Starting phenix.real_space_refine on Mon Jun 23 22:12:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ahr_9626/06_2025/6ahr_9626_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ahr_9626/06_2025/6ahr_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/cci-nas-00/data/ceres_data/6ahr_9626/06_2025/6ahr_9626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ahr_9626/06_2025/6ahr_9626.map" model { file = "/net/cci-nas-00/data/ceres_data/6ahr_9626/06_2025/6ahr_9626_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ahr_9626/06_2025/6ahr_9626_neut.cif" } 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. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.74, per 1000 atoms: 0.53 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.8 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: 10.73 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: 11.71 Time building geometry restraints manager: 7.36 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: 0.00 - 3.29: 40535 3.29 - 6.57: 454 6.57 - 9.86: 85 9.86 - 13.14: 7 13.14 - 16.43: 1 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 3.120 nonbonded pdb=" O2' C A 326 " pdb=" O5' U A 327 " model vdw 1.851 3.040 nonbonded pdb=" O2' G A 12 " pdb=" OP1 G A 13 " model vdw 1.873 3.040 nonbonded pdb=" N6 A A 269 " pdb=" N3 A A 315 " model vdw 1.942 3.200 nonbonded pdb=" OP1 C A 328 " pdb=" NH2 ARG L 139 " model vdw 1.959 3.120 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = (chain 'J' and resid 2 through 237) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 70.180 Find NCS groups from input model: 0.420 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.370 ------------------------------------------------------------------------------- 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 : 0.007 0.690 29134 Z= 0.295 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 Details of bonding type rmsd hydrogen bonds : bond 0.14656 ( 1088) hydrogen bonds : angle 6.96339 ( 2934) metal coordination : bond 0.62085 ( 2) covalent geometry : bond 0.00399 (29132) covalent geometry : angle 0.95586 (41082) *********************** 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 to be fit. rotamer outliers: 3 poor density : 973 time to evaluate : 2.394 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: 0.5236 time to fit residues: 746.0253 Evaluate side-chains 470 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 2.503 ------------------------------------------------------------------------------- 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: 6.9990 chunk 74 optimal weight: 0.9990 chunk 147 optimal weight: 0.0000 chunk 117 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 555 ASN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 720 GLN B 802 HIS B 872 HIS B 891 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 ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN 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 27 GLN K 103 ASN K 107 HIS L 34 GLN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.121881 restraints weight = 84684.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.125120 restraints weight = 47537.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.126344 restraints weight = 29470.981| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 29134 Z= 0.198 Angle : 0.756 15.517 41082 Z= 0.383 Chirality : 0.041 0.188 4923 Planarity : 0.006 0.073 3950 Dihedral : 21.352 179.775 8256 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.55 % Favored : 89.37 % Rotamer: Outliers : 4.85 % Allowed : 15.21 % Favored : 79.94 % 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: -2.92 (0.15), residues: 2559 helix: -0.85 (0.16), residues: 919 sheet: -0.86 (0.21), residues: 544 loop : -3.53 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 631 HIS 0.009 0.001 HIS C 42 PHE 0.026 0.002 PHE L 260 TYR 0.023 0.002 TYR H 19 ARG 0.011 0.001 ARG J 76 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 1088) hydrogen bonds : angle 5.18457 ( 2934) metal coordination : bond 0.02098 ( 2) covalent geometry : bond 0.00380 (29132) covalent geometry : angle 0.75605 (41082) *********************** 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 639 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 529 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLU cc_start: 0.8898 (pt0) cc_final: 0.8424 (tt0) REVERT: B 144 MET cc_start: 0.5362 (ptp) cc_final: 0.5009 (ptp) REVERT: B 214 MET cc_start: 0.7638 (mmm) cc_final: 0.6782 (mmm) REVERT: B 238 MET cc_start: 0.7914 (ttt) cc_final: 0.7673 (ttm) REVERT: B 246 ASP cc_start: 0.7061 (t0) cc_final: 0.6855 (t0) REVERT: B 522 LYS cc_start: 0.7992 (tttt) cc_final: 0.7700 (tttp) REVERT: B 561 SER cc_start: 0.8892 (p) cc_final: 0.8621 (p) REVERT: B 653 TYR cc_start: 0.8359 (m-80) cc_final: 0.8007 (m-80) REVERT: B 957 LEU cc_start: 0.7381 (mt) cc_final: 0.6949 (mp) REVERT: B 966 PHE cc_start: 0.7392 (m-10) cc_final: 0.5892 (p90) REVERT: B 980 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6526 (mm-30) REVERT: C 41 MET cc_start: 0.7622 (tmm) cc_final: 0.7205 (mtt) REVERT: E 98 PHE cc_start: 0.6958 (m-80) cc_final: 0.6621 (m-80) REVERT: F 59 GLN cc_start: 0.2818 (OUTLIER) cc_final: 0.2611 (pp30) REVERT: G 74 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8487 (tp) REVERT: I 133 LEU cc_start: 0.4679 (tt) cc_final: 0.4158 (mm) REVERT: I 155 VAL cc_start: 0.8491 (t) cc_final: 0.8228 (p) REVERT: I 223 THR cc_start: 0.8140 (m) cc_final: 0.7879 (p) REVERT: J 8 ASP cc_start: 0.6799 (m-30) cc_final: 0.6506 (m-30) REVERT: J 142 ILE cc_start: 0.7508 (mm) cc_final: 0.7090 (mm) REVERT: J 202 ASP cc_start: 0.7126 (p0) cc_final: 0.6649 (p0) REVERT: J 233 GLU cc_start: 0.8493 (tp30) cc_final: 0.8200 (tp30) REVERT: K 91 THR cc_start: 0.7129 (m) cc_final: 0.6681 (p) REVERT: K 121 GLN cc_start: 0.4589 (OUTLIER) cc_final: 0.3435 (pp30) REVERT: L 218 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6241 (tp-100) REVERT: L 279 CYS cc_start: 0.5029 (t) cc_final: 0.4611 (t) REVERT: L 319 ASP cc_start: 0.7684 (m-30) cc_final: 0.7463 (m-30) outliers start: 110 outliers final: 58 residues processed: 603 average time/residue: 0.6611 time to fit residues: 630.8686 Evaluate side-chains 468 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 406 time to evaluate : 6.489 ------------------------------------------------------------------------------- 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 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 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 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 22 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 59 GLN 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 74 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain H residue 107 VAL 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 16 LYS 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 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 126 CYS 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 K residue 121 GLN Chi-restraints excluded: chain L residue 17 CYS Chi-restraints excluded: chain L residue 20 SER 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 218 GLN Chi-restraints excluded: chain L residue 255 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 80 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 284 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 263 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN B 658 ASN B 710 GLN C 42 HIS ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN H 42 GLN I 86 HIS I 114 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.141288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.120075 restraints weight = 84250.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.123249 restraints weight = 46802.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.124440 restraints weight = 29394.974| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29134 Z= 0.131 Angle : 0.687 15.783 41082 Z= 0.341 Chirality : 0.040 0.221 4923 Planarity : 0.006 0.052 3950 Dihedral : 21.171 174.687 8255 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.55 % Favored : 89.33 % Rotamer: Outliers : 5.11 % Allowed : 18.34 % Favored : 76.54 % 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: -2.48 (0.16), residues: 2559 helix: -0.26 (0.16), residues: 924 sheet: -0.83 (0.21), residues: 551 loop : -3.40 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 626 HIS 0.009 0.001 HIS C 42 PHE 0.034 0.002 PHE G 93 TYR 0.028 0.002 TYR L 339 ARG 0.015 0.001 ARG C 163 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 1088) hydrogen bonds : angle 4.86560 ( 2934) metal coordination : bond 0.00140 ( 2) covalent geometry : bond 0.00284 (29132) covalent geometry : angle 0.68744 (41082) *********************** 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 580 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 464 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLU cc_start: 0.8979 (pt0) cc_final: 0.8424 (tt0) REVERT: B 144 MET cc_start: 0.5297 (ptp) cc_final: 0.5005 (ptp) REVERT: B 214 MET cc_start: 0.7244 (mmm) cc_final: 0.6786 (mmm) REVERT: B 522 LYS cc_start: 0.8004 (tttt) cc_final: 0.7454 (tmtt) REVERT: B 561 SER cc_start: 0.8891 (p) cc_final: 0.8646 (p) REVERT: B 654 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8261 (ttpt) REVERT: B 678 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8206 (mmmm) REVERT: B 865 SER cc_start: 0.7805 (p) cc_final: 0.7482 (t) REVERT: B 978 CYS cc_start: 0.8426 (p) cc_final: 0.7804 (m) REVERT: B 980 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6593 (mp0) REVERT: C 163 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7468 (mmm160) REVERT: D 212 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5474 (t80) REVERT: E 8 TYR cc_start: 0.7812 (m-80) cc_final: 0.7504 (m-80) REVERT: E 124 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6713 (mm) REVERT: H 13 TYR cc_start: 0.6458 (m-80) cc_final: 0.6180 (m-10) REVERT: H 76 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7247 (ptt180) REVERT: I 23 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7807 (tm-30) REVERT: I 133 LEU cc_start: 0.4221 (tt) cc_final: 0.3424 (mt) REVERT: I 223 THR cc_start: 0.8231 (m) cc_final: 0.7973 (p) REVERT: J 142 ILE cc_start: 0.7450 (mm) cc_final: 0.6975 (mm) REVERT: J 165 MET cc_start: 0.7207 (mmt) cc_final: 0.6716 (mmt) REVERT: J 169 THR cc_start: 0.8332 (p) cc_final: 0.8034 (t) REVERT: J 233 GLU cc_start: 0.8510 (tp30) cc_final: 0.8287 (tp30) REVERT: K 11 PHE cc_start: 0.7611 (m-80) cc_final: 0.7259 (m-80) REVERT: K 91 THR cc_start: 0.6989 (m) cc_final: 0.6624 (p) REVERT: L 209 VAL cc_start: 0.7176 (t) cc_final: 0.6696 (t) REVERT: L 279 CYS cc_start: 0.5700 (t) cc_final: 0.5475 (t) outliers start: 116 outliers final: 71 residues processed: 537 average time/residue: 0.4090 time to fit residues: 341.0244 Evaluate side-chains 485 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 409 time to evaluate : 2.366 ------------------------------------------------------------------------------- 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 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 312 TRP 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 586 LEU Chi-restraints excluded: chain B residue 654 LYS 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 124 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 179 LYS 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 115 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU 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 115 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 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 180 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 244 THR 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 17 CYS Chi-restraints excluded: chain L residue 20 SER 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 148 ILE Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 98 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 HIS B 160 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN E 111 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN I 114 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.134144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.111680 restraints weight = 84550.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.115092 restraints weight = 45907.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.115810 restraints weight = 28604.690| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3980 r_free = 0.3980 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29134 Z= 0.162 Angle : 0.710 14.982 41082 Z= 0.354 Chirality : 0.040 0.199 4923 Planarity : 0.005 0.054 3950 Dihedral : 21.026 173.577 8255 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.75 % Favored : 89.18 % Rotamer: Outliers : 5.73 % Allowed : 19.00 % Favored : 75.26 % 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: -2.24 (0.16), residues: 2559 helix: 0.02 (0.16), residues: 941 sheet: -0.68 (0.22), residues: 534 loop : -3.38 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 708 HIS 0.008 0.001 HIS C 42 PHE 0.041 0.002 PHE G 93 TYR 0.033 0.002 TYR L 339 ARG 0.010 0.001 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 1088) hydrogen bonds : angle 4.78848 ( 2934) metal coordination : bond 0.00192 ( 2) covalent geometry : bond 0.00343 (29132) covalent geometry : angle 0.70993 (41082) *********************** 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 591 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 461 time to evaluate : 2.747 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: 0.8957 (pt0) cc_final: 0.8284 (tt0) REVERT: B 139 MET cc_start: 0.7199 (tmm) cc_final: 0.6992 (tmm) REVERT: B 144 MET cc_start: 0.5879 (ptp) cc_final: 0.5542 (ptp) REVERT: B 224 GLU cc_start: 0.7454 (tt0) cc_final: 0.7134 (tp30) REVERT: B 261 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: B 262 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B 429 MET cc_start: 0.7260 (ptp) cc_final: 0.7047 (ptm) REVERT: B 489 LEU cc_start: 0.9025 (mt) cc_final: 0.8546 (mt) REVERT: B 626 TRP cc_start: 0.7659 (m100) cc_final: 0.7337 (m-90) REVERT: B 654 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8404 (ttpt) REVERT: B 978 CYS cc_start: 0.8464 (p) cc_final: 0.7923 (m) REVERT: B 980 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6771 (mm-30) REVERT: C 41 MET cc_start: 0.5780 (ttp) cc_final: 0.5524 (ttm) REVERT: C 154 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6857 (ptt-90) REVERT: E 93 ARG cc_start: 0.4643 (mpp80) cc_final: 0.3649 (mpp80) REVERT: F 41 LYS cc_start: 0.6873 (pttt) cc_final: 0.6496 (pttt) REVERT: F 50 MET cc_start: 0.7193 (mmp) cc_final: 0.6610 (mpp) REVERT: G 70 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7588 (p90) REVERT: G 84 ILE cc_start: 0.8725 (pp) cc_final: 0.8303 (pt) REVERT: I 121 ASP cc_start: 0.6437 (t70) cc_final: 0.6215 (t70) REVERT: I 133 LEU cc_start: 0.4128 (tt) cc_final: 0.3495 (mt) REVERT: I 143 ASN cc_start: 0.7633 (m-40) cc_final: 0.7245 (t0) REVERT: J 40 ASP cc_start: 0.6746 (t0) cc_final: 0.6181 (t70) REVERT: J 142 ILE cc_start: 0.8132 (mm) cc_final: 0.7746 (mm) REVERT: J 233 GLU cc_start: 0.8756 (tp30) cc_final: 0.8236 (tp30) REVERT: K 13 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.7509 (ptm160) REVERT: K 91 THR cc_start: 0.7494 (m) cc_final: 0.7081 (p) REVERT: L 5 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7381 (ttm170) REVERT: L 320 SER cc_start: 0.8861 (m) cc_final: 0.8523 (p) REVERT: L 329 HIS cc_start: 0.8467 (t70) cc_final: 0.8216 (t-90) outliers start: 130 outliers final: 87 residues processed: 540 average time/residue: 0.4026 time to fit residues: 341.0839 Evaluate side-chains 480 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 388 time to evaluate : 2.627 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 TRP 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 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 808 SER 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 972 PHE Chi-restraints excluded: chain B residue 987 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 154 ARG 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 102 LEU Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 126 LEU 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 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 103 ARG 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 42 LYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL 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 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 212 LEU Chi-restraints excluded: chain J residue 244 THR 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 K residue 76 THR Chi-restraints excluded: chain L residue 17 CYS 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 120 ASP Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 123 THR 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 218 GLN Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 278 LEU 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 82 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 255 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 235 optimal weight: 0.0070 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 0.0670 chunk 174 optimal weight: 9.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN B 570 GLN B 720 GLN C 26 ASN E 41 HIS F 48 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.134708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.112661 restraints weight = 83045.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.115569 restraints weight = 47450.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.116207 restraints weight = 30305.506| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3991 r_free = 0.3991 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29134 Z= 0.124 Angle : 0.677 14.695 41082 Z= 0.331 Chirality : 0.039 0.195 4923 Planarity : 0.005 0.054 3950 Dihedral : 20.907 175.400 8255 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.63 % Favored : 89.29 % Rotamer: Outliers : 5.29 % Allowed : 21.30 % Favored : 73.41 % 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: -2.01 (0.16), residues: 2559 helix: 0.27 (0.17), residues: 943 sheet: -0.56 (0.22), residues: 549 loop : -3.35 (0.16), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 324 HIS 0.015 0.001 HIS B 138 PHE 0.022 0.002 PHE G 93 TYR 0.037 0.002 TYR H 19 ARG 0.024 0.001 ARG F 147 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 1088) hydrogen bonds : angle 4.66566 ( 2934) metal coordination : bond 0.00084 ( 2) covalent geometry : bond 0.00273 (29132) covalent geometry : angle 0.67701 (41082) *********************** 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 554 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 434 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 GLU cc_start: 0.8956 (pt0) cc_final: 0.8269 (tt0) REVERT: B 144 MET cc_start: 0.5833 (ptp) cc_final: 0.5477 (ptp) REVERT: B 224 GLU cc_start: 0.7493 (tt0) cc_final: 0.7214 (tp30) REVERT: B 261 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: B 262 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 489 LEU cc_start: 0.8916 (mt) cc_final: 0.8489 (mt) REVERT: B 564 GLU cc_start: 0.7200 (tt0) cc_final: 0.6935 (tm-30) REVERT: B 626 TRP cc_start: 0.7722 (m100) cc_final: 0.7510 (m-90) REVERT: B 632 ILE cc_start: 0.9300 (tp) cc_final: 0.9033 (pt) REVERT: B 670 MET cc_start: 0.8639 (mpp) cc_final: 0.8202 (mpp) REVERT: B 978 CYS cc_start: 0.8451 (p) cc_final: 0.7978 (m) REVERT: B 980 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6802 (mm-30) REVERT: C 163 ARG cc_start: 0.8931 (mmt90) cc_final: 0.8589 (mmm-85) REVERT: D 179 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7707 (pttt) REVERT: F 41 LYS cc_start: 0.7035 (pttt) cc_final: 0.6597 (pttt) REVERT: F 88 LEU cc_start: 0.7965 (tp) cc_final: 0.7588 (tp) REVERT: G 20 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7716 (t80) REVERT: G 52 CYS cc_start: 0.7805 (t) cc_final: 0.7564 (t) REVERT: G 70 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7606 (p90) REVERT: G 84 ILE cc_start: 0.8695 (pp) cc_final: 0.8300 (pt) REVERT: H 21 TYR cc_start: 0.8000 (m-80) cc_final: 0.7591 (m-10) REVERT: I 133 LEU cc_start: 0.4198 (tt) cc_final: 0.3368 (mt) REVERT: I 143 ASN cc_start: 0.7668 (m-40) cc_final: 0.7275 (t0) REVERT: J 142 ILE cc_start: 0.8167 (mm) cc_final: 0.7829 (mm) REVERT: J 165 MET cc_start: 0.7061 (mmt) cc_final: 0.6530 (mmt) REVERT: J 169 THR cc_start: 0.8580 (p) cc_final: 0.8352 (t) REVERT: J 233 GLU cc_start: 0.8806 (tp30) cc_final: 0.8356 (tp30) REVERT: K 11 PHE cc_start: 0.7407 (m-80) cc_final: 0.6834 (m-80) REVERT: K 58 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8116 (ptmt) REVERT: K 91 THR cc_start: 0.7422 (m) cc_final: 0.7034 (p) REVERT: L 5 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7328 (ttm170) REVERT: L 88 LYS cc_start: 0.8594 (mttt) cc_final: 0.8285 (mttm) REVERT: L 207 PRO cc_start: 0.6352 (Cg_exo) cc_final: 0.6136 (Cg_endo) REVERT: L 320 SER cc_start: 0.8719 (m) cc_final: 0.8417 (p) outliers start: 120 outliers final: 79 residues processed: 510 average time/residue: 0.3887 time to fit residues: 315.1087 Evaluate side-chains 475 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 391 time to evaluate : 2.453 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 TRP 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 477 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 808 SER 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 228 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 131 LEU 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 D residue 212 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 66 VAL 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 20 TYR 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 74 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 77 ILE 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 42 LYS Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 212 LEU 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 87 CYS Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 187 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 THR 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 70 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 120 ASP 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 255 ASN Chi-restraints excluded: chain L residue 278 LEU 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 172 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 272 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS K 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.131957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109621 restraints weight = 82887.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.112246 restraints weight = 46214.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.112905 restraints weight = 30156.346| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.7066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29134 Z= 0.137 Angle : 0.684 14.061 41082 Z= 0.336 Chirality : 0.039 0.269 4923 Planarity : 0.005 0.069 3950 Dihedral : 20.845 175.594 8255 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.75 % Favored : 89.21 % Rotamer: Outliers : 5.07 % Allowed : 21.60 % Favored : 73.32 % 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: -1.89 (0.16), residues: 2559 helix: 0.39 (0.17), residues: 944 sheet: -0.59 (0.22), residues: 554 loop : -3.27 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 324 HIS 0.006 0.001 HIS B 138 PHE 0.015 0.002 PHE F 28 TYR 0.041 0.002 TYR J 156 ARG 0.011 0.001 ARG F 147 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1088) hydrogen bonds : angle 4.67867 ( 2934) metal coordination : bond 0.00126 ( 2) covalent geometry : bond 0.00292 (29132) covalent geometry : angle 0.68430 (41082) *********************** 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 550 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 435 time to evaluate : 2.628 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: B 114 GLU cc_start: 0.8947 (pt0) cc_final: 0.8271 (tt0) REVERT: B 139 MET cc_start: 0.7292 (tmm) cc_final: 0.7065 (tmm) REVERT: B 144 MET cc_start: 0.5928 (ptp) cc_final: 0.5719 (ptp) REVERT: B 154 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5745 (ppt170) REVERT: B 241 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7877 (mpp80) REVERT: B 261 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: B 262 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8378 (pp) REVERT: B 489 LEU cc_start: 0.9041 (mt) cc_final: 0.8645 (mt) REVERT: B 522 LYS cc_start: 0.7836 (tttm) cc_final: 0.7515 (tptt) REVERT: B 564 GLU cc_start: 0.7353 (tt0) cc_final: 0.7037 (tm-30) REVERT: B 628 MET cc_start: 0.8404 (mmp) cc_final: 0.8095 (mmp) REVERT: B 636 TYR cc_start: 0.6490 (m-80) cc_final: 0.6104 (m-80) REVERT: B 670 MET cc_start: 0.8662 (mpp) cc_final: 0.8145 (mpp) REVERT: B 978 CYS cc_start: 0.8485 (p) cc_final: 0.8000 (m) REVERT: B 980 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6833 (mm-30) REVERT: C 163 ARG cc_start: 0.8827 (mmt90) cc_final: 0.8528 (mmm-85) REVERT: D 179 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7749 (pttt) REVERT: D 215 LYS cc_start: 0.0800 (mttt) cc_final: 0.0547 (mttt) REVERT: E 75 GLN cc_start: 0.8243 (pm20) cc_final: 0.7959 (pm20) REVERT: E 93 ARG cc_start: 0.4595 (mpp80) cc_final: 0.4354 (mpp80) REVERT: F 41 LYS cc_start: 0.7198 (pttt) cc_final: 0.6225 (pttp) REVERT: G 40 ASN cc_start: 0.6466 (t0) cc_final: 0.6252 (t0) REVERT: G 46 LYS cc_start: 0.8050 (tttt) cc_final: 0.7610 (tttt) REVERT: G 52 CYS cc_start: 0.7756 (t) cc_final: 0.7365 (t) REVERT: G 70 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7530 (p90) REVERT: G 84 ILE cc_start: 0.8838 (pp) cc_final: 0.8423 (pt) REVERT: H 86 TRP cc_start: 0.8205 (t-100) cc_final: 0.7820 (t-100) REVERT: I 133 LEU cc_start: 0.4382 (tt) cc_final: 0.3457 (mt) REVERT: I 143 ASN cc_start: 0.7793 (m-40) cc_final: 0.7335 (t0) REVERT: J 142 ILE cc_start: 0.8708 (mm) cc_final: 0.8414 (mm) REVERT: J 165 MET cc_start: 0.7165 (mmt) cc_final: 0.6588 (mmt) REVERT: J 233 GLU cc_start: 0.8843 (tp30) cc_final: 0.8400 (tp30) REVERT: K 11 PHE cc_start: 0.7477 (m-80) cc_final: 0.7100 (m-80) REVERT: K 47 LYS cc_start: 0.7466 (tttt) cc_final: 0.6738 (tptt) REVERT: K 58 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8140 (ptmt) REVERT: K 91 THR cc_start: 0.7517 (m) cc_final: 0.7058 (p) REVERT: K 113 ARG cc_start: 0.7292 (ttt180) cc_final: 0.7011 (mtp180) REVERT: L 5 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7518 (ttm170) REVERT: L 41 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5171 (ttp-170) REVERT: L 88 LYS cc_start: 0.8644 (mttt) cc_final: 0.8347 (mttm) REVERT: L 317 PHE cc_start: 0.5922 (m-80) cc_final: 0.4974 (m-80) REVERT: L 320 SER cc_start: 0.8951 (m) cc_final: 0.8628 (p) outliers start: 115 outliers final: 74 residues processed: 508 average time/residue: 0.3927 time to fit residues: 318.0357 Evaluate side-chains 477 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 396 time to evaluate : 2.831 ------------------------------------------------------------------------------- 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 154 ARG 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 241 ARG Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 808 SER 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 C residue 228 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 131 LEU 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 81 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 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 70 TYR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 74 ILE 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 42 LYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 87 CYS 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 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 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 105 ASN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 ILE 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 278 LEU 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 171 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 166 optimal weight: 30.0000 chunk 220 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 720 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.109526 restraints weight = 82645.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.112502 restraints weight = 49397.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.113069 restraints weight = 30295.332| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29134 Z= 0.124 Angle : 0.677 14.006 41082 Z= 0.330 Chirality : 0.039 0.258 4923 Planarity : 0.005 0.091 3950 Dihedral : 20.805 177.680 8255 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.67 % Favored : 89.29 % Rotamer: Outliers : 4.67 % Allowed : 23.41 % Favored : 71.91 % 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: -1.82 (0.16), residues: 2559 helix: 0.43 (0.17), residues: 947 sheet: -0.54 (0.22), residues: 558 loop : -3.22 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 324 HIS 0.010 0.001 HIS C 42 PHE 0.027 0.002 PHE K 16 TYR 0.029 0.002 TYR L 339 ARG 0.014 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 1088) hydrogen bonds : angle 4.58524 ( 2934) metal coordination : bond 0.00073 ( 2) covalent geometry : bond 0.00264 (29132) covalent geometry : angle 0.67689 (41082) *********************** 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 547 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 441 time to evaluate : 2.422 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: B 114 GLU cc_start: 0.8908 (pt0) cc_final: 0.8241 (tt0) REVERT: B 139 MET cc_start: 0.7392 (tmm) cc_final: 0.6913 (tmm) REVERT: B 154 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.5866 (ppt170) REVERT: B 243 LEU cc_start: 0.8796 (tt) cc_final: 0.8579 (tt) REVERT: B 261 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: B 262 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 330 TRP cc_start: 0.6826 (OUTLIER) cc_final: 0.5971 (t60) REVERT: B 489 LEU cc_start: 0.9057 (mt) cc_final: 0.8511 (mt) REVERT: B 522 LYS cc_start: 0.7855 (tttm) cc_final: 0.7539 (tptt) REVERT: B 564 GLU cc_start: 0.7332 (tt0) cc_final: 0.6994 (tm-30) REVERT: B 619 ASP cc_start: 0.7763 (m-30) cc_final: 0.6966 (m-30) REVERT: B 626 TRP cc_start: 0.7643 (m-90) cc_final: 0.7404 (m-90) REVERT: B 636 TYR cc_start: 0.6434 (m-80) cc_final: 0.6155 (m-80) REVERT: B 670 MET cc_start: 0.8649 (mpp) cc_final: 0.8134 (mpp) REVERT: B 865 SER cc_start: 0.7791 (p) cc_final: 0.7393 (t) REVERT: B 951 PRO cc_start: 0.7845 (Cg_exo) cc_final: 0.7630 (Cg_endo) REVERT: B 978 CYS cc_start: 0.8461 (p) cc_final: 0.7999 (m) REVERT: B 980 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6781 (mm-30) REVERT: C 163 ARG cc_start: 0.8785 (mmt90) cc_final: 0.8487 (mmm-85) REVERT: E 75 GLN cc_start: 0.8260 (pm20) cc_final: 0.7950 (pm20) REVERT: E 124 ILE cc_start: 0.7275 (mm) cc_final: 0.7057 (mm) REVERT: F 41 LYS cc_start: 0.7155 (pttt) cc_final: 0.6731 (pttt) REVERT: G 46 LYS cc_start: 0.8000 (tttt) cc_final: 0.7426 (tttt) REVERT: G 70 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7335 (p90) REVERT: G 84 ILE cc_start: 0.8851 (pp) cc_final: 0.8463 (pt) REVERT: I 133 LEU cc_start: 0.4056 (tt) cc_final: 0.3232 (mt) REVERT: I 143 ASN cc_start: 0.7787 (m-40) cc_final: 0.7320 (t0) REVERT: J 142 ILE cc_start: 0.8771 (mm) cc_final: 0.8497 (mm) REVERT: J 147 ASP cc_start: 0.7225 (t70) cc_final: 0.6935 (t0) REVERT: J 165 MET cc_start: 0.7147 (mmt) cc_final: 0.6652 (mmt) REVERT: J 233 GLU cc_start: 0.8857 (tp30) cc_final: 0.8478 (tp30) REVERT: K 11 PHE cc_start: 0.7601 (m-80) cc_final: 0.7277 (m-80) REVERT: K 47 LYS cc_start: 0.7535 (tttt) cc_final: 0.6746 (tptt) REVERT: K 58 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8137 (ptmt) REVERT: K 113 ARG cc_start: 0.7241 (ttt180) cc_final: 0.7004 (mtp180) REVERT: L 41 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.5078 (ttp-170) REVERT: L 88 LYS cc_start: 0.8676 (mttt) cc_final: 0.8412 (mttm) REVERT: L 160 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7205 (ptpt) REVERT: L 328 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 106 outliers final: 72 residues processed: 507 average time/residue: 0.3834 time to fit residues: 310.9001 Evaluate side-chains 489 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 410 time to evaluate : 2.794 ------------------------------------------------------------------------------- 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 154 ARG 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 261 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 330 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL 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 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 C residue 228 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 69 CYS 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 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 70 TYR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 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 212 LEU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 34 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 105 ASN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 142 MET 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 249 SER Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 181 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN C 185 ASN E 102 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 114 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 ASN L 184 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.118124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094964 restraints weight = 83356.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097060 restraints weight = 52318.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097512 restraints weight = 33961.833| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.9307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 29134 Z= 0.298 Angle : 0.924 13.737 41082 Z= 0.465 Chirality : 0.048 0.306 4923 Planarity : 0.007 0.082 3950 Dihedral : 21.229 167.182 8255 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.00 % Favored : 87.96 % Rotamer: Outliers : 5.34 % Allowed : 24.03 % Favored : 70.63 % 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: -2.40 (0.16), residues: 2559 helix: -0.15 (0.16), residues: 935 sheet: -0.92 (0.22), residues: 530 loop : -3.31 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP H 86 HIS 0.013 0.002 HIS G 131 PHE 0.042 0.004 PHE B 310 TYR 0.028 0.003 TYR L 339 ARG 0.011 0.001 ARG B 576 Details of bonding type rmsd hydrogen bonds : bond 0.06278 ( 1088) hydrogen bonds : angle 5.44685 ( 2934) metal coordination : bond 0.00334 ( 2) covalent geometry : bond 0.00640 (29132) covalent geometry : angle 0.92378 (41082) *********************** 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 567 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 446 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.7656 (tmm) cc_final: 0.6310 (tmm) REVERT: B 154 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5309 (ppt170) REVERT: B 224 GLU cc_start: 0.7816 (tt0) cc_final: 0.7588 (tm-30) REVERT: B 241 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8031 (mpp80) REVERT: B 489 LEU cc_start: 0.9246 (mt) cc_final: 0.8745 (mt) REVERT: B 564 GLU cc_start: 0.8035 (tt0) cc_final: 0.7710 (tm-30) REVERT: B 619 ASP cc_start: 0.7931 (m-30) cc_final: 0.7350 (m-30) REVERT: B 626 TRP cc_start: 0.8105 (m-90) cc_final: 0.7840 (m-90) REVERT: B 670 MET cc_start: 0.8835 (mpp) cc_final: 0.7882 (mtt) REVERT: B 978 CYS cc_start: 0.8549 (p) cc_final: 0.8001 (m) REVERT: B 980 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7123 (mm-30) REVERT: F 41 LYS cc_start: 0.7605 (pttt) cc_final: 0.6738 (pttp) REVERT: F 95 THR cc_start: 0.8821 (m) cc_final: 0.8360 (p) REVERT: G 38 TYR cc_start: 0.8567 (m-80) cc_final: 0.8312 (m-10) REVERT: G 46 LYS cc_start: 0.8117 (tttt) cc_final: 0.7576 (tttt) REVERT: G 70 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7709 (p90) REVERT: G 84 ILE cc_start: 0.9188 (pp) cc_final: 0.8816 (pt) REVERT: H 68 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7858 (mm-30) REVERT: H 80 SER cc_start: 0.8618 (p) cc_final: 0.8204 (m) REVERT: H 88 SER cc_start: 0.8869 (m) cc_final: 0.8632 (t) REVERT: I 121 ASP cc_start: 0.7145 (t70) cc_final: 0.6894 (t70) REVERT: I 143 ASN cc_start: 0.8135 (m-40) cc_final: 0.7453 (t0) REVERT: J 147 ASP cc_start: 0.7208 (t70) cc_final: 0.6995 (t0) REVERT: J 165 MET cc_start: 0.7558 (mmt) cc_final: 0.7088 (mmt) REVERT: J 233 GLU cc_start: 0.8896 (tp30) cc_final: 0.8284 (tm-30) REVERT: J 239 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.5252 (p90) REVERT: K 47 LYS cc_start: 0.8567 (tttt) cc_final: 0.7414 (tptt) REVERT: K 58 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8326 (ptmt) REVERT: L 44 PHE cc_start: 0.7645 (p90) cc_final: 0.7425 (p90) REVERT: L 59 LEU cc_start: 0.9292 (tt) cc_final: 0.9023 (pp) REVERT: L 88 LYS cc_start: 0.9013 (mttt) cc_final: 0.8749 (mttp) REVERT: L 147 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8651 (p) REVERT: L 160 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7583 (ptpt) REVERT: L 194 MET cc_start: 0.6787 (mmp) cc_final: 0.6274 (mmp) REVERT: L 278 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (mp) outliers start: 121 outliers final: 84 residues processed: 527 average time/residue: 0.3737 time to fit residues: 313.9280 Evaluate side-chains 461 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 370 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 154 ARG 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 241 ARG Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 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 477 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 666 CYS Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 889 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 B residue 1017 PHE 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 151 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 25 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 93 ARG 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 F residue 7 VAL 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 70 TYR Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 185 VAL 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 105 VAL Chi-restraints excluded: chain J residue 136 TYR Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 187 ILE 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 34 LEU Chi-restraints excluded: chain K residue 42 GLU 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 K residue 103 ASN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 147 SER 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 202 ILE Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 346 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 91 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 83 optimal weight: 0.0070 chunk 234 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN C 149 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN G 89 GLN ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.119621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.096870 restraints weight = 82693.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.098676 restraints weight = 48150.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099243 restraints weight = 34148.835| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.9639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29134 Z= 0.198 Angle : 0.805 13.957 41082 Z= 0.401 Chirality : 0.043 0.278 4923 Planarity : 0.006 0.061 3950 Dihedral : 21.169 176.002 8255 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.61 % Favored : 88.35 % Rotamer: Outliers : 4.54 % Allowed : 26.98 % Favored : 68.47 % 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: -2.28 (0.16), residues: 2559 helix: 0.03 (0.17), residues: 943 sheet: -0.97 (0.21), residues: 551 loop : -3.31 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 324 HIS 0.007 0.001 HIS L 337 PHE 0.042 0.002 PHE C 43 TYR 0.045 0.002 TYR G 20 ARG 0.010 0.001 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 1088) hydrogen bonds : angle 5.16326 ( 2934) metal coordination : bond 0.00239 ( 2) covalent geometry : bond 0.00433 (29132) covalent geometry : angle 0.80460 (41082) *********************** 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 519 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 416 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 MET cc_start: 0.7651 (tmm) cc_final: 0.6250 (tmm) REVERT: B 154 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5539 (ppt170) REVERT: B 224 GLU cc_start: 0.7903 (tt0) cc_final: 0.7597 (tm-30) REVERT: B 241 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7875 (mpp80) REVERT: B 243 LEU cc_start: 0.9089 (tt) cc_final: 0.8743 (tt) REVERT: B 489 LEU cc_start: 0.9200 (mt) cc_final: 0.8648 (mt) REVERT: B 508 THR cc_start: 0.8239 (m) cc_final: 0.7776 (p) REVERT: B 564 GLU cc_start: 0.7794 (tt0) cc_final: 0.7542 (tm-30) REVERT: B 622 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6238 (tt) REVERT: B 636 TYR cc_start: 0.7434 (m-80) cc_final: 0.7002 (m-80) REVERT: B 670 MET cc_start: 0.8655 (mpp) cc_final: 0.8050 (mtt) REVERT: B 978 CYS cc_start: 0.8499 (p) cc_final: 0.8055 (m) REVERT: B 980 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7079 (mm-30) REVERT: C 163 ARG cc_start: 0.8991 (mmt90) cc_final: 0.8481 (mmm-85) REVERT: E 124 ILE cc_start: 0.8460 (mm) cc_final: 0.8161 (tt) REVERT: F 41 LYS cc_start: 0.7605 (pttt) cc_final: 0.7107 (pttp) REVERT: G 38 TYR cc_start: 0.8532 (m-80) cc_final: 0.8297 (m-10) REVERT: G 46 LYS cc_start: 0.7856 (tttt) cc_final: 0.7399 (tttt) REVERT: G 70 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7420 (p90) REVERT: G 84 ILE cc_start: 0.9144 (pp) cc_final: 0.8845 (pt) REVERT: I 143 ASN cc_start: 0.8204 (m-40) cc_final: 0.7633 (t0) REVERT: I 183 LYS cc_start: 0.7940 (tppt) cc_final: 0.7727 (mmtm) REVERT: J 165 MET cc_start: 0.7110 (mmt) cc_final: 0.6741 (mmt) REVERT: J 233 GLU cc_start: 0.8733 (tp30) cc_final: 0.8123 (tm-30) REVERT: J 239 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.4751 (p90) REVERT: K 47 LYS cc_start: 0.8383 (tttt) cc_final: 0.7161 (tptt) REVERT: K 58 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8262 (ptmt) REVERT: K 80 ARG cc_start: 0.6369 (mmt180) cc_final: 0.5816 (mmt180) REVERT: L 17 CYS cc_start: 0.8330 (m) cc_final: 0.7540 (t) REVERT: L 42 VAL cc_start: 0.9397 (t) cc_final: 0.9125 (p) REVERT: L 59 LEU cc_start: 0.9240 (tt) cc_final: 0.8950 (pp) REVERT: L 160 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7535 (ptpt) REVERT: L 278 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (mp) outliers start: 103 outliers final: 80 residues processed: 486 average time/residue: 0.4059 time to fit residues: 316.3909 Evaluate side-chains 457 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 370 time to evaluate : 2.674 ------------------------------------------------------------------------------- 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 154 ARG 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 238 MET Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 808 SER 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 187 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 VAL 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 81 LEU Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 7 VAL 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 109 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 187 ILE 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 34 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 ILE 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 202 ILE Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 325 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 128 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN I 46 GLN I 65 GLN I 86 HIS K 103 ASN L 100 HIS ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.093081 restraints weight = 82785.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.095469 restraints weight = 50121.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.096069 restraints weight = 33165.085| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 1.0291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 29134 Z= 0.236 Angle : 0.858 14.504 41082 Z= 0.428 Chirality : 0.045 0.318 4923 Planarity : 0.006 0.064 3950 Dihedral : 21.250 173.759 8255 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 4.81 % Allowed : 27.60 % Favored : 67.59 % 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: -2.44 (0.16), residues: 2559 helix: -0.14 (0.16), residues: 949 sheet: -1.08 (0.21), residues: 549 loop : -3.37 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 554 HIS 0.018 0.002 HIS L 296 PHE 0.037 0.003 PHE C 43 TYR 0.035 0.003 TYR L 339 ARG 0.009 0.001 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 1088) hydrogen bonds : angle 5.29956 ( 2934) metal coordination : bond 0.00290 ( 2) covalent geometry : bond 0.00518 (29132) covalent geometry : angle 0.85842 (41082) ********************** 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 519 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 410 time to evaluate : 2.659 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: B 139 MET cc_start: 0.7740 (tmm) cc_final: 0.6142 (tmm) REVERT: B 241 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7952 (mpp80) REVERT: B 243 LEU cc_start: 0.9172 (tt) cc_final: 0.8807 (tt) REVERT: B 489 LEU cc_start: 0.9181 (mt) cc_final: 0.8762 (mt) REVERT: B 636 TYR cc_start: 0.7530 (m-80) cc_final: 0.7044 (m-80) REVERT: B 670 MET cc_start: 0.8640 (mpp) cc_final: 0.8003 (mtt) REVERT: B 951 PRO cc_start: 0.8187 (Cg_exo) cc_final: 0.7854 (Cg_endo) REVERT: B 978 CYS cc_start: 0.8416 (p) cc_final: 0.8036 (m) REVERT: B 980 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7069 (mm-30) REVERT: C 50 ASP cc_start: 0.8366 (m-30) cc_final: 0.8051 (m-30) REVERT: C 163 ARG cc_start: 0.8893 (mmt90) cc_final: 0.8666 (mmm-85) REVERT: C 194 ARG cc_start: 0.8210 (ttp80) cc_final: 0.8007 (ttp80) REVERT: E 98 PHE cc_start: 0.7496 (m-10) cc_final: 0.7056 (m-10) REVERT: F 41 LYS cc_start: 0.7682 (pttt) cc_final: 0.7131 (pttp) REVERT: F 95 THR cc_start: 0.8900 (m) cc_final: 0.8537 (p) REVERT: G 38 TYR cc_start: 0.8551 (m-80) cc_final: 0.8283 (m-10) REVERT: G 46 LYS cc_start: 0.7845 (tttt) cc_final: 0.7391 (tttt) REVERT: G 70 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7541 (p90) REVERT: G 84 ILE cc_start: 0.9118 (pp) cc_final: 0.8787 (pt) REVERT: I 143 ASN cc_start: 0.8432 (m-40) cc_final: 0.7667 (t0) REVERT: I 192 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6562 (tp30) REVERT: J 165 MET cc_start: 0.7362 (mmt) cc_final: 0.6852 (mmt) REVERT: J 233 GLU cc_start: 0.8729 (tp30) cc_final: 0.8436 (tp30) REVERT: J 239 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.4888 (p90) REVERT: K 47 LYS cc_start: 0.8699 (tttt) cc_final: 0.7595 (tptt) REVERT: K 58 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8302 (ptmt) REVERT: K 80 ARG cc_start: 0.6361 (mmt180) cc_final: 0.5799 (mmt180) REVERT: L 17 CYS cc_start: 0.8458 (m) cc_final: 0.8183 (t) REVERT: L 42 VAL cc_start: 0.9513 (t) cc_final: 0.9246 (p) REVERT: L 55 GLU cc_start: 0.8358 (pm20) cc_final: 0.8129 (pm20) REVERT: L 344 PHE cc_start: 0.6949 (m-80) cc_final: 0.6642 (m-10) outliers start: 109 outliers final: 87 residues processed: 478 average time/residue: 0.4393 time to fit residues: 338.2021 Evaluate side-chains 482 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 392 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 238 MET Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 808 SER 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 124 LEU 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 C residue 221 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 VAL 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 6 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 93 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 7 VAL 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 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 74 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 138 LYS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 174 LEU 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 25 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 GLU 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 102 LEU Chi-restraints excluded: chain L residue 105 ASN Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 224 SER Chi-restraints excluded: chain L residue 249 SER Chi-restraints excluded: chain L residue 320 SER Chi-restraints excluded: chain L residue 325 GLU Chi-restraints excluded: chain L residue 328 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN I 27 HIS I 36 ASN I 86 HIS ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.119034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.096649 restraints weight = 82187.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.098347 restraints weight = 48304.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099206 restraints weight = 33105.768| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 1.0361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29134 Z= 0.160 Angle : 0.807 14.679 41082 Z= 0.396 Chirality : 0.043 0.287 4923 Planarity : 0.006 0.104 3950 Dihedral : 21.183 179.589 8255 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.18 % Favored : 88.78 % Rotamer: Outliers : 3.62 % Allowed : 30.16 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2559 helix: 0.02 (0.17), residues: 955 sheet: -0.96 (0.22), residues: 550 loop : -3.36 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 324 HIS 0.012 0.001 HIS I 27 PHE 0.039 0.002 PHE C 43 TYR 0.049 0.002 TYR G 20 ARG 0.012 0.001 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 1088) hydrogen bonds : angle 5.09371 ( 2934) metal coordination : bond 0.00153 ( 2) covalent geometry : bond 0.00355 (29132) covalent geometry : angle 0.80733 (41082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10376.63 seconds wall clock time: 183 minutes 38.26 seconds (11018.26 seconds total)