Starting phenix.real_space_refine on Mon Sep 14 16:36:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_7809.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_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_7809/09_2026/6d6r_7809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_7809.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_7809.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_7809.cif" model { file = "/net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_7809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d6r_7809/09_2026/6d6r_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): 0.28s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 13} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 966 Classifications: {'DNA': 13, 'RNAv2': 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: 31 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: 6.92, 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: 3.23 Conformation dependent library (CDL) restraints added in 1.3 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: 3.66 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: 7.29 Time building geometry restraints manager: 4.17 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 2.00e-02 2.50e+03 1.92e+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: 43289 2.49 - 4.98: 562 4.98 - 7.47: 18 7.47 - 9.96: 1 9.96 - 12.45: 2 Bond angle restraints: 43872 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=" N3 DT O 16 " pdb=" C4 DT O 16 " pdb=" O4 DT O 16 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT O 8 " pdb=" C4 DT O 8 " pdb=" O4 DT O 8 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" O4 DT O 16 " pdb=" C4 DT O 16 " pdb=" C5 DT O 16 " ideal model delta sigma weight residual 124.90 122.05 2.85 7.00e-01 2.04e+00 1.65e+01 angle pdb=" N3 DT O 13 " pdb=" C4 DT O 13 " pdb=" O4 DT O 13 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 43867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.55: 19427 33.55 - 67.10: 209 67.10 - 100.65: 21 100.65 - 134.20: 1 134.20 - 167.76: 1 Dihedral angle restraints: 19659 sinusoidal: 8434 harmonic: 11225 Sorted by residual: dihedral pdb=" C4' C O 49 " pdb=" C3' C O 49 " pdb=" C2' C O 49 " pdb=" C1' C O 49 " ideal model delta sinusoidal sigma weight residual 36.34 -36.41 72.75 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' A O 53 " pdb=" C3' A O 53 " pdb=" C2' A O 53 " pdb=" C1' A O 53 " ideal model delta sinusoidal sigma weight residual 36.34 -36.19 72.53 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' A O 62 " pdb=" C3' A O 62 " pdb=" C2' A O 62 " pdb=" C1' A O 62 " ideal model delta sinusoidal sigma weight residual 36.34 -35.66 72.01 1 3.10e+00 1.04e-01 6.90e+02 ... (remaining 19656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4989 0.166 - 0.333: 64 0.333 - 0.499: 0 0.499 - 0.666: 0 0.666 - 0.832: 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 2.17 -3.01 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C2' A O 62 " pdb=" C3' A O 62 " pdb=" O2' A O 62 " pdb=" C1' A O 62 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' C O 17 " pdb=" C3' C O 17 " pdb=" O2' C O 17 " pdb=" C1' C O 17 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.220 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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= 0.328 Angle : 0.702 12.446 43875 Z= 0.387 Chirality : 0.053 0.832 5054 Planarity : 0.004 0.051 5456 Dihedral : 10.614 167.755 12395 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/Z covalent geometry : bond 0.00790 / 0.33 (32289) covalent geometry : angle 0.70197 / 0.39 (43872) hydrogen bonds : bond 0.12567 / 8.60 ( 1372) hydrogen bonds : angle 6.26290 / 4.41 ( 3856) metal coordination : bond 0.10796 / 5.33 ( 4) metal coordination : angle 1.35140 / 0.73 ( 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 : 1.190 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: 0.6948 (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: 0.7586 (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: 0.7828 (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: 0.2287 time to fit residues: 267.3061 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 : 1.078 ------------------------------------------------------------------------------- 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... A 168 GLN A 188 HIS A 189 HIS B 33 GLN E 19 GLN E 114 ASN E 131 HIS E 162 ASN G 116 HIS H 199 ASN I 173 GLN J 632 GLN ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 919 GLN L 20 GLN L 92 ASN M 300 HIS M 898 ASN M 981 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.115932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094835 restraints weight = 62177.650| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.28 r_work: 0.3246 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32293 Z= 0.180 Angle : 0.772 22.084 43875 Z= 0.373 Chirality : 0.060 1.632 5054 Planarity : 0.005 0.057 5456 Dihedral : 9.579 160.248 4919 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.51 % Allowed : 8.50 % Favored : 89.99 % 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: -2.65 (0.13), residues: 3839 helix: -0.21 (0.14), residues: 1275 sheet: -1.73 (0.18), residues: 760 loop : -2.99 (0.12), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 527 TYR 0.030 0.002 TYR M 279 PHE 0.026 0.002 PHE M 563 TRP 0.015 0.002 TRP K 564 HIS 0.010 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (32289) covalent geometry : angle 0.77202 / 0.37 (43872) hydrogen bonds : bond 0.05042 / 3.49 ( 1372) hydrogen bonds : angle 5.14428 / 3.64 ( 3856) metal coordination : bond 0.01451 / 0.73 ( 4) metal coordination : angle 3.07246 / 1.65 ( 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 483 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 433 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7620 (pp) REVERT: A 229 ARG cc_start: 0.8164 (mpt-90) cc_final: 0.7733 (mmt90) REVERT: A 240 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6560 (pp) REVERT: C 9 GLU cc_start: 0.6113 (mp0) cc_final: 0.5066 (pt0) REVERT: D 143 ASP cc_start: 0.8511 (t70) cc_final: 0.8295 (t0) REVERT: E 233 LYS cc_start: 0.8570 (mptp) cc_final: 0.8251 (mttp) REVERT: F 50 LYS cc_start: 0.8983 (tttt) cc_final: 0.8648 (tttp) REVERT: G 164 TYR cc_start: 0.8988 (t80) cc_final: 0.8581 (t80) REVERT: H 93 GLN cc_start: 0.7508 (pm20) cc_final: 0.7236 (tp40) REVERT: H 94 LYS cc_start: 0.7514 (ttpp) cc_final: 0.7286 (ttpp) REVERT: H 105 ASP cc_start: 0.7805 (t0) cc_final: 0.7507 (t70) REVERT: H 128 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7668 (tm-30) REVERT: H 129 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8004 (mm) REVERT: H 253 ASP cc_start: 0.7837 (t0) cc_final: 0.7554 (p0) REVERT: I 16 ASN cc_start: 0.8002 (m-40) cc_final: 0.7601 (t0) REVERT: K 238 GLN cc_start: 0.7399 (pt0) cc_final: 0.6628 (mm-40) REVERT: K 265 ILE cc_start: 0.7187 (mm) cc_final: 0.6620 (mm) REVERT: K 473 LEU cc_start: 0.6944 (tp) cc_final: 0.6675 (tp) REVERT: K 926 SER cc_start: 0.8624 (m) cc_final: 0.8309 (p) REVERT: L 63 SER cc_start: 0.9090 (t) cc_final: 0.8635 (t) REVERT: L 91 MET cc_start: 0.8770 (mmm) cc_final: 0.8175 (mtt) REVERT: M 386 PHE cc_start: 0.8245 (m-10) cc_final: 0.7791 (m-10) REVERT: M 912 PHE cc_start: 0.7468 (m-10) cc_final: 0.7179 (m-10) REVERT: M 973 TRP cc_start: 0.8450 (t-100) cc_final: 0.8227 (t-100) REVERT: M 1007 MET cc_start: 0.7905 (mmm) cc_final: 0.7572 (mmt) outliers start: 50 outliers final: 26 residues processed: 473 average time/residue: 0.2026 time to fit residues: 153.7427 Evaluate side-chains 373 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 344 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 226 ASN 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 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 286 LYS 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 137 GLU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain K residue 185 ILE Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 738 THR Chi-restraints excluded: chain K residue 808 HIS Chi-restraints excluded: chain K residue 894 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS 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: 4.9990 chunk 21 optimal weight: 0.7980 chunk 308 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 229 GLN F 249 GLN H 101 ASN K 284 ASN M 300 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.112979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.091261 restraints weight = 62541.817| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.26 r_work: 0.3178 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 32293 Z= 0.180 Angle : 0.693 22.445 43875 Z= 0.338 Chirality : 0.055 1.641 5054 Planarity : 0.004 0.060 5456 Dihedral : 9.431 169.855 4919 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.26 % Allowed : 9.73 % Favored : 88.00 % 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: -1.83 (0.13), residues: 3839 helix: 0.43 (0.15), residues: 1287 sheet: -1.28 (0.18), residues: 765 loop : -2.48 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 396 TYR 0.020 0.002 TYR K 772 PHE 0.030 0.002 PHE M 563 TRP 0.023 0.002 TRP K 405 HIS 0.010 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (32289) covalent geometry : angle 0.69265 / 0.34 (43872) hydrogen bonds : bond 0.04662 / 3.20 ( 1372) hydrogen bonds : angle 4.83926 / 3.44 ( 3856) metal coordination : bond 0.01413 / 0.71 ( 4) metal coordination : angle 2.17926 / 1.15 ( 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 456 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 381 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7589 (pp) REVERT: A 229 ARG cc_start: 0.8243 (mpt-90) cc_final: 0.7720 (mmt90) REVERT: A 240 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6575 (pp) REVERT: B 22 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7696 (ptt90) REVERT: C 226 MET cc_start: 0.8775 (tpt) cc_final: 0.8405 (tpt) REVERT: D 63 GLU cc_start: 0.8360 (tt0) cc_final: 0.7914 (tt0) REVERT: D 143 ASP cc_start: 0.8662 (t70) cc_final: 0.8453 (t0) REVERT: E 233 LYS cc_start: 0.8574 (mptp) cc_final: 0.8141 (mttp) REVERT: F 50 LYS cc_start: 0.9079 (tttt) cc_final: 0.8731 (tttp) REVERT: G 103 ASP cc_start: 0.7902 (p0) cc_final: 0.7678 (p0) REVERT: G 173 ASP cc_start: 0.8210 (m-30) cc_final: 0.7976 (m-30) REVERT: G 250 LEU cc_start: 0.8514 (tp) cc_final: 0.8001 (mt) REVERT: H 105 ASP cc_start: 0.7826 (t0) cc_final: 0.7510 (t70) REVERT: H 128 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7732 (tm-30) REVERT: H 253 ASP cc_start: 0.8019 (t0) cc_final: 0.7621 (p0) REVERT: H 282 MET cc_start: 0.8212 (mmm) cc_final: 0.7957 (mtp) REVERT: I 120 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7892 (mmmt) REVERT: I 164 MET cc_start: 0.8260 (mtp) cc_final: 0.8025 (mtm) REVERT: K 96 GLN cc_start: 0.7536 (tt0) cc_final: 0.7056 (tm-30) REVERT: K 186 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5892 (mm-30) REVERT: K 238 GLN cc_start: 0.7384 (pt0) cc_final: 0.6650 (mm-40) REVERT: K 265 ILE cc_start: 0.7541 (mm) cc_final: 0.6841 (mm) REVERT: K 667 MET cc_start: 0.7661 (mmm) cc_final: 0.7287 (mmm) REVERT: K 772 TYR cc_start: 0.8242 (t80) cc_final: 0.8030 (t80) REVERT: K 926 SER cc_start: 0.8575 (m) cc_final: 0.8263 (p) REVERT: L 91 MET cc_start: 0.8801 (mmm) cc_final: 0.8335 (mtt) REVERT: M 253 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7954 (mt-10) REVERT: M 386 PHE cc_start: 0.8474 (m-10) cc_final: 0.8152 (m-10) REVERT: M 426 ASN cc_start: 0.8298 (m110) cc_final: 0.7851 (m110) REVERT: M 487 MET cc_start: 0.6722 (tpp) cc_final: 0.6291 (tpp) REVERT: M 511 TRP cc_start: 0.8493 (m-10) cc_final: 0.8184 (m-10) REVERT: M 912 PHE cc_start: 0.7735 (m-10) cc_final: 0.7522 (m-10) outliers start: 75 outliers final: 42 residues processed: 435 average time/residue: 0.1967 time to fit residues: 138.1387 Evaluate side-chains 380 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 334 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 A residue 226 ASN 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 197 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain I residue 8 CYS 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 K residue 171 VAL Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 432 VAL 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 M residue 170 CYS 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: 4.9990 chunk 371 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 326 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 249 GLN J 632 GLN K 583 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082395 restraints weight = 62499.556| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.14 r_work: 0.3157 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32293 Z= 0.166 Angle : 0.662 20.276 43875 Z= 0.323 Chirality : 0.053 1.627 5054 Planarity : 0.004 0.060 5456 Dihedral : 9.343 174.187 4919 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.65 % Allowed : 11.00 % Favored : 86.35 % 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: -1.41 (0.13), residues: 3839 helix: 0.73 (0.15), residues: 1281 sheet: -0.99 (0.18), residues: 748 loop : -2.20 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 78 TYR 0.014 0.001 TYR F 252 PHE 0.020 0.002 PHE M 563 TRP 0.017 0.002 TRP M 973 HIS 0.011 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (32289) covalent geometry : angle 0.66139 / 0.32 (43872) hydrogen bonds : bond 0.04426 / 3.03 ( 1372) hydrogen bonds : angle 4.64019 / 3.31 ( 3856) metal coordination : bond 0.01105 / 0.55 ( 4) metal coordination : angle 1.77649 / 0.95 ( 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 445 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 357 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7429 (pp) REVERT: A 229 ARG cc_start: 0.8255 (mpt-90) cc_final: 0.7701 (mmt90) REVERT: A 240 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6541 (pp) REVERT: B 22 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8021 (ptt90) REVERT: B 186 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7984 (pt) REVERT: C 138 ASP cc_start: 0.8446 (m-30) cc_final: 0.8224 (m-30) REVERT: D 63 GLU cc_start: 0.8319 (tt0) cc_final: 0.8050 (tt0) REVERT: D 143 ASP cc_start: 0.8619 (t70) cc_final: 0.8403 (t0) REVERT: D 172 LYS cc_start: 0.7956 (pttp) cc_final: 0.7739 (ptmm) REVERT: E 33 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7193 (ptt90) REVERT: E 74 PRO cc_start: 0.8212 (Cg_endo) cc_final: 0.7832 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8596 (mptp) cc_final: 0.8255 (mttp) REVERT: F 50 LYS cc_start: 0.9115 (tttt) cc_final: 0.8750 (tttp) REVERT: F 111 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.7093 (mtp85) REVERT: G 103 ASP cc_start: 0.7926 (p0) cc_final: 0.7704 (p0) REVERT: G 158 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7574 (mm110) REVERT: G 161 ASP cc_start: 0.8501 (m-30) cc_final: 0.8078 (m-30) REVERT: G 182 ASP cc_start: 0.8197 (t0) cc_final: 0.7897 (t0) REVERT: G 188 ASN cc_start: 0.8328 (p0) cc_final: 0.7910 (p0) REVERT: G 250 LEU cc_start: 0.8576 (tp) cc_final: 0.8051 (mt) REVERT: H 105 ASP cc_start: 0.7793 (t0) cc_final: 0.7469 (t70) REVERT: H 129 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8080 (mm) REVERT: H 253 ASP cc_start: 0.8050 (t0) cc_final: 0.7665 (p0) REVERT: H 282 MET cc_start: 0.8198 (mmm) cc_final: 0.7968 (mtp) REVERT: I 164 MET cc_start: 0.8185 (mtp) cc_final: 0.7934 (mtm) REVERT: I 173 GLN cc_start: 0.7134 (tt0) cc_final: 0.6760 (tt0) REVERT: K 96 GLN cc_start: 0.7509 (tt0) cc_final: 0.7188 (tm-30) REVERT: K 201 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5104 (mm) REVERT: K 238 GLN cc_start: 0.7187 (pt0) cc_final: 0.6578 (mm-40) REVERT: K 265 ILE cc_start: 0.7666 (mm) cc_final: 0.6969 (mm) REVERT: K 289 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7040 (tm-30) REVERT: K 470 LEU cc_start: 0.8783 (mp) cc_final: 0.8505 (tp) REVERT: K 542 GLU cc_start: 0.7103 (pm20) cc_final: 0.6849 (pm20) REVERT: K 667 MET cc_start: 0.7768 (mmm) cc_final: 0.7371 (mmm) REVERT: M 386 PHE cc_start: 0.8565 (m-10) cc_final: 0.8213 (m-10) REVERT: M 454 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9278 (pp) REVERT: M 487 MET cc_start: 0.6779 (tpp) cc_final: 0.6270 (tpp) REVERT: M 491 MET cc_start: 0.7475 (mpp) cc_final: 0.7243 (mmt) REVERT: M 511 TRP cc_start: 0.8507 (m-10) cc_final: 0.8211 (m-10) REVERT: M 569 MET cc_start: 0.8604 (ttp) cc_final: 0.8375 (ttp) outliers start: 88 outliers final: 54 residues processed: 420 average time/residue: 0.1960 time to fit residues: 132.8122 Evaluate side-chains 390 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 206 LEU 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 C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 49 GLN 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 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 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 E residue 286 LYS 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 128 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 42 MET 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 495 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 894 LEU Chi-restraints excluded: chain L residue 59 ILE 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 512 ILE Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 848 MET 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: 2.9990 chunk 117 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 228 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS F 127 GLN F 249 GLN J 632 GLN K 920 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089452 restraints weight = 62465.630| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.19 r_work: 0.3152 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32293 Z= 0.138 Angle : 0.627 20.650 43875 Z= 0.306 Chirality : 0.051 1.549 5054 Planarity : 0.004 0.061 5456 Dihedral : 9.270 177.937 4919 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.71 % Allowed : 11.84 % Favored : 85.44 % 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: -1.13 (0.13), residues: 3839 helix: 0.96 (0.15), residues: 1274 sheet: -0.82 (0.18), residues: 744 loop : -2.01 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 396 TYR 0.022 0.001 TYR K 258 PHE 0.018 0.001 PHE M 912 TRP 0.016 0.001 TRP H 96 HIS 0.009 0.001 HIS K 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (32289) covalent geometry : angle 0.62701 / 0.31 (43872) hydrogen bonds : bond 0.04181 / 2.86 ( 1372) hydrogen bonds : angle 4.51199 / 3.21 ( 3856) metal coordination : bond 0.00859 / 0.43 ( 4) metal coordination : angle 1.53313 / 0.82 ( 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 449 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 359 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8748 (m-80) cc_final: 0.8327 (m-80) REVERT: A 121 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7392 (pp) REVERT: A 180 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.6881 (ptp-170) REVERT: B 22 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7908 (ptt90) REVERT: C 28 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 138 ASP cc_start: 0.8494 (m-30) cc_final: 0.8233 (m-30) REVERT: D 63 GLU cc_start: 0.8313 (tt0) cc_final: 0.8025 (tt0) REVERT: D 143 ASP cc_start: 0.8641 (t70) cc_final: 0.8439 (t0) REVERT: E 33 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7112 (ptt90) REVERT: E 74 PRO cc_start: 0.8201 (Cg_endo) cc_final: 0.7828 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8651 (mptp) cc_final: 0.8282 (mttp) REVERT: F 50 LYS cc_start: 0.9105 (tttt) cc_final: 0.8669 (tttp) REVERT: F 111 ARG cc_start: 0.7682 (ptp-110) cc_final: 0.7102 (mtp85) REVERT: F 257 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7978 (mt0) REVERT: G 103 ASP cc_start: 0.7927 (p0) cc_final: 0.7662 (p0) REVERT: G 182 ASP cc_start: 0.8158 (t0) cc_final: 0.7859 (t0) REVERT: G 188 ASN cc_start: 0.8369 (p0) cc_final: 0.7938 (p0) REVERT: G 250 LEU cc_start: 0.8539 (tp) cc_final: 0.8073 (mt) REVERT: H 93 GLN cc_start: 0.7664 (tp40) cc_final: 0.7406 (tp-100) REVERT: H 105 ASP cc_start: 0.7822 (t0) cc_final: 0.7489 (t70) REVERT: H 107 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8879 (m) REVERT: H 129 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8020 (mm) REVERT: H 253 ASP cc_start: 0.8053 (t0) cc_final: 0.7709 (p0) REVERT: H 269 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8088 (ttpt) REVERT: H 282 MET cc_start: 0.8164 (mmm) cc_final: 0.7958 (mtp) REVERT: I 164 MET cc_start: 0.8194 (mtp) cc_final: 0.7963 (mtm) REVERT: I 173 GLN cc_start: 0.7149 (tt0) cc_final: 0.6776 (tt0) REVERT: K 96 GLN cc_start: 0.7522 (tt0) cc_final: 0.7186 (tm-30) REVERT: K 201 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5447 (mm) REVERT: K 238 GLN cc_start: 0.7184 (pt0) cc_final: 0.6577 (mm-40) REVERT: K 265 ILE cc_start: 0.7722 (mm) cc_final: 0.7053 (mm) REVERT: K 289 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7015 (tm-30) REVERT: K 470 LEU cc_start: 0.8802 (mp) cc_final: 0.8499 (tp) REVERT: K 667 MET cc_start: 0.7837 (mmm) cc_final: 0.7437 (mmm) REVERT: K 817 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7213 (tt) REVERT: M 253 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7878 (mt-10) REVERT: M 386 PHE cc_start: 0.8562 (m-10) cc_final: 0.8183 (m-10) REVERT: M 454 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9273 (pp) REVERT: M 487 MET cc_start: 0.6838 (tpp) cc_final: 0.6289 (tpp) REVERT: M 491 MET cc_start: 0.7610 (mpp) cc_final: 0.7290 (mmp) REVERT: M 529 MET cc_start: 0.8402 (mtm) cc_final: 0.8158 (mtp) REVERT: M 553 LYS cc_start: 0.7511 (pttm) cc_final: 0.6915 (tttt) REVERT: M 569 MET cc_start: 0.8648 (ttp) cc_final: 0.8415 (ttp) REVERT: M 872 MET cc_start: 0.8343 (tpp) cc_final: 0.7914 (ttm) REVERT: M 912 PHE cc_start: 0.7528 (m-10) cc_final: 0.7231 (m-10) outliers start: 90 outliers final: 53 residues processed: 426 average time/residue: 0.1987 time to fit residues: 136.1866 Evaluate side-chains 398 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 49 GLN 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 189 GLU 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 E residue 286 LYS Chi-restraints excluded: chain F residue 216 MET 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 H residue 1 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 269 LYS Chi-restraints excluded: chain H residue 277 MET Chi-restraints excluded: chain I residue 8 CYS 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 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 449 LEU 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 920 HIS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 507 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 375 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 170 optimal weight: 0.2980 chunk 96 optimal weight: 0.5980 chunk 310 optimal weight: 0.6980 chunk 258 optimal weight: 0.1980 chunk 231 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 311 optimal weight: 0.0050 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS D 173 GLN E 275 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090118 restraints weight = 62367.255| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.19 r_work: 0.3165 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3703 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= 0.115 Angle : 0.609 19.948 43875 Z= 0.298 Chirality : 0.050 1.425 5054 Planarity : 0.003 0.060 5456 Dihedral : 9.208 179.375 4919 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.44 % Allowed : 12.78 % Favored : 84.78 % 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: -0.88 (0.13), residues: 3839 helix: 1.18 (0.15), residues: 1274 sheet: -0.70 (0.18), residues: 749 loop : -1.87 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 78 TYR 0.014 0.001 TYR K 531 PHE 0.033 0.001 PHE K 904 TRP 0.016 0.001 TRP H 96 HIS 0.019 0.001 HIS K 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (32289) covalent geometry : angle 0.60913 / 0.30 (43872) hydrogen bonds : bond 0.03918 / 2.67 ( 1372) hydrogen bonds : angle 4.38019 / 3.12 ( 3856) metal coordination : bond 0.00587 / 0.29 ( 4) metal coordination : angle 1.42298 / 0.76 ( 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 433 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7347 (pp) REVERT: A 180 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.6858 (mtt-85) REVERT: A 240 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6486 (pp) REVERT: C 28 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7903 (tm-30) REVERT: D 63 GLU cc_start: 0.8299 (tt0) cc_final: 0.8021 (tt0) REVERT: D 143 ASP cc_start: 0.8665 (t70) cc_final: 0.8432 (t0) REVERT: E 74 PRO cc_start: 0.8195 (Cg_endo) cc_final: 0.7817 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8648 (mptp) cc_final: 0.8279 (mttp) REVERT: F 20 TYR cc_start: 0.6615 (m-80) cc_final: 0.6197 (m-80) REVERT: F 50 LYS cc_start: 0.9081 (tttt) cc_final: 0.8678 (tttp) REVERT: F 111 ARG cc_start: 0.7725 (ptp-110) cc_final: 0.7152 (mtp85) REVERT: F 257 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7977 (mt0) REVERT: G 103 ASP cc_start: 0.7942 (p0) cc_final: 0.7654 (p0) REVERT: G 182 ASP cc_start: 0.8219 (t0) cc_final: 0.7843 (t0) REVERT: G 188 ASN cc_start: 0.8348 (p0) cc_final: 0.7929 (p0) REVERT: G 250 LEU cc_start: 0.8533 (tp) cc_final: 0.8094 (mt) REVERT: H 93 GLN cc_start: 0.7515 (tp40) cc_final: 0.7240 (tp40) REVERT: H 105 ASP cc_start: 0.7809 (t0) cc_final: 0.7443 (t70) REVERT: H 107 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8908 (m) REVERT: H 129 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8006 (mm) REVERT: H 253 ASP cc_start: 0.8030 (t0) cc_final: 0.7696 (p0) REVERT: H 269 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8026 (ttpt) REVERT: H 282 MET cc_start: 0.8258 (mmm) cc_final: 0.7989 (mtp) REVERT: I 120 LYS cc_start: 0.8335 (mmmm) cc_final: 0.7978 (mmmt) REVERT: I 164 MET cc_start: 0.8133 (mtp) cc_final: 0.7877 (mtm) REVERT: I 173 GLN cc_start: 0.7174 (tt0) cc_final: 0.6778 (tt0) REVERT: K 96 GLN cc_start: 0.7497 (tt0) cc_final: 0.7170 (tm-30) REVERT: K 201 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5551 (mm) REVERT: K 238 GLN cc_start: 0.7206 (pt0) cc_final: 0.6613 (mm-40) REVERT: K 265 ILE cc_start: 0.7721 (mm) cc_final: 0.7066 (mm) REVERT: K 289 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6983 (tm-30) REVERT: K 470 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8458 (tt) REVERT: K 667 MET cc_start: 0.7836 (mmm) cc_final: 0.7346 (mmm) REVERT: K 817 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7219 (tt) REVERT: L 78 ARG cc_start: 0.8003 (ptt90) cc_final: 0.7729 (ppt170) REVERT: M 253 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7889 (mt-10) REVERT: M 386 PHE cc_start: 0.8578 (m-10) cc_final: 0.8219 (m-10) REVERT: M 450 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8392 (mtm-85) REVERT: M 454 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9268 (pp) REVERT: M 487 MET cc_start: 0.6833 (tpp) cc_final: 0.6281 (tpp) REVERT: M 491 MET cc_start: 0.7681 (mpp) cc_final: 0.7334 (mmp) REVERT: M 529 MET cc_start: 0.8508 (mtm) cc_final: 0.8266 (mtp) REVERT: M 553 LYS cc_start: 0.7105 (pttm) cc_final: 0.6845 (ptmt) REVERT: M 563 PHE cc_start: 0.8300 (t80) cc_final: 0.7962 (t80) REVERT: M 569 MET cc_start: 0.8672 (ttp) cc_final: 0.8442 (ttp) REVERT: M 872 MET cc_start: 0.8355 (tpp) cc_final: 0.7947 (ttm) REVERT: M 973 TRP cc_start: 0.8437 (t-100) cc_final: 0.8204 (t-100) outliers start: 81 outliers final: 53 residues processed: 408 average time/residue: 0.1956 time to fit residues: 128.3678 Evaluate side-chains 387 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 112 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain D residue 49 GLN 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 189 GLU 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 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 H residue 1 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 269 LYS Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 41 LEU 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 201 LEU Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU 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 M residue 116 LEU Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 507 LYS Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1033 ASP 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: 2.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS ** K 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 920 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079409 restraints weight = 63180.167| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.15 r_work: 0.3096 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 32293 Z= 0.209 Angle : 0.665 19.438 43875 Z= 0.326 Chirality : 0.050 1.280 5054 Planarity : 0.004 0.062 5456 Dihedral : 9.295 179.720 4919 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.13 % Allowed : 12.84 % Favored : 84.03 % 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: -0.89 (0.13), residues: 3839 helix: 1.09 (0.15), residues: 1282 sheet: -0.66 (0.18), residues: 752 loop : -1.84 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 623 TYR 0.024 0.002 TYR M 583 PHE 0.026 0.002 PHE K 904 TRP 0.016 0.002 TRP K 564 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (32289) covalent geometry : angle 0.66484 / 0.33 (43872) hydrogen bonds : bond 0.04390 / 3.00 ( 1372) hydrogen bonds : angle 4.46998 / 3.19 ( 3856) metal coordination : bond 0.00902 / 0.45 ( 4) metal coordination : angle 1.24964 / 0.69 ( 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 449 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 345 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7660 (pp) REVERT: A 200 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: A 229 ARG cc_start: 0.8285 (mpt-90) cc_final: 0.7495 (mmt90) REVERT: A 240 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6706 (pp) REVERT: B 22 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8194 (ptt90) REVERT: B 186 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8125 (pt) REVERT: C 28 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8045 (tm-30) REVERT: D 76 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8486 (tt) REVERT: D 143 ASP cc_start: 0.8664 (t70) cc_final: 0.8461 (t0) REVERT: E 33 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7123 (ptt90) REVERT: E 74 PRO cc_start: 0.8294 (Cg_endo) cc_final: 0.7937 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8727 (mptp) cc_final: 0.8367 (mttp) REVERT: F 50 LYS cc_start: 0.9176 (tttt) cc_final: 0.8821 (tttp) REVERT: F 111 ARG cc_start: 0.7718 (ptp-110) cc_final: 0.7186 (mtp85) REVERT: G 103 ASP cc_start: 0.8057 (p0) cc_final: 0.7525 (p0) REVERT: G 105 GLN cc_start: 0.8520 (mp10) cc_final: 0.8163 (mp10) REVERT: G 182 ASP cc_start: 0.8335 (t0) cc_final: 0.7916 (t0) REVERT: G 188 ASN cc_start: 0.8547 (p0) cc_final: 0.8147 (p0) REVERT: G 250 LEU cc_start: 0.8591 (tp) cc_final: 0.8094 (mt) REVERT: H 93 GLN cc_start: 0.7659 (tp40) cc_final: 0.7339 (tp40) REVERT: H 105 ASP cc_start: 0.7826 (t0) cc_final: 0.7486 (t70) REVERT: H 107 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8939 (m) REVERT: H 129 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8090 (mm) REVERT: H 253 ASP cc_start: 0.8158 (t0) cc_final: 0.7802 (p0) REVERT: H 269 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8147 (ttpt) REVERT: H 282 MET cc_start: 0.8241 (mmm) cc_final: 0.8026 (mtp) REVERT: I 173 GLN cc_start: 0.7292 (tt0) cc_final: 0.6940 (tt0) REVERT: K 96 GLN cc_start: 0.7569 (tt0) cc_final: 0.7304 (tm-30) REVERT: K 201 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5550 (mm) REVERT: K 238 GLN cc_start: 0.7218 (pt0) cc_final: 0.6693 (mm-40) REVERT: K 265 ILE cc_start: 0.7776 (mm) cc_final: 0.7128 (mm) REVERT: K 289 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7118 (tm-30) REVERT: K 470 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8542 (tp) REVERT: K 667 MET cc_start: 0.8025 (mmm) cc_final: 0.7602 (mmm) REVERT: K 817 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7337 (tt) REVERT: K 926 SER cc_start: 0.8605 (m) cc_final: 0.8230 (p) REVERT: L 78 ARG cc_start: 0.8192 (ptt90) cc_final: 0.7843 (ppt90) REVERT: M 386 PHE cc_start: 0.8669 (m-10) cc_final: 0.8287 (m-10) REVERT: M 454 ILE cc_start: 0.9528 (OUTLIER) cc_final: 0.9287 (pp) REVERT: M 487 MET cc_start: 0.6784 (tpp) cc_final: 0.6205 (tpp) REVERT: M 491 MET cc_start: 0.7718 (mpp) cc_final: 0.7341 (mmp) REVERT: M 553 LYS cc_start: 0.6963 (pttm) cc_final: 0.6751 (ptmt) REVERT: M 888 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7802 (mm) outliers start: 104 outliers final: 66 residues processed: 420 average time/residue: 0.1960 time to fit residues: 132.5358 Evaluate side-chains 403 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 322 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 226 ASN 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 167 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 233 CYS Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 68 LYS 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 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 E residue 286 LYS Chi-restraints excluded: chain F residue 219 LEU 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 1 MET Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 269 LYS Chi-restraints excluded: chain I residue 8 CYS 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 287 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU Chi-restraints excluded: chain K residue 738 THR 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 909 VAL Chi-restraints excluded: chain L residue 59 ILE 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 507 LYS Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1033 ASP 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: 0.7980 chunk 336 optimal weight: 0.8980 chunk 356 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 303 optimal weight: 0.0770 chunk 245 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 367 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS M 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.102782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080659 restraints weight = 62932.093| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.18 r_work: 0.3121 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 32293 Z= 0.132 Angle : 0.613 18.321 43875 Z= 0.300 Chirality : 0.048 1.136 5054 Planarity : 0.004 0.058 5456 Dihedral : 9.230 178.758 4919 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.74 % Allowed : 13.83 % Favored : 83.42 % 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: -0.71 (0.13), residues: 3839 helix: 1.27 (0.15), residues: 1278 sheet: -0.57 (0.19), residues: 747 loop : -1.76 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 623 TYR 0.018 0.001 TYR M 583 PHE 0.016 0.001 PHE B 106 TRP 0.016 0.001 TRP H 96 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (32289) covalent geometry : angle 0.61279 / 0.30 (43872) hydrogen bonds : bond 0.04005 / 2.74 ( 1372) hydrogen bonds : angle 4.34724 / 3.10 ( 3856) metal coordination : bond 0.00380 / 0.19 ( 4) metal coordination : angle 1.11475 / 0.61 ( 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 427 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 336 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7522 (pp) REVERT: A 200 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6949 (mt0) REVERT: A 229 ARG cc_start: 0.8250 (mpt-90) cc_final: 0.8003 (mtt90) REVERT: A 240 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6619 (pp) REVERT: B 186 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8061 (pt) REVERT: C 15 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7494 (mtm110) REVERT: C 28 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 217 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8210 (pp) REVERT: C 226 MET cc_start: 0.8903 (tpt) cc_final: 0.8694 (tpt) REVERT: D 143 ASP cc_start: 0.8658 (t70) cc_final: 0.8419 (t0) REVERT: E 33 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7003 (ptt90) REVERT: E 74 PRO cc_start: 0.8258 (Cg_endo) cc_final: 0.7874 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8726 (mptp) cc_final: 0.8308 (mttp) REVERT: F 20 TYR cc_start: 0.6771 (m-80) cc_final: 0.6361 (m-80) REVERT: F 50 LYS cc_start: 0.9139 (tttt) cc_final: 0.8724 (tttp) REVERT: F 111 ARG cc_start: 0.7772 (ptp-110) cc_final: 0.7240 (mtp85) REVERT: G 103 ASP cc_start: 0.8070 (p0) cc_final: 0.7802 (p0) REVERT: G 182 ASP cc_start: 0.8277 (t0) cc_final: 0.7815 (t0) REVERT: G 188 ASN cc_start: 0.8539 (p0) cc_final: 0.8110 (p0) REVERT: G 250 LEU cc_start: 0.8532 (tp) cc_final: 0.8073 (mt) REVERT: H 93 GLN cc_start: 0.7570 (tp40) cc_final: 0.7281 (tp40) REVERT: H 105 ASP cc_start: 0.7850 (t0) cc_final: 0.7495 (t70) REVERT: H 107 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8902 (m) REVERT: H 129 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8068 (mm) REVERT: H 253 ASP cc_start: 0.8115 (t0) cc_final: 0.7696 (p0) REVERT: H 269 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8058 (ttpt) REVERT: H 282 MET cc_start: 0.8237 (mmm) cc_final: 0.8005 (mtp) REVERT: I 173 GLN cc_start: 0.7226 (tt0) cc_final: 0.6870 (tt0) REVERT: K 158 GLU cc_start: 0.7575 (tp30) cc_final: 0.7343 (tt0) REVERT: K 201 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5575 (mm) REVERT: K 238 GLN cc_start: 0.7306 (pt0) cc_final: 0.6696 (mm-40) REVERT: K 265 ILE cc_start: 0.7790 (mm) cc_final: 0.7180 (mm) REVERT: K 470 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8410 (tt) REVERT: K 817 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7274 (tt) REVERT: L 78 ARG cc_start: 0.8080 (ptt90) cc_final: 0.7820 (ppt90) REVERT: M 143 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8037 (t80) REVERT: M 386 PHE cc_start: 0.8637 (m-10) cc_final: 0.8227 (m-10) REVERT: M 450 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8298 (mtm-85) REVERT: M 454 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9261 (pp) REVERT: M 491 MET cc_start: 0.7761 (mpp) cc_final: 0.7347 (mmp) REVERT: M 516 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: M 553 LYS cc_start: 0.7062 (pttm) cc_final: 0.6811 (ptmt) REVERT: M 595 TYR cc_start: 0.6407 (m-10) cc_final: 0.6162 (m-10) REVERT: M 836 LYS cc_start: 0.3481 (mptt) cc_final: 0.3195 (mmtm) REVERT: M 872 MET cc_start: 0.8440 (tpp) cc_final: 0.7982 (ttm) REVERT: M 888 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7918 (mm) outliers start: 91 outliers final: 56 residues processed: 404 average time/residue: 0.1907 time to fit residues: 123.9765 Evaluate side-chains 394 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 321 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 121 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL 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 15 ARG Chi-restraints excluded: chain C residue 200 VAL 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 68 LYS 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 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 63 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 269 LYS Chi-restraints excluded: chain I residue 8 CYS 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 K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 449 LEU 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 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 L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 143 PHE Chi-restraints excluded: chain M residue 170 CYS Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 507 LYS Chi-restraints excluded: chain M residue 513 SER Chi-restraints excluded: chain M residue 516 GLU Chi-restraints excluded: chain M residue 888 LEU Chi-restraints excluded: chain M residue 1033 ASP 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: 0.2980 chunk 214 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 286 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS M 490 ASN 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 = 0.102428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.080257 restraints weight = 62848.449| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.18 r_work: 0.3111 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 32293 Z= 0.142 Angle : 0.618 16.946 43875 Z= 0.302 Chirality : 0.047 0.985 5054 Planarity : 0.004 0.061 5456 Dihedral : 9.191 177.938 4919 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.80 % Allowed : 13.92 % Favored : 83.27 % Cbeta Deviations : 0.03 % 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: -0.63 (0.13), residues: 3839 helix: 1.31 (0.15), residues: 1279 sheet: -0.45 (0.18), residues: 760 loop : -1.72 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 42 TYR 0.016 0.001 TYR M 583 PHE 0.039 0.002 PHE K 666 TRP 0.017 0.001 TRP H 96 HIS 0.008 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (32289) covalent geometry : angle 0.61816 / 0.30 (43872) hydrogen bonds : bond 0.03981 / 2.72 ( 1372) hydrogen bonds : angle 4.31716 / 3.08 ( 3856) metal coordination : bond 0.00489 / 0.24 ( 4) metal coordination : angle 1.12835 / 0.61 ( 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 429 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 336 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7515 (pp) REVERT: A 200 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6919 (mt0) REVERT: A 229 ARG cc_start: 0.8215 (mpt-90) cc_final: 0.7967 (mtt90) REVERT: A 240 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6622 (pp) REVERT: B 186 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8093 (pt) REVERT: C 15 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7511 (mtm110) REVERT: C 28 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 217 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8257 (pp) REVERT: C 226 MET cc_start: 0.8924 (tpt) cc_final: 0.8710 (tpt) REVERT: D 143 ASP cc_start: 0.8660 (t70) cc_final: 0.8438 (t0) REVERT: E 33 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6980 (ptt90) REVERT: E 74 PRO cc_start: 0.8253 (Cg_endo) cc_final: 0.7885 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8743 (mptp) cc_final: 0.8315 (mttp) REVERT: F 50 LYS cc_start: 0.9111 (tttt) cc_final: 0.8683 (tttp) REVERT: F 111 ARG cc_start: 0.7719 (ptp-110) cc_final: 0.7192 (mtp85) REVERT: G 103 ASP cc_start: 0.8122 (p0) cc_final: 0.7811 (p0) REVERT: G 182 ASP cc_start: 0.8263 (t0) cc_final: 0.7747 (t0) REVERT: G 188 ASN cc_start: 0.8605 (p0) cc_final: 0.8198 (p0) REVERT: G 195 GLN cc_start: 0.7699 (mp10) cc_final: 0.7497 (pt0) REVERT: G 250 LEU cc_start: 0.8557 (tp) cc_final: 0.8126 (mt) REVERT: H 105 ASP cc_start: 0.7853 (t0) cc_final: 0.7496 (t70) REVERT: H 107 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8904 (m) REVERT: H 128 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7779 (tm-30) REVERT: H 129 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7963 (mm) REVERT: H 253 ASP cc_start: 0.8135 (t0) cc_final: 0.7691 (p0) REVERT: H 269 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8046 (ttpt) REVERT: I 173 GLN cc_start: 0.7238 (tt0) cc_final: 0.6886 (tt0) REVERT: K 201 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5573 (mm) REVERT: K 238 GLN cc_start: 0.7297 (pt0) cc_final: 0.6666 (mm-40) REVERT: K 265 ILE cc_start: 0.7843 (mm) cc_final: 0.7262 (mm) REVERT: K 470 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8407 (tt) REVERT: K 667 MET cc_start: 0.7917 (mmm) cc_final: 0.7681 (mmm) REVERT: K 817 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7295 (tt) REVERT: L 78 ARG cc_start: 0.8105 (ptt90) cc_final: 0.7779 (ppt90) REVERT: M 143 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8039 (t80) REVERT: M 386 PHE cc_start: 0.8655 (m-10) cc_final: 0.8244 (m-10) REVERT: M 450 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8294 (mtm-85) REVERT: M 454 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9256 (pp) REVERT: M 553 LYS cc_start: 0.7102 (pttm) cc_final: 0.6861 (ptmt) REVERT: M 595 TYR cc_start: 0.6409 (m-10) cc_final: 0.6112 (m-10) REVERT: M 836 LYS cc_start: 0.3567 (mptt) cc_final: 0.3350 (mmtm) REVERT: M 872 MET cc_start: 0.8457 (tpp) cc_final: 0.7996 (ttm) REVERT: M 888 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7927 (mm) outliers start: 93 outliers final: 65 residues processed: 405 average time/residue: 0.1967 time to fit residues: 127.4770 Evaluate side-chains 400 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 319 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL 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 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 200 VAL 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 79 ILE 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 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 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 63 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 269 LYS Chi-restraints excluded: chain I residue 8 CYS 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 K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 566 MET Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU 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 L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 143 PHE 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 490 ASN Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain M residue 507 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 182 optimal weight: 0.9990 chunk 167 optimal weight: 0.4980 chunk 330 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 225 optimal weight: 0.2980 chunk 359 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.102791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080671 restraints weight = 62653.382| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.17 r_work: 0.3120 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32293 Z= 0.128 Angle : 0.617 16.883 43875 Z= 0.300 Chirality : 0.046 0.940 5054 Planarity : 0.004 0.057 5456 Dihedral : 9.166 177.378 4919 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.68 % Allowed : 14.07 % 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: -0.53 (0.13), residues: 3839 helix: 1.39 (0.15), residues: 1279 sheet: -0.41 (0.19), residues: 745 loop : -1.65 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 42 TYR 0.016 0.001 TYR M 583 PHE 0.029 0.001 PHE K 666 TRP 0.015 0.001 TRP H 96 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (32289) covalent geometry : angle 0.61680 / 0.30 (43872) hydrogen bonds : bond 0.03874 / 2.65 ( 1372) hydrogen bonds : angle 4.27114 / 3.05 ( 3856) metal coordination : bond 0.00349 / 0.17 ( 4) metal coordination : angle 1.05689 / 0.59 ( 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 416 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 327 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7490 (pp) REVERT: A 200 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: A 229 ARG cc_start: 0.8219 (mpt-90) cc_final: 0.7427 (mmt90) REVERT: A 240 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6597 (pp) REVERT: B 186 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8087 (pt) REVERT: B 236 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7346 (ttt90) REVERT: C 15 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7518 (mtm110) REVERT: C 28 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 217 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8270 (pp) REVERT: C 226 MET cc_start: 0.8915 (tpt) cc_final: 0.8705 (tpt) REVERT: D 143 ASP cc_start: 0.8645 (t70) cc_final: 0.8426 (t0) REVERT: E 33 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.6919 (ptt90) REVERT: E 72 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6979 (tm-30) REVERT: E 74 PRO cc_start: 0.8216 (Cg_endo) cc_final: 0.7841 (Cg_exo) REVERT: E 233 LYS cc_start: 0.8743 (mptp) cc_final: 0.8101 (mttp) REVERT: F 50 LYS cc_start: 0.9097 (tttt) cc_final: 0.8673 (tttp) REVERT: F 111 ARG cc_start: 0.7715 (ptp-110) cc_final: 0.7189 (mtp85) REVERT: G 103 ASP cc_start: 0.8186 (p0) cc_final: 0.7835 (p0) REVERT: G 182 ASP cc_start: 0.8265 (t0) cc_final: 0.7747 (t0) REVERT: G 188 ASN cc_start: 0.8569 (p0) cc_final: 0.8150 (p0) REVERT: G 195 GLN cc_start: 0.7761 (mp10) cc_final: 0.7517 (pt0) REVERT: G 250 LEU cc_start: 0.8540 (tp) cc_final: 0.8134 (mt) REVERT: H 105 ASP cc_start: 0.7838 (t0) cc_final: 0.7485 (t70) REVERT: H 107 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8904 (m) REVERT: H 129 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8051 (mm) REVERT: H 253 ASP cc_start: 0.8106 (t0) cc_final: 0.7674 (p0) REVERT: H 269 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8019 (ttpt) REVERT: I 173 GLN cc_start: 0.7222 (tt0) cc_final: 0.6871 (tt0) REVERT: K 201 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5552 (mm) REVERT: K 238 GLN cc_start: 0.7259 (pt0) cc_final: 0.6664 (mm-40) REVERT: K 265 ILE cc_start: 0.7842 (mm) cc_final: 0.7267 (mm) REVERT: K 470 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8420 (tt) REVERT: K 667 MET cc_start: 0.7888 (mmm) cc_final: 0.7592 (mmm) REVERT: K 817 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7281 (tt) REVERT: M 143 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8030 (t80) REVERT: M 386 PHE cc_start: 0.8605 (m-10) cc_final: 0.8214 (m-10) REVERT: M 450 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8282 (mtm-85) REVERT: M 454 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9235 (pp) REVERT: M 553 LYS cc_start: 0.7182 (pttm) cc_final: 0.6938 (ptmt) REVERT: M 595 TYR cc_start: 0.6444 (m-10) cc_final: 0.6187 (m-10) REVERT: M 836 LYS cc_start: 0.3573 (mptt) cc_final: 0.3357 (mmtm) REVERT: M 872 MET cc_start: 0.8463 (tpp) cc_final: 0.8000 (ttm) REVERT: M 888 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7945 (mm) outliers start: 89 outliers final: 64 residues processed: 389 average time/residue: 0.1935 time to fit residues: 121.0184 Evaluate side-chains 398 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL 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 167 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 200 VAL 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 68 LYS 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 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 63 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 168 GLN Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 269 LYS Chi-restraints excluded: chain I residue 8 CYS 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 K residue 171 VAL Chi-restraints excluded: chain K residue 201 LEU Chi-restraints excluded: chain K residue 287 VAL Chi-restraints excluded: chain K residue 432 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 470 LEU Chi-restraints excluded: chain K residue 550 SER Chi-restraints excluded: chain K residue 566 MET Chi-restraints excluded: chain K residue 581 VAL Chi-restraints excluded: chain K residue 595 LEU 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 909 VAL Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 143 PHE 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 507 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 46 optimal weight: 0.9980 chunk 317 optimal weight: 3.9990 chunk 307 optimal weight: 0.0670 chunk 324 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 355 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 HIS M 317 GLN M 490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.102644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080504 restraints weight = 63220.590| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.18 r_work: 0.3119 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32293 Z= 0.129 Angle : 0.615 18.191 43875 Z= 0.298 Chirality : 0.046 0.952 5054 Planarity : 0.004 0.057 5456 Dihedral : 9.131 176.882 4919 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.65 % Allowed : 14.26 % Favored : 83.09 % 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: -0.47 (0.14), residues: 3839 helix: 1.44 (0.15), residues: 1282 sheet: -0.32 (0.19), residues: 752 loop : -1.65 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 42 TYR 0.015 0.001 TYR M 583 PHE 0.029 0.001 PHE A 77 TRP 0.016 0.001 TRP H 96 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (32289) covalent geometry : angle 0.61497 / 0.30 (43872) hydrogen bonds : bond 0.03857 / 2.63 ( 1372) hydrogen bonds : angle 4.24698 / 3.03 ( 3856) metal coordination : bond 0.00369 / 0.18 ( 4) metal coordination : angle 1.02485 / 0.57 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8860.96 seconds wall clock time: 152 minutes 17.67 seconds (9137.67 seconds total)