848 (mm) REVERT: B 330 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.5929 (t60) REVERT: B 553 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5120 (pt) REVERT: B 564 GLU cc_start: 0.7782 (tt0) cc_final: 0.7486 (tm-30) REVERT: B 567 ILE cc_start: -0.0300 (OUTLIER) cc_final: -0.0604 (tp) REVERT: B 619 ASP cc_start: 0.7750 (m-30) cc_final: 0.6893 (m-30) REVERT: B 626 TRP cc_start: 0.8108 (m100) cc_final: 0.7750 (m-90) REVERT: B 636 TYR cc_start: 0.7434 (m-80) cc_final: 0.6985 (m-80) REVERT: B 670 MET cc_start: 0.8306 (mpp) cc_final: 0.7711 (mtt) REVERT: B 980 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6795 (mm-30) REVERT: E 69 CYS cc_start: 0.6394 (t) cc_final: 0.6096 (t) REVERT: E 123 LEU cc_start: 0.8826 (mt) cc_final: 0.8495 (tp) REVERT: F 41 LYS cc_start: 0.7189 (pttt) cc_final: 0.6440 (pttp) REVERT: G 20 TYR cc_start: 0.7965 (t80) cc_final: 0.7742 (t80) REVERT: G 38 TYR cc_start: 0.8508 (m-80) cc_final: 0.7940 (m-10) REVERT: G 70 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7679 (p90) REVERT: G 84 ILE cc_start: 0.9039 (pp) cc_final: 0.8702 (pt) REVERT: H 52 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7627 (t80) REVERT: H 68 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7590 (mm-30) REVERT: H 112 LEU cc_start: 0.8344 (tp) cc_final: 0.8002 (tp) REVERT: I 143 ASN cc_start: 0.8085 (m-40) cc_final: 0.7413 (t0) REVERT: I 178 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7910 (pt0) REVERT: J 43 GLU cc_start: 0.6011 (mp0) cc_final: 0.5773 (pm20) REVERT: J 147 ASP cc_start: 0.6912 (t70) cc_final: 0.6646 (t0) REVERT: J 165 MET cc_start: 0.7407 (mmt) cc_final: 0.7060 (mmt) REVERT: J 174 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9074 (mm) REVERT: J 233 GLU cc_start: 0.8899 (tp30) cc_final: 0.8222 (tm-30) REVERT: J 239 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.4745 (p90) REVERT: K 47 LYS cc_start: 0.8120 (tttt) cc_final: 0.7106 (tptt) REVERT: K 113 ARG cc_start: 0.7624 (ttp-170) cc_final: 0.7274 (mtp180) REVERT: L 17 CYS cc_start: 0.8271 (m) cc_final: 0.7708 (t) REVERT: L 41 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5744 (ttp-170) REVERT: L 59 LEU cc_start: 0.9140 (tt) cc_final: 0.8923 (pp) REVERT: L 88 LYS cc_start: 0.8523 (mttt) cc_final: 0.8192 (mmmm) REVERT: L 166 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8248 (p) REVERT: L 349 TYR cc_start: 0.6334 (p90) cc_final: 0.6004 (p90) outliers start: 155 outliers final: 109 residues processed: 538 average time/residue: 0.3957 time to fit residues: 338.5111 Evaluate side-chains 523 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 401 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 330 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 ARG Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 72 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 187 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 234 THR Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 278 optimal weight: 0.5980 chunk 174 optimal weight: 0.0370 chunk 169 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 1.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 185 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 969 GLN C 27 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.9031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.253 29132 Z= 0.259 Angle : 0.730 13.649 41082 Z= 0.359 Chirality : 0.042 0.483 4923 Planarity : 0.005 0.060 3950 Dihedral : 21.034 174.246 8255 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 6.31 % Allowed : 25.26 % Favored : 68.43 % Cbeta Deviations : 0.04 % 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: -2.30 (0.16), residues: 2559 helix: 0.02 (0.17), residues: 959 sheet: -1.01 (0.22), residues: 559 loop : -3.38 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 324 HIS 0.016 0.001 HIS B 138 PHE 0.030 0.002 PHE E 53 TYR 0.029 0.002 TYR C 29 ARG 0.006 0.001 ARG E 120 *********************** 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 580 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 437 time to evaluate : 2.440 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: B 114 GLU cc_start: 0.8696 (pt0) cc_final: 0.8144 (tt0) REVERT: B 139 MET cc_start: 0.7218 (tmm) cc_final: 0.6915 (tmm) REVERT: B 224 GLU cc_start: 0.7800 (tt0) cc_final: 0.7425 (tm-30) REVERT: B 261 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 294 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7739 (mm) REVERT: B 567 ILE cc_start: -0.0010 (OUTLIER) cc_final: -0.0267 (tp) REVERT: B 619 ASP cc_start: 0.7809 (m-30) cc_final: 0.6907 (m-30) REVERT: B 622 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6191 (tt) REVERT: B 626 TRP cc_start: 0.8016 (m100) cc_final: 0.7725 (m-90) REVERT: B 636 TYR cc_start: 0.7274 (m-80) cc_final: 0.6958 (m-80) REVERT: B 670 MET cc_start: 0.8255 (mpp) cc_final: 0.7567 (mtt) REVERT: B 980 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6948 (mm-30) REVERT: E 32 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8820 (pp) REVERT: E 69 CYS cc_start: 0.6394 (t) cc_final: 0.6082 (t) REVERT: E 123 LEU cc_start: 0.8745 (mt) cc_final: 0.8407 (tp) REVERT: F 41 LYS cc_start: 0.7149 (pttt) cc_final: 0.6402 (pttp) REVERT: G 38 TYR cc_start: 0.8494 (m-80) cc_final: 0.7900 (m-10) REVERT: G 70 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7533 (p90) REVERT: G 84 ILE cc_start: 0.8998 (pp) cc_final: 0.8681 (pt) REVERT: G 87 GLN cc_start: 0.8548 (mt0) cc_final: 0.8285 (mt0) REVERT: H 52 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7654 (t80) REVERT: H 112 LEU cc_start: 0.8104 (tp) cc_final: 0.7680 (tp) REVERT: I 143 ASN cc_start: 0.8080 (m-40) cc_final: 0.7509 (t0) REVERT: I 178 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7778 (pt0) REVERT: J 43 GLU cc_start: 0.5852 (mp0) cc_final: 0.5470 (pm20) REVERT: J 142 ILE cc_start: 0.9311 (mm) cc_final: 0.9017 (mm) REVERT: J 165 MET cc_start: 0.7267 (mmt) cc_final: 0.6941 (mmt) REVERT: J 233 GLU cc_start: 0.8893 (tp30) cc_final: 0.8284 (tm-30) REVERT: J 239 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.4580 (p90) REVERT: K 47 LYS cc_start: 0.8071 (tttt) cc_final: 0.7094 (tptt) REVERT: K 113 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.7220 (mtp180) REVERT: L 17 CYS cc_start: 0.8363 (m) cc_final: 0.7575 (t) REVERT: L 41 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6479 (tmm-80) REVERT: L 59 LEU cc_start: 0.9175 (tt) cc_final: 0.8894 (pp) REVERT: L 88 LYS cc_start: 0.8763 (mttt) cc_final: 0.8464 (mmmm) REVERT: L 160 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7515 (ptpt) REVERT: L 349 TYR cc_start: 0.6475 (p90) cc_final: 0.6216 (p90) outliers start: 143 outliers final: 107 residues processed: 530 average time/residue: 0.3911 time to fit residues: 323.4355 Evaluate side-chains 521 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 404 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 969 GLN Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LYS Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 119 ARG Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 72 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 112 ASN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 255 ASN Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Chi-restraints excluded: chain L residue 352 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 166 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.9312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 29132 Z= 0.233 Angle : 0.728 14.260 41082 Z= 0.356 Chirality : 0.041 0.372 4923 Planarity : 0.005 0.060 3950 Dihedral : 21.010 173.992 8255 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 6.00 % Allowed : 26.19 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.04 % 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: -2.23 (0.16), residues: 2559 helix: 0.09 (0.17), residues: 959 sheet: -0.99 (0.21), residues: 555 loop : -3.35 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 324 HIS 0.006 0.001 HIS I 27 PHE 0.039 0.002 PHE C 43 TYR 0.025 0.002 TYR L 37 ARG 0.008 0.001 ARG F 100 *********************** 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 550 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 414 time to evaluate : 2.954 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: B 114 GLU cc_start: 0.8641 (pt0) cc_final: 0.8140 (tt0) REVERT: B 139 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6163 (tmm) REVERT: B 241 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7886 (mpp80) REVERT: B 243 LEU cc_start: 0.9132 (tt) cc_final: 0.8887 (tt) REVERT: B 261 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 294 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7640 (mm) REVERT: B 330 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.6354 (t60) REVERT: B 567 ILE cc_start: 0.0128 (OUTLIER) cc_final: -0.0108 (tp) REVERT: B 619 ASP cc_start: 0.7790 (m-30) cc_final: 0.6912 (m-30) REVERT: B 622 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6244 (tt) REVERT: B 626 TRP cc_start: 0.8048 (m100) cc_final: 0.7744 (m-90) REVERT: B 628 MET cc_start: 0.8365 (mmm) cc_final: 0.8158 (mmp) REVERT: B 636 TYR cc_start: 0.7353 (m-80) cc_final: 0.7046 (m-80) REVERT: B 670 MET cc_start: 0.8171 (mpp) cc_final: 0.7926 (mtt) REVERT: B 978 CYS cc_start: 0.8519 (p) cc_final: 0.7958 (m) REVERT: B 980 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6770 (mm-30) REVERT: D 199 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7994 (mptt) REVERT: E 14 VAL cc_start: 0.8766 (t) cc_final: 0.8505 (m) REVERT: E 69 CYS cc_start: 0.6413 (t) cc_final: 0.6118 (t) REVERT: E 75 GLN cc_start: 0.8221 (pm20) cc_final: 0.7984 (pm20) REVERT: E 123 LEU cc_start: 0.8727 (mt) cc_final: 0.8394 (tp) REVERT: F 41 LYS cc_start: 0.7133 (pttt) cc_final: 0.6472 (pttp) REVERT: G 38 TYR cc_start: 0.8497 (m-80) cc_final: 0.7963 (m-10) REVERT: G 48 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: G 70 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7468 (p90) REVERT: G 84 ILE cc_start: 0.9016 (pp) cc_final: 0.8747 (pt) REVERT: G 97 GLN cc_start: 0.7517 (tp40) cc_final: 0.7166 (tp40) REVERT: I 143 ASN cc_start: 0.8109 (m-40) cc_final: 0.7564 (t0) REVERT: J 142 ILE cc_start: 0.9358 (mm) cc_final: 0.9076 (mm) REVERT: J 165 MET cc_start: 0.7234 (mmt) cc_final: 0.6941 (mmt) REVERT: J 174 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9022 (mm) REVERT: J 177 MET cc_start: 0.7707 (mtt) cc_final: 0.7433 (ttt) REVERT: J 233 GLU cc_start: 0.8779 (tp30) cc_final: 0.8248 (tm-30) REVERT: J 239 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.4668 (p90) REVERT: K 47 LYS cc_start: 0.8416 (tttt) cc_final: 0.7222 (tptt) REVERT: K 80 ARG cc_start: 0.6727 (mmt180) cc_final: 0.6001 (mmt180) REVERT: K 113 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6985 (mtp180) REVERT: L 17 CYS cc_start: 0.8260 (m) cc_final: 0.7579 (t) REVERT: L 41 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6673 (tmm-80) REVERT: L 59 LEU cc_start: 0.9116 (tt) cc_final: 0.8839 (pp) REVERT: L 160 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7484 (ptpt) REVERT: L 241 PHE cc_start: 0.8645 (t80) cc_final: 0.8329 (t80) REVERT: L 349 TYR cc_start: 0.6763 (p90) cc_final: 0.6540 (p90) outliers start: 136 outliers final: 105 residues processed: 504 average time/residue: 0.3752 time to fit residues: 301.8025 Evaluate side-chains 516 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 397 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 330 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 72 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 202 ILE Chi-restraints excluded: chain L residue 254 ASN Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Chi-restraints excluded: chain L residue 352 GLN Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 3.9990 chunk 266 optimal weight: 0.0670 chunk 243 optimal weight: 0.0770 chunk 259 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN J 37 HIS L 100 HIS ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.9609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.231 29132 Z= 0.249 Angle : 0.736 14.169 41082 Z= 0.360 Chirality : 0.041 0.468 4923 Planarity : 0.005 0.060 3950 Dihedral : 21.025 174.265 8255 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 5.82 % Allowed : 26.90 % Favored : 67.28 % Cbeta Deviations : 0.04 % 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: -2.22 (0.16), residues: 2559 helix: 0.13 (0.17), residues: 960 sheet: -1.03 (0.21), residues: 559 loop : -3.34 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 858 HIS 0.019 0.001 HIS C 42 PHE 0.032 0.002 PHE E 53 TYR 0.028 0.002 TYR L 37 ARG 0.007 0.001 ARG C 194 *********************** 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 551 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 419 time to evaluate : 2.757 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: B 114 GLU cc_start: 0.8665 (pt0) cc_final: 0.8162 (tt0) REVERT: B 139 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6246 (tmm) REVERT: B 241 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7903 (mpp80) REVERT: B 243 LEU cc_start: 0.9117 (tt) cc_final: 0.8892 (tt) REVERT: B 261 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 294 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7723 (mm) REVERT: B 619 ASP cc_start: 0.7803 (m-30) cc_final: 0.6905 (m-30) REVERT: B 622 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6245 (tt) REVERT: B 628 MET cc_start: 0.8339 (mmm) cc_final: 0.8134 (mmp) REVERT: B 636 TYR cc_start: 0.7422 (m-80) cc_final: 0.7118 (m-80) REVERT: B 670 MET cc_start: 0.8016 (mpp) cc_final: 0.7428 (mtt) REVERT: B 978 CYS cc_start: 0.8534 (p) cc_final: 0.7970 (m) REVERT: B 980 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 50 ASP cc_start: 0.8636 (m-30) cc_final: 0.8387 (m-30) REVERT: D 130 LEU cc_start: 0.8878 (mm) cc_final: 0.8587 (mm) REVERT: D 199 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7996 (mptt) REVERT: E 69 CYS cc_start: 0.6467 (t) cc_final: 0.6139 (t) REVERT: E 75 GLN cc_start: 0.8138 (pm20) cc_final: 0.7925 (pm20) REVERT: E 123 LEU cc_start: 0.8736 (mt) cc_final: 0.8406 (tp) REVERT: F 41 LYS cc_start: 0.7251 (pttt) cc_final: 0.6612 (pttp) REVERT: G 38 TYR cc_start: 0.8519 (m-80) cc_final: 0.8008 (m-10) REVERT: G 48 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: G 70 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7450 (p90) REVERT: G 84 ILE cc_start: 0.9043 (pp) cc_final: 0.8780 (pt) REVERT: G 97 GLN cc_start: 0.7449 (tp40) cc_final: 0.7110 (tp40) REVERT: I 143 ASN cc_start: 0.8110 (m-40) cc_final: 0.7520 (t0) REVERT: I 160 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6638 (pp) REVERT: I 178 GLN cc_start: 0.8345 (pt0) cc_final: 0.7756 (tm-30) REVERT: J 165 MET cc_start: 0.7260 (mmt) cc_final: 0.6964 (mmt) REVERT: J 174 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9031 (mm) REVERT: J 233 GLU cc_start: 0.8769 (tp30) cc_final: 0.8270 (tm-30) REVERT: J 239 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.4608 (p90) REVERT: K 47 LYS cc_start: 0.8405 (tttt) cc_final: 0.7234 (tptt) REVERT: K 107 HIS cc_start: 0.5041 (m90) cc_final: 0.4794 (m90) REVERT: K 113 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7072 (mtp180) REVERT: L 6 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7350 (mtm-85) REVERT: L 17 CYS cc_start: 0.8337 (m) cc_final: 0.7976 (t) REVERT: L 59 LEU cc_start: 0.9090 (tt) cc_final: 0.8834 (pp) REVERT: L 160 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7522 (ptpt) REVERT: L 241 PHE cc_start: 0.8740 (t80) cc_final: 0.8437 (t80) REVERT: L 349 TYR cc_start: 0.6882 (p90) cc_final: 0.6658 (p90) outliers start: 132 outliers final: 111 residues processed: 500 average time/residue: 0.3849 time to fit residues: 307.3882 Evaluate side-chains 518 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 395 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 72 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 254 ASN Chi-restraints excluded: chain L residue 255 ASN Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Chi-restraints excluded: chain L residue 352 GLN Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN C 42 HIS ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN I 65 GLN ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.9812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 29132 Z= 0.230 Angle : 0.746 14.278 41082 Z= 0.363 Chirality : 0.041 0.310 4923 Planarity : 0.005 0.063 3950 Dihedral : 21.034 174.375 8255 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 5.91 % Allowed : 27.16 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.21 (0.16), residues: 2559 helix: 0.11 (0.17), residues: 959 sheet: -0.97 (0.21), residues: 551 loop : -3.32 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 324 HIS 0.012 0.001 HIS C 42 PHE 0.048 0.002 PHE C 43 TYR 0.035 0.002 TYR G 20 ARG 0.009 0.000 ARG C 194 ********************** 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 536 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 402 time to evaluate : 3.269 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: B 114 GLU cc_start: 0.8666 (pt0) cc_final: 0.8163 (tt0) REVERT: B 139 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.5904 (tmm) REVERT: B 241 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7874 (mpp80) REVERT: B 243 LEU cc_start: 0.9114 (tt) cc_final: 0.8898 (tt) REVERT: B 261 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 294 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7704 (mm) REVERT: B 330 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.6394 (t60) REVERT: B 619 ASP cc_start: 0.7804 (m-30) cc_final: 0.6941 (m-30) REVERT: B 622 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.5970 (tt) REVERT: B 628 MET cc_start: 0.8362 (mmm) cc_final: 0.8149 (mmp) REVERT: B 636 TYR cc_start: 0.7355 (m-80) cc_final: 0.7054 (m-80) REVERT: B 670 MET cc_start: 0.7952 (mpp) cc_final: 0.7408 (mtt) REVERT: B 978 CYS cc_start: 0.8469 (p) cc_final: 0.7901 (m) REVERT: B 980 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6765 (mm-30) REVERT: C 30 ILE cc_start: 0.7074 (tp) cc_final: 0.6843 (tp) REVERT: C 41 MET cc_start: 0.8473 (mtp) cc_final: 0.8263 (mtp) REVERT: C 50 ASP cc_start: 0.8652 (m-30) cc_final: 0.8330 (m-30) REVERT: D 130 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (mm) REVERT: D 199 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7935 (mptt) REVERT: E 69 CYS cc_start: 0.6416 (t) cc_final: 0.6186 (t) REVERT: E 123 LEU cc_start: 0.8800 (mt) cc_final: 0.8457 (tp) REVERT: F 1 MET cc_start: 0.2886 (OUTLIER) cc_final: -0.1824 (ptp) REVERT: F 41 LYS cc_start: 0.7265 (pttt) cc_final: 0.6511 (pttp) REVERT: G 38 TYR cc_start: 0.8511 (m-80) cc_final: 0.7993 (m-10) REVERT: G 48 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: G 70 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7454 (p90) REVERT: G 84 ILE cc_start: 0.9043 (pp) cc_final: 0.8782 (pt) REVERT: G 97 GLN cc_start: 0.7706 (tp40) cc_final: 0.7342 (tp40) REVERT: I 143 ASN cc_start: 0.8161 (m-40) cc_final: 0.7562 (t0) REVERT: I 160 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6507 (pp) REVERT: I 178 GLN cc_start: 0.8328 (pt0) cc_final: 0.7747 (tm-30) REVERT: J 165 MET cc_start: 0.7305 (mmt) cc_final: 0.6952 (mmt) REVERT: J 174 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9039 (mm) REVERT: J 233 GLU cc_start: 0.8727 (tp30) cc_final: 0.8266 (tm-30) REVERT: J 239 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.4710 (p90) REVERT: K 47 LYS cc_start: 0.8382 (tttt) cc_final: 0.7232 (tptt) REVERT: K 80 ARG cc_start: 0.6692 (mmt180) cc_final: 0.5976 (mmt180) REVERT: K 107 HIS cc_start: 0.5020 (m90) cc_final: 0.4772 (m90) REVERT: K 113 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7070 (mtp180) REVERT: L 6 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7339 (mtm-85) REVERT: L 17 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7986 (t) REVERT: L 42 VAL cc_start: 0.9377 (t) cc_final: 0.9051 (p) REVERT: L 152 GLU cc_start: 0.7755 (pm20) cc_final: 0.7272 (pm20) REVERT: L 160 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7544 (ptpt) REVERT: L 241 PHE cc_start: 0.8701 (t80) cc_final: 0.8449 (t80) REVERT: L 277 TYR cc_start: 0.7825 (t80) cc_final: 0.7596 (t80) REVERT: L 349 TYR cc_start: 0.6905 (p90) cc_final: 0.6660 (p90) outliers start: 134 outliers final: 108 residues processed: 480 average time/residue: 0.3976 time to fit residues: 307.5082 Evaluate side-chains 515 residues out of total 2268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 391 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 330 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 440 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 910 LYS Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain B residue 1017 PHE Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 72 LYS Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 239 PHE Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 254 ASN Chi-restraints excluded: chain L residue 255 ASN Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Chi-restraints excluded: chain L residue 352 GLN Chi-restraints excluded: chain L residue 360 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 211 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN G 87 GLN ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.123409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.100831 restraints weight = 81945.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.103520 restraints weight = 48240.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.103850 restraints weight = 31509.976| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.9842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29132 Z= 0.187 Angle : 0.732 14.173 41082 Z= 0.352 Chirality : 0.040 0.312 4923 Planarity : 0.005 0.061 3950 Dihedral : 20.968 174.328 8255 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.94 % Favored : 88.94 % Rotamer: Outliers : 4.59 % Allowed : 28.62 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.12 (0.16), residues: 2559 helix: 0.18 (0.17), residues: 959 sheet: -0.94 (0.22), residues: 564 loop : -3.28 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 324 HIS 0.020 0.001 HIS C 42 PHE 0.074 0.002 PHE C 43 TYR 0.030 0.002 TYR L 38 ARG 0.009 0.000 ARG C 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6459.44 seconds wall clock time: 117 minutes 18.91 seconds (7038.91 seconds total)