Starting phenix.real_space_refine on Thu Nov 20 07:36:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d6r_7809/11_2025/6d6r_7809.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d6r_7809/11_2025/6d6r_7809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d6r_7809/11_2025/6d6r_7809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d6r_7809/11_2025/6d6r_7809.map" model { file = "/net/cci-nas-00/data/ceres_data/6d6r_7809/11_2025/6d6r_7809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d6r_7809/11_2025/6d6r_7809.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 196 5.16 5 C 19695 2.51 5 N 5611 2.21 5 O 6074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31639 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "B" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1824 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 7, 'TRANS': 233} Chain: "C" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2020 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 14, 'TRANS': 250} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1566 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2194 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "F" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1859 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 232} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 1 Chain: "H" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2263 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Chain: "I" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1407 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 86 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "K" Number of atoms: 6856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6856 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 40, 'TRANS': 812} Chain breaks: 6 Chain: "L" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 573 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5648 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 683} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 966 Classifications: {'DNA': 13, 'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 6, 'rna3p': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {' C%rna3p_pyr:plan': 2, ' C%rna3p_pyr:plan2': 2, ' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 40 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17538 SG CYS K 31 45.199 135.961 78.802 1.00 75.54 S ATOM 17564 SG CYS K 36 45.007 136.828 82.641 1.00 92.82 S ATOM 17580 SG CYS K 39 43.986 133.311 81.292 1.00 97.97 S Time building chain proxies: 6.94, per 1000 atoms: 0.22 Number of scatterers: 31639 At special positions: 0 Unit cell: (164.78, 191.53, 174.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 196 16.00 P 61 15.00 Mg 1 11.99 O 6074 8.00 N 5611 7.00 C 19695 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 159 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 31 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 39 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 36 " Number of angles added : 3 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 48 sheets defined 34.9% alpha, 20.8% beta 14 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.784A pdb=" N ALA A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 243 through 277 removed outlier: 3.800A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.004A pdb=" N THR B 82 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.597A pdb=" N ALA B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.133A pdb=" N LEU B 114 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.965A pdb=" N ALA B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 208 through 243 removed outlier: 4.307A pdb=" N VAL B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 removed outlier: 4.055A pdb=" N PHE C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 116 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 147 through 163 removed outlier: 3.908A pdb=" N ALA C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 245 through 272 removed outlier: 4.166A pdb=" N ASP C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 106 Processing helix chain 'D' and resid 129 through 144 removed outlier: 4.147A pdb=" N ASN D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 202 through 232 Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 147 through 162 Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'E' and resid 250 through 281 removed outlier: 3.759A pdb=" N GLU E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 285 Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 118 through 131 Processing helix chain 'F' and resid 157 through 173 Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 233 through 270 Proline residue: F 253 - end of helix Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.582A pdb=" N ILE G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 225 removed outlier: 3.981A pdb=" N GLY G 222 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 223 " --> pdb=" O GLN G 219 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 257 Processing helix chain 'G' and resid 261 through 274 Processing helix chain 'H' and resid 12 through 16 removed outlier: 4.344A pdb=" N SER H 15 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 12 through 16' Processing helix chain 'H' and resid 124 through 134 removed outlier: 4.975A pdb=" N ARG H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY H 133 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 179 removed outlier: 3.515A pdb=" N LEU H 178 " --> pdb=" O SER H 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL H 179 " --> pdb=" O PRO H 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 175 through 179' Processing helix chain 'H' and resid 227 through 247 removed outlier: 4.690A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 263 Processing helix chain 'H' and resid 273 through 293 Processing helix chain 'I' and resid 16 through 20 removed outlier: 3.561A pdb=" N GLY I 20 " --> pdb=" O LEU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 61 removed outlier: 3.540A pdb=" N GLU I 60 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 57 through 61' Processing helix chain 'I' and resid 117 through 122 Processing helix chain 'K' and resid 69 through 76 Processing helix chain 'K' and resid 76 through 82 removed outlier: 3.501A pdb=" N LEU K 80 " --> pdb=" O GLN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 102 through 114 removed outlier: 3.589A pdb=" N TYR K 106 " --> pdb=" O SER K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 164 removed outlier: 4.369A pdb=" N SER K 164 " --> pdb=" O LEU K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 187 removed outlier: 3.755A pdb=" N LYS K 181 " --> pdb=" O ASP K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 201 Processing helix chain 'K' and resid 205 through 210 Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.882A pdb=" N LYS K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 437 removed outlier: 4.640A pdb=" N GLU K 431 " --> pdb=" O GLU K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 452 removed outlier: 3.524A pdb=" N LEU K 452 " --> pdb=" O VAL K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 513 removed outlier: 4.459A pdb=" N PHE K 512 " --> pdb=" O ASP K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 526 removed outlier: 3.864A pdb=" N GLN K 521 " --> pdb=" O ASN K 517 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG K 526 " --> pdb=" O GLU K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 547 Processing helix chain 'K' and resid 589 through 599 Processing helix chain 'K' and resid 606 through 627 removed outlier: 3.909A pdb=" N LEU K 616 " --> pdb=" O GLY K 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 657 through 682 removed outlier: 3.615A pdb=" N SER K 661 " --> pdb=" O ARG K 657 " (cutoff:3.500A) Processing helix chain 'K' and resid 699 through 709 Processing helix chain 'K' and resid 717 through 726 removed outlier: 3.676A pdb=" N LEU K 721 " --> pdb=" O THR K 717 " (cutoff:3.500A) Processing helix chain 'K' and resid 736 through 746 Processing helix chain 'K' and resid 782 through 796 Processing helix chain 'K' and resid 801 through 805 Processing helix chain 'K' and resid 806 through 843 Processing helix chain 'L' and resid 10 through 15 Processing helix chain 'L' and resid 16 through 21 removed outlier: 3.625A pdb=" N GLN L 20 " --> pdb=" O MET L 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG L 21 " --> pdb=" O LYS L 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 16 through 21' Processing helix chain 'L' and resid 63 through 68 removed outlier: 3.719A pdb=" N CYS L 67 " --> pdb=" O SER L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'M' and resid 141 through 153 removed outlier: 3.561A pdb=" N ASN M 153 " --> pdb=" O GLN M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 181 Processing helix chain 'M' and resid 192 through 207 Processing helix chain 'M' and resid 229 through 239 Processing helix chain 'M' and resid 254 through 259 removed outlier: 3.597A pdb=" N ASP M 259 " --> pdb=" O TYR M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 273 removed outlier: 4.442A pdb=" N TRP M 266 " --> pdb=" O ARG M 262 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU M 267 " --> pdb=" O GLY M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 301 Processing helix chain 'M' and resid 339 through 354 removed outlier: 4.081A pdb=" N PHE M 343 " --> pdb=" O ARG M 339 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 384 Processing helix chain 'M' and resid 396 through 407 Processing helix chain 'M' and resid 414 through 429 Processing helix chain 'M' and resid 438 through 451 Proline residue: M 446 - end of helix Processing helix chain 'M' and resid 460 through 474 Processing helix chain 'M' and resid 483 through 488 removed outlier: 3.931A pdb=" N MET M 487 " --> pdb=" O GLU M 483 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 522 Processing helix chain 'M' and resid 544 through 553 Processing helix chain 'M' and resid 566 through 575 Processing helix chain 'M' and resid 580 through 588 Processing helix chain 'M' and resid 588 through 593 Processing helix chain 'M' and resid 598 through 609 Processing helix chain 'M' and resid 832 through 840 Processing helix chain 'M' and resid 847 through 861 removed outlier: 3.770A pdb=" N LEU M 851 " --> pdb=" O GLN M 847 " (cutoff:3.500A) Processing helix chain 'M' and resid 871 through 878 Processing helix chain 'M' and resid 884 through 893 removed outlier: 3.625A pdb=" N LEU M 888 " --> pdb=" O ASP M 884 " (cutoff:3.500A) Processing helix chain 'M' and resid 901 through 914 removed outlier: 4.022A pdb=" N ALA M 905 " --> pdb=" O SER M 901 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR M 906 " --> pdb=" O ALA M 902 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE M 912 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing helix chain 'M' and resid 925 through 949 Proline residue: M 931 - end of helix removed outlier: 3.555A pdb=" N GLN M 934 " --> pdb=" O GLY M 930 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA M 949 " --> pdb=" O VAL M 945 " (cutoff:3.500A) Processing helix chain 'M' and resid 954 through 961 removed outlier: 3.545A pdb=" N TYR M 958 " --> pdb=" O ASP M 954 " (cutoff:3.500A) Processing helix chain 'M' and resid 966 through 975 Processing helix chain 'M' and resid 978 through 982 Processing helix chain 'M' and resid 989 through 1015 removed outlier: 4.023A pdb=" N ILE M 993 " --> pdb=" O PHE M 989 " (cutoff:3.500A) Processing helix chain 'M' and resid 1017 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 82 removed outlier: 6.625A pdb=" N PHE A 77 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 136 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN A 79 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU A 138 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLU A 81 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.781A pdb=" N MET A 225 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 219 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 233 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A 233 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA B 202 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 235 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET B 200 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER A 237 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LEU B 198 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 187 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 185 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET B 200 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN B 183 " --> pdb=" O MET B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.473A pdb=" N LYS B 46 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN B 119 " --> pdb=" O PRO B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.145A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 171 removed outlier: 3.963A pdb=" N GLU C 167 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS C 183 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 12.524A pdb=" N THR C 169 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N LEU C 181 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N ASN C 171 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N VAL C 179 " --> pdb=" O ASN C 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.862A pdb=" N VAL C 194 " --> pdb=" O MET C 226 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS C 234 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP C 227 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU C 232 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.275A pdb=" N SER D 53 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER D 115 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.874A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 78 through 84 removed outlier: 6.891A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP E 133 " --> pdb=" O CYS E 125 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS E 125 " --> pdb=" O TRP E 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 78 through 84 removed outlier: 6.891A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 35 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 165 through 166 Processing sheet with id=AB5, first strand: chain 'E' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 209 through 211 removed outlier: 4.384A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS E 238 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.814A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS F 61 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG F 95 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL F 146 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 97 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA F 148 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP F 99 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU F 150 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.454A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 195 through 197 removed outlier: 4.454A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 28 Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 34 Processing sheet with id=AC3, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.713A pdb=" N ILE L 59 " --> pdb=" O VAL G 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 191 through 192 removed outlier: 3.734A pdb=" N GLY G 191 " --> pdb=" O TYR G 164 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER G 140 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LYS G 124 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS G 130 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 198 through 201 removed outlier: 3.704A pdb=" N LEU G 227 " --> pdb=" O PHE L 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 26 through 27 removed outlier: 3.650A pdb=" N GLY H 58 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER H 59 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET H 40 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N VAL H 69 " --> pdb=" O MET H 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'H' and resid 164 through 165 removed outlier: 6.873A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU H 109 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL H 91 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS H 97 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.894A pdb=" N ALA H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 21 through 24 removed outlier: 7.233A pdb=" N VAL I 55 " --> pdb=" O GLY I 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 26 through 29 Processing sheet with id=AD3, first strand: chain 'I' and resid 93 through 94 removed outlier: 3.769A pdb=" N MET I 93 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL I 90 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA I 83 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE I 78 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL I 85 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER I 76 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE I 87 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS I 74 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR I 89 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE I 127 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 93 through 94 removed outlier: 3.769A pdb=" N MET I 93 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL I 90 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG I 100 " --> pdb=" O TYR I 142 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU I 144 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR I 102 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU I 143 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE I 127 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 165 through 168 removed outlier: 3.587A pdb=" N ILE I 167 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 2 through 10 Processing sheet with id=AD7, first strand: chain 'K' and resid 87 through 90 removed outlier: 3.677A pdb=" N TYR K 121 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 174 through 175 Processing sheet with id=AD9, first strand: chain 'K' and resid 274 through 277 removed outlier: 6.964A pdb=" N ILE K 291 " --> pdb=" O ILE K 349 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY K 347 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU K 295 " --> pdb=" O VAL K 345 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL K 345 " --> pdb=" O GLU K 295 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 383 through 385 removed outlier: 5.391A pdb=" N LEU K 360 " --> pdb=" O ARG K 396 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG K 396 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ARG K 397 " --> pdb=" O ASN K 419 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN K 419 " --> pdb=" O ARG K 397 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE K 399 " --> pdb=" O VAL K 417 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 468 through 469 removed outlier: 3.740A pdb=" N GLU K 468 " --> pdb=" O LYS K 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL K 581 " --> pdb=" O GLU K 468 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS K 574 " --> pdb=" O GLU K 565 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 477 through 478 removed outlier: 7.012A pdb=" N SER K 477 " --> pdb=" O LEU K 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 530 through 531 Processing sheet with id=AE5, first strand: chain 'K' and resid 637 through 638 removed outlier: 3.612A pdb=" N ARG K 638 " --> pdb=" O GLN K 652 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN K 652 " --> pdb=" O ARG K 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 688 through 690 Processing sheet with id=AE7, first strand: chain 'K' and resid 846 through 848 removed outlier: 6.049A pdb=" N VAL K 846 " --> pdb=" O ILE K 911 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE K 911 " --> pdb=" O VAL K 846 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 851 through 852 Processing sheet with id=AE9, first strand: chain 'K' and resid 886 through 888 Processing sheet with id=AF1, first strand: chain 'M' and resid 99 through 103 removed outlier: 6.641A pdb=" N VAL M 157 " --> pdb=" O PHE M 281 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER M 283 " --> pdb=" O VAL M 157 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL M 159 " --> pdb=" O SER M 283 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG M 184 " --> pdb=" O VAL M 246 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TRP M 248 " --> pdb=" O ARG M 184 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 329 through 332 removed outlier: 7.441A pdb=" N HIS M 318 " --> pdb=" O VAL M 331 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN M 317 " --> pdb=" O VAL M 535 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU M 537 " --> pdb=" O GLN M 317 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR M 319 " --> pdb=" O LEU M 537 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL M 539 " --> pdb=" O TYR M 319 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE M 321 " --> pdb=" O VAL M 539 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL M 496 " --> pdb=" O ILE M 536 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N MET M 538 " --> pdb=" O VAL M 496 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE M 498 " --> pdb=" O MET M 538 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY M 453 " --> pdb=" O PHE M 480 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 864 through 865 removed outlier: 3.596A pdb=" N VAL M 869 " --> pdb=" O THR M 865 " (cutoff:3.500A) 1350 hydrogen bonds defined for protein. 3792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10430 1.34 - 1.46: 5378 1.46 - 1.58: 16070 1.58 - 1.69: 120 1.69 - 1.81: 291 Bond restraints: 32289 Sorted by residual: bond pdb=" O3A ANP M2001 " pdb=" PB ANP M2001 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 1.593 1.681 -0.088 1.50e-02 4.44e+03 3.41e+01 bond pdb=" P C O 17 " pdb=" OP1 C O 17 " ideal model delta sigma weight residual 1.485 1.568 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5' ANP M2001 " pdb=" PA ANP M2001 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.22e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 43395 2.49 - 4.98: 457 4.98 - 7.47: 19 7.47 - 9.96: 1 9.96 - 12.45: 3 Bond angle restraints: 43875 Sorted by residual: angle pdb=" CA PRO K 648 " pdb=" N PRO K 648 " pdb=" CD PRO K 648 " ideal model delta sigma weight residual 112.00 99.55 12.45 1.40e+00 5.10e-01 7.90e+01 angle pdb=" O3' DT O 16 " pdb=" P C O 17 " pdb=" O5' C O 17 " ideal model delta sigma weight residual 104.00 115.00 -11.00 1.50e+00 4.44e-01 5.38e+01 angle pdb=" O1B ANP M2001 " pdb=" PB ANP M2001 " pdb=" O2B ANP M2001 " ideal model delta sigma weight residual 120.08 109.31 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C HIS M 278 " pdb=" N TYR M 279 " pdb=" CA TYR M 279 " ideal model delta sigma weight residual 122.09 116.39 5.70 1.86e+00 2.89e-01 9.38e+00 angle pdb=" N ALA K 600 " pdb=" CA ALA K 600 " pdb=" CB ALA K 600 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 ... (remaining 43870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 19538 33.55 - 67.10: 210 67.10 - 100.65: 32 100.65 - 134.20: 1 134.20 - 167.76: 2 Dihedral angle restraints: 19783 sinusoidal: 8558 harmonic: 11225 Sorted by residual: dihedral pdb=" CA MET K 455 " pdb=" C MET K 455 " pdb=" N PRO K 456 " pdb=" CA PRO K 456 " ideal model delta harmonic sigma weight residual 180.00 131.40 48.60 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" O4' C O 49 " pdb=" C1' C O 49 " pdb=" N1 C O 49 " pdb=" C2 C O 49 " ideal model delta sinusoidal sigma weight residual -128.00 32.68 -160.68 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" CA ASP B 201 " pdb=" C ASP B 201 " pdb=" N ALA B 202 " pdb=" CA ALA B 202 " ideal model delta harmonic sigma weight residual 180.00 149.16 30.84 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 19780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5007 0.119 - 0.238: 45 0.238 - 0.357: 1 0.357 - 0.476: 0 0.476 - 0.595: 1 Chirality restraints: 5054 Sorted by residual: chirality pdb=" P C O 17 " pdb=" OP1 C O 17 " pdb=" OP2 C O 17 " pdb=" O5' C O 17 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" C3' ANP M2001 " pdb=" C2' ANP M2001 " pdb=" C4' ANP M2001 " pdb=" O3' ANP M2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1' A O 58 " pdb=" O4' A O 58 " pdb=" C2' A O 58 " pdb=" N9 A O 58 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5051 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C O 42 " 0.040 2.00e-02 2.50e+03 2.04e-02 9.39e+00 pdb=" N1 C O 42 " -0.043 2.00e-02 2.50e+03 pdb=" C2 C O 42 " -0.010 2.00e-02 2.50e+03 pdb=" O2 C O 42 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C O 42 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C O 42 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C O 42 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C O 42 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C O 42 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 60 " 0.035 2.00e-02 2.50e+03 1.59e-02 6.92e+00 pdb=" N9 A O 60 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A O 60 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A O 60 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A O 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A O 60 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A O 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A O 60 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A O 60 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A O 60 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 41 " 0.034 2.00e-02 2.50e+03 1.48e-02 6.05e+00 pdb=" N9 A O 41 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A O 41 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A O 41 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A O 41 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A O 41 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A O 41 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A O 41 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A O 41 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A O 41 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A O 41 " -0.005 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 157 2.43 - 3.05: 21896 3.05 - 3.67: 44633 3.67 - 4.28: 67056 4.28 - 4.90: 113491 Nonbonded interactions: 247233 Sorted by model distance: nonbonded pdb=" O2' C O 42 " pdb=" O5' A O 43 " model vdw 1.816 3.040 nonbonded pdb=" OG SER B 7 " pdb=" OE1 GLN B 9 " model vdw 1.944 3.040 nonbonded pdb=" OG SER M 189 " pdb=" OG SER M 195 " model vdw 1.956 3.040 nonbonded pdb=" OD1 ASP C 111 " pdb=" ND2 ASN C 115 " model vdw 1.959 3.120 nonbonded pdb=" OE2 GLU M 267 " pdb=" OG SER M 561 " model vdw 1.979 3.040 ... (remaining 247228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.008 0.174 32293 Z= 0.321 Angle : 0.680 12.446 43878 Z= 0.376 Chirality : 0.045 0.595 5054 Planarity : 0.004 0.051 5456 Dihedral : 10.881 167.755 12519 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.11), residues: 3839 helix: -1.97 (0.12), residues: 1234 sheet: -2.38 (0.17), residues: 762 loop : -4.04 (0.10), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 285 TYR 0.039 0.002 TYR M 279 PHE 0.027 0.002 PHE C 154 TRP 0.027 0.002 TRP K 405 HIS 0.011 0.002 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00787 (32289) covalent geometry : angle 0.68017 (43875) hydrogen bonds : bond 0.12567 ( 1372) hydrogen bonds : angle 6.26290 ( 3856) metal coordination : bond 0.10796 ( 4) metal coordination : angle 1.35140 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 769 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ARG cc_start: 0.7300 (mpt-90) cc_final: 0.6949 (mmt90) REVERT: C 9 GLU cc_start: 0.5666 (mp0) cc_final: 0.4826 (pt0) REVERT: C 34 THR cc_start: 0.8801 (m) cc_final: 0.8332 (p) REVERT: C 226 MET cc_start: 0.7587 (tpt) cc_final: 0.7377 (tpt) REVERT: D 68 LYS cc_start: 0.7050 (mtmp) cc_final: 0.6777 (mtpt) REVERT: E 233 LYS cc_start: 0.8184 (mptp) cc_final: 0.7883 (mttp) REVERT: F 50 LYS cc_start: 0.8704 (tttt) cc_final: 0.8451 (tttp) REVERT: G 162 LEU cc_start: 0.8217 (pt) cc_final: 0.8015 (pt) REVERT: H 82 ASP cc_start: 0.7349 (m-30) cc_final: 0.7121 (m-30) REVERT: H 271 ILE cc_start: 0.8078 (pp) cc_final: 0.7827 (pt) REVERT: K 166 ASP cc_start: 0.4839 (m-30) cc_final: 0.4566 (m-30) REVERT: K 238 GLN cc_start: 0.6873 (pt0) cc_final: 0.6586 (mm-40) REVERT: K 265 ILE cc_start: 0.6802 (mm) cc_final: 0.6345 (mm) REVERT: K 470 LEU cc_start: 0.8314 (mp) cc_final: 0.7914 (mp) REVERT: K 488 ASP cc_start: 0.7209 (m-30) cc_final: 0.6921 (m-30) REVERT: K 926 SER cc_start: 0.8475 (m) cc_final: 0.8265 (p) REVERT: L 63 SER cc_start: 0.8930 (t) cc_final: 0.7941 (p) REVERT: L 67 CYS cc_start: 0.7796 (t) cc_final: 0.7438 (m) REVERT: M 329 HIS cc_start: 0.8282 (m90) cc_final: 0.7922 (m90) REVERT: M 489 ILE cc_start: 0.7302 (pp) cc_final: 0.7085 (pp) outliers start: 1 outliers final: 0 residues processed: 770 average time/residue: 0.2496 time to fit residues: 288.6007 Evaluate side-chains 391 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 188 HIS B 33 GLN E 19 GLN E 114 ASN E 131 HIS E 162 ASN G 116 HIS H 101 ASN H 199 ASN J 632 GLN K 284 ASN K 919 GLN L 20 GLN L 92 ASN M 300 HIS ** M 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 981 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.114710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093103 restraints weight = 62263.004| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.21 r_work: 0.3221 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32293 Z= 0.157 Angle : 0.663 9.455 43878 Z= 0.340 Chirality : 0.045 0.257 5054 Planarity : 0.004 0.056 5456 Dihedral : 11.026 168.404 5043 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.57 % Allowed : 8.14 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.13), residues: 3839 helix: 0.04 (0.14), residues: 1284 sheet: -1.63 (0.18), residues: 758 loop : -2.87 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 527 TYR 0.027 0.002 TYR M 279 PHE 0.026 0.002 PHE L 57 TRP 0.017 0.001 TRP K 564 HIS 0.012 0.001 HIS M 981 Details of bonding type rmsd covalent geometry : bond 0.00364 (32289) covalent geometry : angle 0.66234 (43875) hydrogen bonds : bond 0.04476 ( 1372) hydrogen bonds : angle 4.89892 ( 3856) metal coordination : bond 0.01884 ( 4) metal coordination : angle 2.20663 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 458 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8007 (mtp) cc_final: 0.7535 (mtt) REVERT: A 121 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7613 (pp) REVERT: A 229 ARG cc_start: 0.8220 (mpt-90) cc_final: 0.7767 (mmt90) REVERT: A 240 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6410 (pp) REVERT: B 22 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8217 (mtm180) REVERT: B 28 MET cc_start: 0.8876 (mtp) cc_final: 0.8640 (mtm) REVERT: C 34 THR cc_start: 0.8885 (m) cc_final: 0.8514 (p) REVERT: C 111 ASP cc_start: 0.7711 (t0) cc_final: 0.7476 (t0) REVERT: C 167 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: C 226 MET cc_start: 0.8753 (tpt) cc_final: 0.8206 (tpt) REVERT: D 143 ASP cc_start: 0.8625 (t70) cc_final: 0.8403 (t0) REVERT: E 72 GLU cc_start: 0.8038 (mp0) cc_final: 0.7610 (tm-30) REVERT: E 233 LYS cc_start: 0.8590 (mptp) cc_final: 0.8238 (mttp) REVERT: F 50 LYS cc_start: 0.9029 (tttt) cc_final: 0.8593 (tttp) REVERT: F 111 ARG cc_start: 0.7564 (ptp-110) cc_final: 0.7029 (mtp85) REVERT: G 103 ASP cc_start: 0.7893 (p0) cc_final: 0.7525 (p0) REVERT: G 105 GLN cc_start: 0.8530 (mp10) cc_final: 0.8209 (mp10) REVERT: G 164 TYR cc_start: 0.8993 (t80) cc_final: 0.8587 (t80) REVERT: G 250 LEU cc_start: 0.8488 (tp) cc_final: 0.7988 (mt) REVERT: H 105 ASP cc_start: 0.7928 (t0) cc_final: 0.7571 (t70) REVERT: H 128 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7643 (tm-30) REVERT: H 253 ASP cc_start: 0.7917 (t0) cc_final: 0.7533 (p0) REVERT: H 282 MET cc_start: 0.8089 (mmm) cc_final: 0.7862 (mtp) REVERT: I 16 ASN cc_start: 0.8063 (m-40) cc_final: 0.7558 (t0) REVERT: I 164 MET cc_start: 0.8342 (mtp) cc_final: 0.8002 (mtm) REVERT: K 157 ASN cc_start: 0.8077 (m-40) cc_final: 0.7787 (m-40) REVERT: K 186 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5927 (mm-30) REVERT: K 238 GLN cc_start: 0.7431 (pt0) cc_final: 0.6758 (mm-40) REVERT: K 265 ILE cc_start: 0.7537 (mm) cc_final: 0.6836 (mm) REVERT: K 667 MET cc_start: 0.7505 (mmm) cc_final: 0.7231 (mmm) REVERT: K 772 TYR cc_start: 0.8317 (t80) cc_final: 0.8059 (t80) REVERT: K 926 SER cc_start: 0.8593 (m) cc_final: 0.8228 (p) REVERT: L 63 SER cc_start: 0.9065 (t) cc_final: 0.8351 (p) REVERT: L 67 CYS cc_start: 0.7829 (t) cc_final: 0.7573 (m) REVERT: L 91 MET cc_start: 0.8808 (mmm) cc_final: 0.8228 (mtt) REVERT: M 279 TYR cc_start: 0.7441 (p90) cc_final: 0.7194 (p90) REVERT: M 386 PHE cc_start: 0.8337 (m-10) cc_final: 0.7961 (m-10) REVERT: M 426 ASN cc_start: 0.8316 (m110) cc_final: 0.7907 (m110) REVERT: M 487 MET cc_start: 0.6718 (tpp) cc_final: 0.6513 (tpp) REVERT: M 912 PHE cc_start: 0.7438 (m-10) cc_final: 0.7172 (m-10) REVERT: M 921 MET cc_start: 0.6762 (mmt) cc_final: 0.6374 (mmm) outliers start: 52 outliers final: 25 residues processed: 496 average time/residue: 0.2180 time to fit residues: 171.7605 Evaluate side-chains 384 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 354 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 85 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 342 THR Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain M residue 513 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 313 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 295 optimal weight: 0.9990 chunk 360 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 235 GLN D 229 GLN E 275 HIS F 249 GLN M 300 HIS M 317 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.112488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.090573 restraints weight = 62601.474| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.19 r_work: 0.3173 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32293 Z= 0.147 Angle : 0.597 9.525 43878 Z= 0.306 Chirality : 0.043 0.295 5054 Planarity : 0.004 0.058 5456 Dihedral : 10.841 172.788 5043 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.14 % Allowed : 10.46 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3839 helix: 0.79 (0.15), residues: 1279 sheet: -1.10 (0.18), residues: 746 loop : -2.31 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG K 396 TYR 0.023 0.001 TYR M 279 PHE 0.021 0.002 PHE M 563 TRP 0.016 0.001 TRP H 96 HIS 0.007 0.001 HIS K 64 Details of bonding type rmsd covalent geometry : bond 0.00342 (32289) covalent geometry : angle 0.59719 (43875) hydrogen bonds : bond 0.04209 ( 1372) hydrogen bonds : angle 4.57368 ( 3856) metal coordination : bond 0.01188 ( 4) metal coordination : angle 1.56031 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 393 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7927 (mtp) cc_final: 0.7477 (mtt) REVERT: A 121 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7488 (pp) REVERT: A 282 PHE cc_start: 0.8176 (m-80) cc_final: 0.7824 (m-80) REVERT: B 22 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7926 (ptt90) REVERT: B 28 MET cc_start: 0.8946 (mtp) cc_final: 0.8716 (mtm) REVERT: B 171 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8706 (t70) REVERT: C 167 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: C 226 MET cc_start: 0.8741 (tpt) cc_final: 0.8502 (tpt) REVERT: D 63 GLU cc_start: 0.8310 (tt0) cc_final: 0.8049 (tt0) REVERT: D 143 ASP cc_start: 0.8619 (t70) cc_final: 0.8398 (t0) REVERT: E 72 GLU cc_start: 0.8035 (mp0) cc_final: 0.7714 (tm-30) REVERT: E 74 PRO cc_start: 0.8116 (Cg_endo) cc_final: 0.7664 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8612 (mptp) cc_final: 0.8194 (mttp) REVERT: F 50 LYS cc_start: 0.9092 (tttt) cc_final: 0.8739 (tttp) REVERT: F 111 ARG cc_start: 0.7603 (ptp-110) cc_final: 0.7060 (mtp85) REVERT: F 178 ASP cc_start: 0.8390 (t0) cc_final: 0.8180 (t0) REVERT: G 103 ASP cc_start: 0.7979 (p0) cc_final: 0.7522 (p0) REVERT: G 105 GLN cc_start: 0.8496 (mp10) cc_final: 0.8181 (mp10) REVERT: G 164 TYR cc_start: 0.9011 (t80) cc_final: 0.8679 (t80) REVERT: G 250 LEU cc_start: 0.8538 (tp) cc_final: 0.8067 (mt) REVERT: H 105 ASP cc_start: 0.7838 (t0) cc_final: 0.7463 (t70) REVERT: H 129 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7931 (mm) REVERT: H 253 ASP cc_start: 0.8061 (t0) cc_final: 0.7605 (p0) REVERT: H 282 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: K 238 GLN cc_start: 0.7323 (pt0) cc_final: 0.6753 (mm-40) REVERT: K 265 ILE cc_start: 0.7646 (mm) cc_final: 0.6946 (mm) REVERT: K 470 LEU cc_start: 0.8818 (mp) cc_final: 0.8502 (tp) REVERT: K 926 SER cc_start: 0.8591 (m) cc_final: 0.8214 (p) REVERT: L 63 SER cc_start: 0.9106 (t) cc_final: 0.8546 (t) REVERT: L 67 CYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7561 (m) REVERT: L 91 MET cc_start: 0.8800 (mmm) cc_final: 0.8280 (mtt) REVERT: M 279 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7195 (p90) REVERT: M 386 PHE cc_start: 0.8515 (m-10) cc_final: 0.8030 (m-10) REVERT: M 450 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8439 (mtm-85) REVERT: M 487 MET cc_start: 0.6752 (tpp) cc_final: 0.6361 (tpp) REVERT: M 491 MET cc_start: 0.7477 (mpp) cc_final: 0.7258 (mpp) REVERT: M 569 MET cc_start: 0.8635 (ttp) cc_final: 0.8413 (ttp) REVERT: M 872 MET cc_start: 0.8313 (tpp) cc_final: 0.7936 (ttm) REVERT: M 891 MET cc_start: 0.8701 (mtm) cc_final: 0.8440 (mtp) REVERT: M 912 PHE cc_start: 0.7548 (m-10) cc_final: 0.7316 (m-10) outliers start: 71 outliers final: 40 residues processed: 439 average time/residue: 0.2177 time to fit residues: 152.9348 Evaluate side-chains 384 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 336 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 282 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 279 TYR Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 353 optimal weight: 7.9990 chunk 371 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN F 249 GLN G 88 HIS K 583 ASN M 317 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.110337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.088227 restraints weight = 62617.823| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.19 r_work: 0.3128 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32293 Z= 0.153 Angle : 0.590 9.404 43878 Z= 0.300 Chirality : 0.042 0.298 5054 Planarity : 0.004 0.060 5456 Dihedral : 10.812 172.816 5043 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 12.18 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3839 helix: 1.09 (0.15), residues: 1274 sheet: -0.85 (0.18), residues: 757 loop : -2.02 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 396 TYR 0.019 0.001 TYR M 279 PHE 0.018 0.002 PHE M 563 TRP 0.022 0.002 TRP M 511 HIS 0.006 0.001 HIS M 305 Details of bonding type rmsd covalent geometry : bond 0.00361 (32289) covalent geometry : angle 0.59012 (43875) hydrogen bonds : bond 0.04112 ( 1372) hydrogen bonds : angle 4.43473 ( 3856) metal coordination : bond 0.00812 ( 4) metal coordination : angle 1.23458 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 355 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (tt) REVERT: A 121 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7622 (pp) REVERT: A 229 ARG cc_start: 0.8277 (mpt-90) cc_final: 0.7503 (mmt90) REVERT: A 240 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6679 (pp) REVERT: B 22 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8264 (ptt90) REVERT: B 28 MET cc_start: 0.8965 (mtp) cc_final: 0.8751 (mtm) REVERT: B 186 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8142 (pt) REVERT: C 28 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 167 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: C 226 MET cc_start: 0.8901 (tpt) cc_final: 0.8682 (tpt) REVERT: D 143 ASP cc_start: 0.8676 (t70) cc_final: 0.8471 (t0) REVERT: E 33 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7076 (ptt90) REVERT: E 72 GLU cc_start: 0.8203 (mp0) cc_final: 0.7837 (tm-30) REVERT: E 74 PRO cc_start: 0.8174 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8690 (mptp) cc_final: 0.8297 (mttp) REVERT: F 50 LYS cc_start: 0.9106 (tttt) cc_final: 0.8682 (tttp) REVERT: F 111 ARG cc_start: 0.7733 (ptp-110) cc_final: 0.7206 (mtp85) REVERT: G 103 ASP cc_start: 0.8110 (p0) cc_final: 0.7567 (p0) REVERT: G 105 GLN cc_start: 0.8531 (mp10) cc_final: 0.8220 (mp10) REVERT: G 188 ASN cc_start: 0.8509 (p0) cc_final: 0.8096 (p0) REVERT: G 250 LEU cc_start: 0.8532 (tp) cc_final: 0.8080 (mt) REVERT: H 253 ASP cc_start: 0.8139 (t0) cc_final: 0.7774 (p0) REVERT: H 282 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (mtp) REVERT: K 201 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5591 (mm) REVERT: K 238 GLN cc_start: 0.7343 (pt0) cc_final: 0.6775 (mm-40) REVERT: K 265 ILE cc_start: 0.7754 (mm) cc_final: 0.7113 (mm) REVERT: K 470 LEU cc_start: 0.8825 (mp) cc_final: 0.8464 (tt) REVERT: K 667 MET cc_start: 0.7838 (mmm) cc_final: 0.7436 (mmm) REVERT: K 711 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6436 (mm) REVERT: L 67 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7594 (m) REVERT: L 78 ARG cc_start: 0.7931 (ptm-80) cc_final: 0.7657 (ptm-80) REVERT: M 253 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8030 (mt-10) REVERT: M 386 PHE cc_start: 0.8659 (m-10) cc_final: 0.8240 (m-10) REVERT: M 450 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8457 (mtm-85) REVERT: M 487 MET cc_start: 0.6907 (tpp) cc_final: 0.6417 (tpp) REVERT: M 491 MET cc_start: 0.7565 (mpp) cc_final: 0.7265 (mmp) REVERT: M 872 MET cc_start: 0.8451 (tpp) cc_final: 0.8034 (ttm) REVERT: M 891 MET cc_start: 0.8819 (mtm) cc_final: 0.8594 (mtp) outliers start: 87 outliers final: 48 residues processed: 417 average time/residue: 0.2082 time to fit residues: 139.3894 Evaluate side-chains 381 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 282 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 711 LEU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1033 ASP Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 185 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 34 optimal weight: 0.5980 chunk 377 optimal weight: 7.9990 chunk 228 optimal weight: 0.0050 chunk 28 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081878 restraints weight = 62687.764| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.18 r_work: 0.3145 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 32293 Z= 0.117 Angle : 0.549 9.499 43878 Z= 0.280 Chirality : 0.041 0.302 5054 Planarity : 0.003 0.058 5456 Dihedral : 10.707 172.708 5043 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.65 % Allowed : 13.23 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3839 helix: 1.34 (0.15), residues: 1274 sheet: -0.63 (0.19), residues: 749 loop : -1.81 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 123 TYR 0.013 0.001 TYR H 252 PHE 0.025 0.001 PHE K 904 TRP 0.018 0.001 TRP H 96 HIS 0.005 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00269 (32289) covalent geometry : angle 0.54936 (43875) hydrogen bonds : bond 0.03709 ( 1372) hydrogen bonds : angle 4.26774 ( 3856) metal coordination : bond 0.00466 ( 4) metal coordination : angle 0.91436 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 367 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7428 (pp) REVERT: A 229 ARG cc_start: 0.8255 (mpt-90) cc_final: 0.7450 (mmt90) REVERT: A 240 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6563 (pp) REVERT: B 186 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7999 (pt) REVERT: B 236 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7391 (ttt90) REVERT: C 28 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 76 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8515 (tt) REVERT: D 143 ASP cc_start: 0.8701 (t70) cc_final: 0.8469 (t0) REVERT: E 33 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7770 (pmt100) REVERT: E 74 PRO cc_start: 0.8184 (Cg_endo) cc_final: 0.7762 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8707 (mptp) cc_final: 0.8241 (mttp) REVERT: F 50 LYS cc_start: 0.9040 (tttt) cc_final: 0.8624 (tttp) REVERT: F 111 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7215 (mtp85) REVERT: G 103 ASP cc_start: 0.8088 (p0) cc_final: 0.7481 (p0) REVERT: G 105 GLN cc_start: 0.8542 (mp10) cc_final: 0.8214 (mp10) REVERT: G 182 ASP cc_start: 0.8047 (t0) cc_final: 0.7775 (t0) REVERT: G 188 ASN cc_start: 0.8557 (p0) cc_final: 0.8190 (p0) REVERT: G 250 LEU cc_start: 0.8510 (tp) cc_final: 0.8156 (mt) REVERT: H 253 ASP cc_start: 0.8114 (t0) cc_final: 0.7688 (p0) REVERT: H 282 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7905 (mtp) REVERT: I 133 ILE cc_start: 0.5986 (OUTLIER) cc_final: 0.5599 (pt) REVERT: K 158 GLU cc_start: 0.7555 (tp30) cc_final: 0.7315 (tt0) REVERT: K 201 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5529 (mm) REVERT: K 238 GLN cc_start: 0.7307 (pt0) cc_final: 0.6693 (mm-40) REVERT: K 265 ILE cc_start: 0.7767 (mm) cc_final: 0.7153 (mm) REVERT: K 432 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7918 (p) REVERT: K 470 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8485 (tt) REVERT: K 667 MET cc_start: 0.7885 (mmm) cc_final: 0.7448 (mmm) REVERT: K 711 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6316 (mm) REVERT: K 723 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: K 817 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7294 (tt) REVERT: L 67 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7530 (m) REVERT: L 78 ARG cc_start: 0.7899 (ptm-80) cc_final: 0.7663 (ptm-80) REVERT: M 386 PHE cc_start: 0.8670 (m-10) cc_final: 0.8217 (m-10) REVERT: M 450 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8423 (mtm-85) REVERT: M 491 MET cc_start: 0.7569 (mpp) cc_final: 0.7303 (mpp) REVERT: M 553 LYS cc_start: 0.7475 (pttm) cc_final: 0.7072 (ptmt) REVERT: M 836 LYS cc_start: 0.3253 (mptt) cc_final: 0.2896 (mmtm) REVERT: M 872 MET cc_start: 0.8439 (tpp) cc_final: 0.8044 (ttm) REVERT: M 891 MET cc_start: 0.8861 (mtm) cc_final: 0.8620 (mtp) REVERT: M 973 TRP cc_start: 0.8436 (t-100) cc_final: 0.8152 (t-100) outliers start: 88 outliers final: 49 residues processed: 431 average time/residue: 0.2135 time to fit residues: 148.0992 Evaluate side-chains 392 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 329 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 282 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 711 LEU Chi-restraints excluded: chain K residue 723 GLU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1007 MET Chi-restraints excluded: chain M residue 1033 ASP Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 375 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 310 optimal weight: 0.7980 chunk 258 optimal weight: 0.0470 chunk 231 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 311 optimal weight: 0.4980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS H 64 ASN K 371 HIS ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 898 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081701 restraints weight = 62779.236| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.18 r_work: 0.3141 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 32293 Z= 0.114 Angle : 0.544 11.292 43878 Z= 0.276 Chirality : 0.041 0.288 5054 Planarity : 0.003 0.059 5456 Dihedral : 10.664 173.044 5043 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.77 % Allowed : 13.98 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3839 helix: 1.51 (0.15), residues: 1267 sheet: -0.48 (0.19), residues: 763 loop : -1.71 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.013 0.001 TYR M 319 PHE 0.019 0.001 PHE A 77 TRP 0.018 0.001 TRP H 96 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00263 (32289) covalent geometry : angle 0.54372 (43875) hydrogen bonds : bond 0.03626 ( 1372) hydrogen bonds : angle 4.17985 ( 3856) metal coordination : bond 0.00264 ( 4) metal coordination : angle 0.77891 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 121 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7452 (pp) REVERT: A 187 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6786 (pp) REVERT: A 200 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6521 (mt0) REVERT: A 229 ARG cc_start: 0.8252 (mpt-90) cc_final: 0.7466 (mmt90) REVERT: A 240 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6479 (pp) REVERT: A 241 MET cc_start: 0.8494 (mpp) cc_final: 0.8086 (mmt) REVERT: B 186 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8077 (pt) REVERT: C 28 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8210 (tm-30) REVERT: D 76 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8501 (tt) REVERT: D 143 ASP cc_start: 0.8710 (t70) cc_final: 0.8473 (t0) REVERT: E 74 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7766 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8712 (mptp) cc_final: 0.8035 (mttp) REVERT: F 15 GLN cc_start: 0.8171 (pm20) cc_final: 0.7680 (pt0) REVERT: F 50 LYS cc_start: 0.9044 (tttt) cc_final: 0.8630 (tttp) REVERT: F 111 ARG cc_start: 0.7721 (ptp-110) cc_final: 0.7205 (mtp85) REVERT: G 103 ASP cc_start: 0.8032 (p0) cc_final: 0.7416 (p0) REVERT: G 105 GLN cc_start: 0.8563 (mp10) cc_final: 0.8220 (mp10) REVERT: G 188 ASN cc_start: 0.8570 (p0) cc_final: 0.8199 (p0) REVERT: G 250 LEU cc_start: 0.8510 (tp) cc_final: 0.8169 (mt) REVERT: H 253 ASP cc_start: 0.8092 (t0) cc_final: 0.7698 (p0) REVERT: H 282 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (mtp) REVERT: K 158 GLU cc_start: 0.7601 (tp30) cc_final: 0.7291 (tt0) REVERT: K 201 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5898 (mt) REVERT: K 238 GLN cc_start: 0.7308 (pt0) cc_final: 0.6697 (mm-40) REVERT: K 265 ILE cc_start: 0.7782 (mm) cc_final: 0.7174 (mm) REVERT: K 470 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8534 (tt) REVERT: K 581 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8747 (m) REVERT: K 613 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7546 (tp) REVERT: K 667 MET cc_start: 0.7939 (mmm) cc_final: 0.7569 (mmm) REVERT: K 681 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: K 711 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6315 (mm) REVERT: K 723 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: K 817 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7328 (tt) REVERT: L 67 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7471 (m) REVERT: M 227 MET cc_start: 0.7671 (ptt) cc_final: 0.7462 (ptt) REVERT: M 253 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8086 (mt-10) REVERT: M 386 PHE cc_start: 0.8610 (m-10) cc_final: 0.8141 (m-10) REVERT: M 404 LEU cc_start: 0.8654 (mp) cc_final: 0.8368 (tp) REVERT: M 450 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8334 (mtm-85) REVERT: M 487 MET cc_start: 0.6607 (tpp) cc_final: 0.6338 (tpp) REVERT: M 491 MET cc_start: 0.7690 (mpp) cc_final: 0.7392 (mpp) REVERT: M 553 LYS cc_start: 0.7546 (pttm) cc_final: 0.7154 (ptmt) REVERT: M 836 LYS cc_start: 0.3130 (mptt) cc_final: 0.2844 (mmtm) REVERT: M 872 MET cc_start: 0.8465 (tpp) cc_final: 0.8066 (ttm) outliers start: 92 outliers final: 52 residues processed: 421 average time/residue: 0.2115 time to fit residues: 142.1209 Evaluate side-chains 403 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 282 MET Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 711 LEU Chi-restraints excluded: chain K residue 723 GLU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1007 MET Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 279 optimal weight: 0.4980 chunk 222 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 318 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN D 30 HIS H 64 ASN ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.086847 restraints weight = 63147.845| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.18 r_work: 0.3097 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32293 Z= 0.162 Angle : 0.577 9.960 43878 Z= 0.293 Chirality : 0.042 0.277 5054 Planarity : 0.004 0.055 5456 Dihedral : 10.701 174.389 5043 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.07 % Allowed : 14.01 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3839 helix: 1.46 (0.15), residues: 1274 sheet: -0.39 (0.18), residues: 768 loop : -1.69 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 78 TYR 0.015 0.001 TYR M 319 PHE 0.019 0.002 PHE K 416 TRP 0.015 0.001 TRP H 96 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00387 (32289) covalent geometry : angle 0.57650 (43875) hydrogen bonds : bond 0.03937 ( 1372) hydrogen bonds : angle 4.25526 ( 3856) metal coordination : bond 0.00281 ( 4) metal coordination : angle 0.87203 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 336 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8791 (tt) REVERT: A 121 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7666 (pp) REVERT: A 187 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6906 (pp) REVERT: A 200 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6794 (mt0) REVERT: A 229 ARG cc_start: 0.8307 (mpt-90) cc_final: 0.7473 (mmt90) REVERT: A 240 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6581 (pp) REVERT: A 241 MET cc_start: 0.8541 (mpp) cc_final: 0.8100 (mmt) REVERT: B 22 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8196 (ptt90) REVERT: B 176 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: B 186 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8199 (pt) REVERT: C 28 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 76 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8517 (tt) REVERT: D 143 ASP cc_start: 0.8707 (t70) cc_final: 0.8489 (t0) REVERT: E 74 PRO cc_start: 0.8282 (Cg_endo) cc_final: 0.7907 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8756 (mptp) cc_final: 0.8099 (mttp) REVERT: F 20 TYR cc_start: 0.6769 (m-80) cc_final: 0.6177 (m-80) REVERT: F 50 LYS cc_start: 0.9126 (tttt) cc_final: 0.8685 (tttp) REVERT: F 111 ARG cc_start: 0.7764 (ptp-110) cc_final: 0.7246 (mtp85) REVERT: G 103 ASP cc_start: 0.8159 (p0) cc_final: 0.7888 (p0) REVERT: G 182 ASP cc_start: 0.8052 (t0) cc_final: 0.7827 (t0) REVERT: G 188 ASN cc_start: 0.8684 (p0) cc_final: 0.8272 (p0) REVERT: H 129 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8156 (mm) REVERT: H 220 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.6917 (mm) REVERT: H 253 ASP cc_start: 0.8140 (t0) cc_final: 0.7741 (p0) REVERT: K 158 GLU cc_start: 0.7615 (tp30) cc_final: 0.7288 (tt0) REVERT: K 201 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5797 (mm) REVERT: K 238 GLN cc_start: 0.7226 (pt0) cc_final: 0.6670 (mm-40) REVERT: K 265 ILE cc_start: 0.7856 (mm) cc_final: 0.7287 (mm) REVERT: K 470 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8505 (tt) REVERT: K 488 ASP cc_start: 0.7707 (t0) cc_final: 0.7378 (t0) REVERT: K 613 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7566 (tt) REVERT: K 681 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: K 711 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6319 (mm) REVERT: K 760 ASN cc_start: 0.7907 (t0) cc_final: 0.7661 (t0) REVERT: K 817 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7365 (tt) REVERT: L 67 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7584 (m) REVERT: M 386 PHE cc_start: 0.8670 (m-10) cc_final: 0.8147 (m-10) REVERT: M 404 LEU cc_start: 0.8681 (mp) cc_final: 0.8368 (tp) REVERT: M 450 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8357 (mtm-85) REVERT: M 454 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9150 (pp) REVERT: M 487 MET cc_start: 0.6667 (tpp) cc_final: 0.6434 (tpp) REVERT: M 491 MET cc_start: 0.7721 (mpp) cc_final: 0.7385 (mpp) REVERT: M 553 LYS cc_start: 0.7433 (pttm) cc_final: 0.7093 (ptmt) REVERT: M 836 LYS cc_start: 0.3325 (mptt) cc_final: 0.2957 (mmtm) REVERT: M 872 MET cc_start: 0.8518 (tpp) cc_final: 0.8087 (ttm) REVERT: M 921 MET cc_start: 0.6724 (mmm) cc_final: 0.6313 (tpt) outliers start: 102 outliers final: 64 residues processed: 409 average time/residue: 0.2069 time to fit residues: 136.5989 Evaluate side-chains 413 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 330 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 685 HIS Chi-restraints excluded: chain K residue 711 LEU Chi-restraints excluded: chain K residue 723 GLU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1007 MET Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 221 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 303 optimal weight: 0.3980 chunk 245 optimal weight: 0.1980 chunk 205 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 367 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 HIS H 64 ASN ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.102402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080407 restraints weight = 63052.308| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.17 r_work: 0.3114 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32293 Z= 0.124 Angle : 0.550 9.518 43878 Z= 0.279 Chirality : 0.041 0.271 5054 Planarity : 0.003 0.057 5456 Dihedral : 10.654 173.735 5043 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.98 % Allowed : 14.32 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3839 helix: 1.58 (0.15), residues: 1269 sheet: -0.34 (0.19), residues: 759 loop : -1.59 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 78 TYR 0.014 0.001 TYR M 319 PHE 0.016 0.001 PHE K 904 TRP 0.015 0.001 TRP H 96 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00287 (32289) covalent geometry : angle 0.54982 (43875) hydrogen bonds : bond 0.03701 ( 1372) hydrogen bonds : angle 4.17921 ( 3856) metal coordination : bond 0.00263 ( 4) metal coordination : angle 0.75775 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 340 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 121 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7525 (pp) REVERT: A 187 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6901 (pp) REVERT: A 200 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6825 (mt0) REVERT: A 229 ARG cc_start: 0.8260 (mpt-90) cc_final: 0.7456 (mmt90) REVERT: A 240 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6537 (pp) REVERT: A 241 MET cc_start: 0.8527 (mpp) cc_final: 0.8072 (mmt) REVERT: B 22 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8051 (ptt90) REVERT: B 176 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: B 186 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8177 (pt) REVERT: B 188 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8508 (pt) REVERT: C 28 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 217 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8184 (pp) REVERT: D 76 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8509 (tt) REVERT: D 143 ASP cc_start: 0.8705 (t70) cc_final: 0.8489 (t0) REVERT: E 74 PRO cc_start: 0.8214 (Cg_endo) cc_final: 0.7815 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8729 (mptp) cc_final: 0.8384 (mttp) REVERT: F 50 LYS cc_start: 0.9090 (tttt) cc_final: 0.8663 (tttp) REVERT: F 111 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7298 (mtp85) REVERT: G 103 ASP cc_start: 0.8176 (p0) cc_final: 0.7807 (p0) REVERT: H 129 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8288 (mm) REVERT: H 220 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.6918 (mm) REVERT: H 253 ASP cc_start: 0.8118 (t0) cc_final: 0.7786 (p0) REVERT: I 133 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5711 (pt) REVERT: K 201 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5700 (mm) REVERT: K 238 GLN cc_start: 0.7188 (pt0) cc_final: 0.6674 (mm-40) REVERT: K 265 ILE cc_start: 0.7901 (mm) cc_final: 0.7313 (mm) REVERT: K 432 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7977 (p) REVERT: K 470 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8477 (tt) REVERT: K 488 ASP cc_start: 0.7752 (t0) cc_final: 0.7424 (t0) REVERT: K 613 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7306 (tt) REVERT: K 681 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: K 711 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6266 (mm) REVERT: K 712 GLU cc_start: 0.7621 (tp30) cc_final: 0.7382 (tp30) REVERT: K 760 ASN cc_start: 0.7944 (t0) cc_final: 0.7663 (t0) REVERT: K 817 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7365 (tt) REVERT: L 67 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7509 (m) REVERT: L 78 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7834 (ppt90) REVERT: L 91 MET cc_start: 0.8840 (mmm) cc_final: 0.8537 (mtt) REVERT: M 386 PHE cc_start: 0.8661 (m-10) cc_final: 0.8132 (m-10) REVERT: M 404 LEU cc_start: 0.8674 (mp) cc_final: 0.8357 (tp) REVERT: M 450 ARG cc_start: 0.8601 (mtt180) cc_final: 0.8390 (mtm-85) REVERT: M 454 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9060 (pp) REVERT: M 491 MET cc_start: 0.7537 (mpp) cc_final: 0.7258 (mpp) REVERT: M 549 LYS cc_start: 0.8328 (tttm) cc_final: 0.8110 (mmmt) REVERT: M 836 LYS cc_start: 0.3641 (mptt) cc_final: 0.3276 (mmtm) REVERT: M 872 MET cc_start: 0.8471 (tpp) cc_final: 0.8030 (ttm) outliers start: 99 outliers final: 59 residues processed: 414 average time/residue: 0.1978 time to fit residues: 132.2728 Evaluate side-chains 399 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 317 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 711 LEU Chi-restraints excluded: chain K residue 723 GLU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1007 MET Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 231 optimal weight: 0.0980 chunk 214 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS H 64 ASN ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079982 restraints weight = 62944.618| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.17 r_work: 0.3106 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32293 Z= 0.135 Angle : 0.563 9.353 43878 Z= 0.285 Chirality : 0.041 0.260 5054 Planarity : 0.003 0.056 5456 Dihedral : 10.643 174.187 5043 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.83 % Allowed : 14.65 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3839 helix: 1.60 (0.15), residues: 1269 sheet: -0.29 (0.19), residues: 755 loop : -1.56 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 94 TYR 0.014 0.001 TYR M 319 PHE 0.017 0.001 PHE K 416 TRP 0.014 0.001 TRP H 96 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00319 (32289) covalent geometry : angle 0.56261 (43875) hydrogen bonds : bond 0.03737 ( 1372) hydrogen bonds : angle 4.17851 ( 3856) metal coordination : bond 0.00124 ( 4) metal coordination : angle 0.77649 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 334 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 121 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7616 (pp) REVERT: A 187 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6900 (pp) REVERT: A 200 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: A 229 ARG cc_start: 0.8273 (mpt-90) cc_final: 0.7466 (mmt90) REVERT: A 240 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6578 (pp) REVERT: A 241 MET cc_start: 0.8562 (mpp) cc_final: 0.8117 (mmt) REVERT: B 22 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8169 (ptt90) REVERT: B 176 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: B 186 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8208 (pt) REVERT: B 188 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8519 (pt) REVERT: C 28 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8239 (pp20) REVERT: C 217 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8212 (pp) REVERT: D 76 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 143 ASP cc_start: 0.8707 (t70) cc_final: 0.8492 (t0) REVERT: E 74 PRO cc_start: 0.8208 (Cg_endo) cc_final: 0.7805 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8758 (mptp) cc_final: 0.8410 (mttp) REVERT: F 50 LYS cc_start: 0.9108 (tttt) cc_final: 0.8684 (tttp) REVERT: F 111 ARG cc_start: 0.7836 (ptp-110) cc_final: 0.7328 (mtp85) REVERT: G 103 ASP cc_start: 0.8155 (p0) cc_final: 0.7814 (p0) REVERT: G 250 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8382 (mp) REVERT: H 129 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8354 (mm) REVERT: H 220 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6929 (mm) REVERT: H 253 ASP cc_start: 0.8137 (t0) cc_final: 0.7793 (p0) REVERT: I 86 HIS cc_start: 0.7028 (m90) cc_final: 0.6779 (m-70) REVERT: I 133 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5892 (pt) REVERT: K 238 GLN cc_start: 0.7228 (pt0) cc_final: 0.6697 (mm-40) REVERT: K 265 ILE cc_start: 0.7962 (mm) cc_final: 0.7386 (mm) REVERT: K 470 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8501 (tt) REVERT: K 488 ASP cc_start: 0.7731 (t0) cc_final: 0.7407 (t0) REVERT: K 613 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7341 (tt) REVERT: K 665 GLU cc_start: 0.7648 (pp20) cc_final: 0.6985 (mm-30) REVERT: K 681 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: K 711 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6217 (mm) REVERT: K 712 GLU cc_start: 0.7617 (tp30) cc_final: 0.7378 (tp30) REVERT: K 727 GLN cc_start: 0.8696 (mt0) cc_final: 0.8402 (pt0) REVERT: K 760 ASN cc_start: 0.7916 (t0) cc_final: 0.7590 (t0) REVERT: K 817 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7389 (tt) REVERT: L 67 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7459 (m) REVERT: L 78 ARG cc_start: 0.8211 (ptm-80) cc_final: 0.7758 (ppt90) REVERT: L 91 MET cc_start: 0.8836 (mmm) cc_final: 0.8552 (mtt) REVERT: M 386 PHE cc_start: 0.8677 (m-10) cc_final: 0.8137 (m-10) REVERT: M 404 LEU cc_start: 0.8717 (mp) cc_final: 0.8381 (tp) REVERT: M 450 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8402 (mtm-85) REVERT: M 454 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9039 (pp) REVERT: M 487 MET cc_start: 0.7043 (tpp) cc_final: 0.6634 (tpp) REVERT: M 491 MET cc_start: 0.7679 (mpp) cc_final: 0.7336 (mpp) REVERT: M 549 LYS cc_start: 0.8379 (tttm) cc_final: 0.8164 (mmmt) REVERT: M 836 LYS cc_start: 0.3864 (mptt) cc_final: 0.3449 (mmtm) REVERT: M 872 MET cc_start: 0.8488 (tpp) cc_final: 0.8066 (ttm) REVERT: M 921 MET cc_start: 0.6592 (mmm) cc_final: 0.6184 (tpt) REVERT: M 967 MET cc_start: 0.8158 (ttp) cc_final: 0.7787 (ttp) outliers start: 94 outliers final: 63 residues processed: 401 average time/residue: 0.2038 time to fit residues: 131.8273 Evaluate side-chains 411 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 326 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 711 LEU Chi-restraints excluded: chain K residue 723 GLU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain K residue 920 HIS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1007 MET Chi-restraints excluded: chain M residue 1035 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 182 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 330 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 225 optimal weight: 0.0000 chunk 359 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS H 64 ASN ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.103214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081303 restraints weight = 62661.535| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.16 r_work: 0.3133 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32293 Z= 0.107 Angle : 0.541 9.262 43878 Z= 0.274 Chirality : 0.040 0.253 5054 Planarity : 0.003 0.057 5456 Dihedral : 10.599 173.505 5043 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.62 % Allowed : 15.01 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3839 helix: 1.73 (0.15), residues: 1264 sheet: -0.23 (0.19), residues: 754 loop : -1.51 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 623 TYR 0.017 0.001 TYR M 595 PHE 0.015 0.001 PHE K 904 TRP 0.014 0.001 TRP H 96 HIS 0.008 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00242 (32289) covalent geometry : angle 0.54094 (43875) hydrogen bonds : bond 0.03486 ( 1372) hydrogen bonds : angle 4.09569 ( 3856) metal coordination : bond 0.00177 ( 4) metal coordination : angle 0.75339 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7678 Ramachandran restraints generated. 3839 Oldfield, 0 Emsley, 3839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 335 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8769 (tt) REVERT: A 121 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7468 (pp) REVERT: A 187 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6899 (pp) REVERT: A 200 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6845 (mt0) REVERT: A 229 ARG cc_start: 0.8224 (mpt-90) cc_final: 0.7428 (mmt90) REVERT: A 240 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6491 (pp) REVERT: A 241 MET cc_start: 0.8522 (mpp) cc_final: 0.8067 (mmt) REVERT: B 22 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8126 (ptt90) REVERT: B 186 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8131 (pt) REVERT: B 188 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8437 (pt) REVERT: C 28 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8182 (pp20) REVERT: C 217 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8147 (pp) REVERT: D 76 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8493 (tt) REVERT: D 143 ASP cc_start: 0.8702 (t70) cc_final: 0.8479 (t0) REVERT: E 74 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7749 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8741 (mptp) cc_final: 0.8394 (mttp) REVERT: F 50 LYS cc_start: 0.9049 (tttt) cc_final: 0.8616 (tttp) REVERT: F 111 ARG cc_start: 0.7821 (ptp-110) cc_final: 0.7300 (mtp85) REVERT: G 103 ASP cc_start: 0.8154 (p0) cc_final: 0.7756 (p0) REVERT: G 250 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8316 (mp) REVERT: H 220 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6906 (mm) REVERT: H 253 ASP cc_start: 0.8099 (t0) cc_final: 0.7765 (p0) REVERT: I 86 HIS cc_start: 0.6986 (m90) cc_final: 0.6759 (m-70) REVERT: K 64 HIS cc_start: 0.7262 (t70) cc_final: 0.5598 (t70) REVERT: K 238 GLN cc_start: 0.7273 (pt0) cc_final: 0.6717 (mm-40) REVERT: K 265 ILE cc_start: 0.7952 (mm) cc_final: 0.7370 (mm) REVERT: K 432 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7974 (p) REVERT: K 470 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8515 (tt) REVERT: K 488 ASP cc_start: 0.7728 (t0) cc_final: 0.7448 (t0) REVERT: K 613 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7314 (tt) REVERT: K 681 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: K 727 GLN cc_start: 0.8716 (mt0) cc_final: 0.8444 (pt0) REVERT: K 760 ASN cc_start: 0.7906 (t0) cc_final: 0.7566 (t0) REVERT: K 817 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7358 (tt) REVERT: L 63 SER cc_start: 0.9052 (t) cc_final: 0.8655 (p) REVERT: L 67 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7391 (m) REVERT: L 78 ARG cc_start: 0.8081 (ptm-80) cc_final: 0.7710 (ppt90) REVERT: L 91 MET cc_start: 0.8798 (mmm) cc_final: 0.8512 (mtt) REVERT: M 386 PHE cc_start: 0.8662 (m-10) cc_final: 0.8132 (m-10) REVERT: M 404 LEU cc_start: 0.8690 (mp) cc_final: 0.8350 (tp) REVERT: M 454 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.8997 (pp) REVERT: M 487 MET cc_start: 0.7115 (tpp) cc_final: 0.6726 (tpp) REVERT: M 491 MET cc_start: 0.7634 (mpp) cc_final: 0.7294 (mpp) REVERT: M 549 LYS cc_start: 0.8333 (tttm) cc_final: 0.8123 (mmmt) REVERT: M 836 LYS cc_start: 0.3947 (mptt) cc_final: 0.3615 (mmtm) REVERT: M 872 MET cc_start: 0.8467 (tpp) cc_final: 0.8069 (ttm) REVERT: M 921 MET cc_start: 0.6596 (mmm) cc_final: 0.6192 (tpt) REVERT: M 973 TRP cc_start: 0.8487 (t-100) cc_final: 0.8246 (t-100) outliers start: 87 outliers final: 56 residues processed: 400 average time/residue: 0.2092 time to fit residues: 134.6402 Evaluate side-chains 395 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 220 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain K residue 156 TYR Chi-restraints excluded: chain K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 681 GLU Chi-restraints excluded: chain K residue 723 GLU Chi-restraints excluded: chain K residue 733 PHE Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 817 LEU Chi-restraints excluded: chain K residue 832 VAL Chi-restraints excluded: chain K residue 867 TYR Chi-restraints excluded: chain K residue 873 VAL Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain K residue 909 VAL Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 350 LEU Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 1007 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 46 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 324 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 355 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN D 30 HIS H 64 ASN ** K 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078892 restraints weight = 63290.613| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.17 r_work: 0.3085 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32293 Z= 0.168 Angle : 0.588 9.174 43878 Z= 0.297 Chirality : 0.042 0.235 5054 Planarity : 0.004 0.056 5456 Dihedral : 10.641 174.980 5043 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 15.07 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3839 helix: 1.61 (0.15), residues: 1272 sheet: -0.18 (0.19), residues: 765 loop : -1.53 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 623 TYR 0.018 0.001 TYR M 595 PHE 0.020 0.002 PHE B 106 TRP 0.013 0.001 TRP H 96 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00403 (32289) covalent geometry : angle 0.58750 (43875) hydrogen bonds : bond 0.03922 ( 1372) hydrogen bonds : angle 4.22137 ( 3856) metal coordination : bond 0.00175 ( 4) metal coordination : angle 0.95507 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9614.61 seconds wall clock time: 164 minutes 40.54 seconds (9880.54 seconds total)