Starting phenix.real_space_refine on Sat Jun 14 12:55:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr1_19453/06_2025/8rr1_19453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr1_19453/06_2025/8rr1_19453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rr1_19453/06_2025/8rr1_19453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr1_19453/06_2025/8rr1_19453.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr1_19453/06_2025/8rr1_19453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr1_19453/06_2025/8rr1_19453.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 76 5.49 5 S 84 5.16 5 C 9994 2.51 5 N 2864 2.21 5 O 3241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16261 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1827 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "E" Number of atoms: 4950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4950 Classifications: {'peptide': 629} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 590} Chain breaks: 4 Chain: "F" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2287 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Chain: "T" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 27} Link IDs: {'rna2p': 18, 'rna3p': 57} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 10.51, per 1000 atoms: 0.65 Number of scatterers: 16261 At special positions: 0 Unit cell: (112.59, 108.42, 172.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 84 16.00 P 76 15.00 O 3241 8.00 N 2864 7.00 C 9994 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: 5.85 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 644 " pdb="ZN ZN E 901 " - pdb=" ND1 HIS E 548 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 546 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 724 " 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 14 sheets defined 49.0% alpha, 13.6% beta 26 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 6.24 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.699A pdb=" N ALA A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.528A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.561A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 186 removed outlier: 4.445A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.512A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.513A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.852A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 137 removed outlier: 3.529A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 166 through 187 removed outlier: 4.572A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 20 through 33 removed outlier: 3.700A pdb=" N LEU C 24 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 46 through 55 removed outlier: 4.099A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.701A pdb=" N VAL C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.578A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.682A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 186 removed outlier: 4.703A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.535A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.666A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.093A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 137 removed outlier: 3.694A pdb=" N MET D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 131 " --> pdb=" O ASN D 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.402A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.577A pdb=" N VAL D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 90 through 98 Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 152 removed outlier: 3.617A pdb=" N LYS E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 323 through 331 removed outlier: 3.828A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 360 Processing helix chain 'E' and resid 379 through 391 Processing helix chain 'E' and resid 442 through 452 removed outlier: 3.547A pdb=" N PHE E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 467 removed outlier: 3.563A pdb=" N SER E 466 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA E 467 " --> pdb=" O TYR E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 529 Processing helix chain 'E' and resid 531 through 538 Processing helix chain 'E' and resid 554 through 570 Processing helix chain 'E' and resid 582 through 595 removed outlier: 4.182A pdb=" N ALA E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP E 587 " --> pdb=" O GLN E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 600 No H-bonds generated for 'chain 'E' and resid 598 through 600' Processing helix chain 'E' and resid 608 through 611 Processing helix chain 'E' and resid 618 through 633 Processing helix chain 'E' and resid 670 through 677 removed outlier: 3.939A pdb=" N VAL E 674 " --> pdb=" O CYS E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 690 through 692 No H-bonds generated for 'chain 'E' and resid 690 through 692' Processing helix chain 'E' and resid 693 through 700 Processing helix chain 'E' and resid 704 through 716 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 763 removed outlier: 4.351A pdb=" N LYS E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 792 Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.949A pdb=" N PHE F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 154 removed outlier: 3.541A pdb=" N GLN F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 148 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.553A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 213 removed outlier: 4.489A pdb=" N ASN F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 210 through 213' Processing helix chain 'F' and resid 216 through 237 removed outlier: 3.620A pdb=" N ASN F 237 " --> pdb=" O TRP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.612A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 329 removed outlier: 3.723A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 removed outlier: 3.612A pdb=" N TYR F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 337 through 341' Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.856A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 12 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 89 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 14 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.602A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.700A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.912A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 167 removed outlier: 6.788A pdb=" N ASP E 106 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER E 139 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 85 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 74 " --> pdb=" O PHE E 85 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.761A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU E 339 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS E 367 " --> pdb=" O VAL E 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 602 through 606 removed outlier: 6.091A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA E 540 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N VAL E 579 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 542 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER E 511 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 542 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU E 513 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 506 " --> pdb=" O THR E 510 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N THR E 502 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 486 " --> pdb=" O ALA E 501 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 634 through 638 removed outlier: 6.876A pdb=" N VAL E 654 " --> pdb=" O GLU E 635 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE E 637 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA E 652 " --> pdb=" O PHE E 637 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS E 685 " --> pdb=" O ASN E 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.493A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 342 through 344 removed outlier: 4.745A pdb=" N GLY F 383 " --> pdb=" O GLN F 343 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4229 1.33 - 1.46: 3577 1.46 - 1.58: 8624 1.58 - 1.70: 149 1.70 - 1.82: 133 Bond restraints: 16712 Sorted by residual: bond pdb=" N VAL E 732 " pdb=" CA VAL E 732 " ideal model delta sigma weight residual 1.461 1.490 -0.030 8.70e-03 1.32e+04 1.16e+01 bond pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 6.89e+00 bond pdb=" O5' A T 66 " pdb=" C5' A T 66 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.90e+00 bond pdb=" N TYR F 341 " pdb=" CA TYR F 341 " ideal model delta sigma weight residual 1.455 1.484 -0.030 1.38e-02 5.25e+03 4.58e+00 bond pdb=" CA SER E 736 " pdb=" CB SER E 736 " ideal model delta sigma weight residual 1.530 1.496 0.033 1.58e-02 4.01e+03 4.47e+00 ... (remaining 16707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 22733 2.49 - 4.99: 225 4.99 - 7.48: 37 7.48 - 9.97: 2 9.97 - 12.46: 2 Bond angle restraints: 22999 Sorted by residual: angle pdb=" CB MET E 713 " pdb=" CG MET E 713 " pdb=" SD MET E 713 " ideal model delta sigma weight residual 112.70 125.16 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" N LEU F 338 " pdb=" CA LEU F 338 " pdb=" C LEU F 338 " ideal model delta sigma weight residual 111.07 106.78 4.29 1.07e+00 8.73e-01 1.60e+01 angle pdb=" C4' G T 67 " pdb=" C3' G T 67 " pdb=" O3' G T 67 " ideal model delta sigma weight residual 109.40 114.98 -5.58 1.50e+00 4.44e-01 1.38e+01 angle pdb=" C4' A T 66 " pdb=" C3' A T 66 " pdb=" C2' A T 66 " ideal model delta sigma weight residual 102.60 98.93 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" N GLU E 130 " pdb=" CA GLU E 130 " pdb=" C GLU E 130 " ideal model delta sigma weight residual 112.38 108.00 4.38 1.22e+00 6.72e-01 1.29e+01 ... (remaining 22994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 9410 25.94 - 51.87: 575 51.87 - 77.81: 168 77.81 - 103.75: 24 103.75 - 129.69: 1 Dihedral angle restraints: 10178 sinusoidal: 4727 harmonic: 5451 Sorted by residual: dihedral pdb=" C5' C T 65 " pdb=" C4' C T 65 " pdb=" C3' C T 65 " pdb=" O3' C T 65 " ideal model delta sinusoidal sigma weight residual 147.00 111.49 35.51 1 8.00e+00 1.56e-02 2.79e+01 dihedral pdb=" O4' C T 64 " pdb=" C2' C T 64 " pdb=" C1' C T 64 " pdb=" C3' C T 64 " ideal model delta sinusoidal sigma weight residual 25.00 -10.18 35.18 1 8.00e+00 1.56e-02 2.74e+01 dihedral pdb=" C4' C T 64 " pdb=" O4' C T 64 " pdb=" C1' C T 64 " pdb=" C2' C T 64 " ideal model delta sinusoidal sigma weight residual 3.00 -29.17 32.17 1 8.00e+00 1.56e-02 2.30e+01 ... (remaining 10175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2549 0.101 - 0.202: 137 0.202 - 0.303: 0 0.303 - 0.404: 2 0.404 - 0.505: 12 Chirality restraints: 2700 Sorted by residual: chirality pdb=" P G T 15 " pdb=" OP1 G T 15 " pdb=" OP2 G T 15 " pdb=" O5' G T 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" P A T 14 " pdb=" OP1 A T 14 " pdb=" OP2 A T 14 " pdb=" O5' A T 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" P A T 63 " pdb=" OP1 A T 63 " pdb=" OP2 A T 63 " pdb=" O5' A T 63 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 2697 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 337 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C PRO F 337 " -0.043 2.00e-02 2.50e+03 pdb=" O PRO F 337 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU F 338 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U T 56 " -0.017 2.00e-02 2.50e+03 1.49e-02 5.00e+00 pdb=" N1 U T 56 " 0.036 2.00e-02 2.50e+03 pdb=" C2 U T 56 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U T 56 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U T 56 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U T 56 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U T 56 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U T 56 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U T 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 203 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO A 204 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.027 5.00e-02 4.00e+02 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 115 2.56 - 3.15: 12628 3.15 - 3.73: 26503 3.73 - 4.32: 36138 4.32 - 4.90: 59913 Nonbonded interactions: 135297 Sorted by model distance: nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 1.976 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 902 " model vdw 2.058 2.230 nonbonded pdb=" OD1 ASP C 41 " pdb=" N LEU C 42 " model vdw 2.159 3.120 nonbonded pdb=" O SER E 545 " pdb=" ND1 HIS E 546 " model vdw 2.163 3.120 nonbonded pdb=" OD1 ASN F 222 " pdb=" O2' G T 9 " model vdw 2.188 3.040 ... (remaining 135292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 207 or resid 211 through 261)) selection = (chain 'B' and (resid 7 through 207 or resid 211 through 261)) selection = (chain 'C' and (resid 7 through 207 or resid 211 through 261)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.78 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: 16.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 48.290 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16717 Z= 0.151 Angle : 0.587 12.463 22999 Z= 0.305 Chirality : 0.053 0.505 2700 Planarity : 0.004 0.049 2709 Dihedral : 17.669 129.685 6674 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 0.13 % Allowed : 12.82 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1898 helix: 1.83 (0.18), residues: 823 sheet: 0.29 (0.29), residues: 337 loop : -0.52 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 659 HIS 0.008 0.001 HIS E 546 PHE 0.009 0.001 PHE F 97 TYR 0.006 0.001 TYR F 137 ARG 0.006 0.000 ARG E 435 Details of bonding type rmsd hydrogen bonds : bond 0.17083 ( 748) hydrogen bonds : angle 6.78954 ( 2082) metal coordination : bond 0.00660 ( 5) covalent geometry : bond 0.00268 (16712) covalent geometry : angle 0.58652 (22999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.9005 (mtt) cc_final: 0.8788 (mtt) REVERT: E 715 MET cc_start: 0.8684 (ttp) cc_final: 0.8381 (ttm) REVERT: F 96 GLU cc_start: 0.9546 (mp0) cc_final: 0.9318 (pm20) REVERT: F 100 MET cc_start: 0.8944 (ppp) cc_final: 0.8584 (ppp) outliers start: 2 outliers final: 1 residues processed: 99 average time/residue: 1.4576 time to fit residues: 161.9593 Evaluate side-chains 89 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 30.0000 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.048218 restraints weight = 45980.729| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.81 r_work: 0.2621 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16717 Z= 0.230 Angle : 0.575 8.156 22999 Z= 0.293 Chirality : 0.043 0.195 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.830 131.915 3211 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 1.79 % Allowed : 12.82 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1898 helix: 2.11 (0.18), residues: 817 sheet: 0.14 (0.29), residues: 341 loop : -0.29 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 115 HIS 0.009 0.001 HIS E 546 PHE 0.010 0.001 PHE E 735 TYR 0.014 0.001 TYR F 137 ARG 0.005 0.000 ARG E 630 Details of bonding type rmsd hydrogen bonds : bond 0.04813 ( 748) hydrogen bonds : angle 4.89654 ( 2082) metal coordination : bond 0.00442 ( 5) covalent geometry : bond 0.00527 (16712) covalent geometry : angle 0.57493 (22999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 ASP cc_start: 0.8494 (t0) cc_final: 0.8284 (t0) REVERT: E 683 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9040 (tm) REVERT: E 715 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8944 (ttm) REVERT: F 96 GLU cc_start: 0.9601 (mp0) cc_final: 0.9344 (pm20) REVERT: F 100 MET cc_start: 0.9023 (ppp) cc_final: 0.8675 (ppp) outliers start: 28 outliers final: 9 residues processed: 112 average time/residue: 1.4046 time to fit residues: 180.6784 Evaluate side-chains 94 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain F residue 101 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 174 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.048212 restraints weight = 45571.924| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.80 r_work: 0.2627 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16717 Z= 0.202 Angle : 0.544 8.590 22999 Z= 0.275 Chirality : 0.042 0.201 2700 Planarity : 0.004 0.053 2709 Dihedral : 15.752 130.269 3211 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 2.05 % Allowed : 13.14 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1898 helix: 2.03 (0.18), residues: 840 sheet: 0.14 (0.28), residues: 339 loop : -0.39 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 115 HIS 0.008 0.001 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.008 0.001 TYR F 135 ARG 0.003 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 748) hydrogen bonds : angle 4.63775 ( 2082) metal coordination : bond 0.00528 ( 5) covalent geometry : bond 0.00461 (16712) covalent geometry : angle 0.54434 (22999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: C 64 ASP cc_start: 0.8517 (t0) cc_final: 0.8294 (t0) REVERT: D 70 ASP cc_start: 0.8780 (m-30) cc_final: 0.8577 (m-30) REVERT: D 160 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: E 453 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8939 (mm) REVERT: E 547 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9013 (tp) REVERT: E 683 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9009 (tm) REVERT: E 715 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8931 (ttm) REVERT: F 96 GLU cc_start: 0.9592 (mp0) cc_final: 0.9365 (pm20) REVERT: F 100 MET cc_start: 0.9159 (ppp) cc_final: 0.8830 (ppp) outliers start: 32 outliers final: 10 residues processed: 113 average time/residue: 1.1276 time to fit residues: 145.1364 Evaluate side-chains 99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 142 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 174 optimal weight: 0.0070 chunk 51 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049641 restraints weight = 45290.517| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.82 r_work: 0.2666 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16717 Z= 0.112 Angle : 0.499 9.129 22999 Z= 0.249 Chirality : 0.041 0.189 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.632 127.119 3211 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.54 % Allowed : 13.85 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1898 helix: 2.10 (0.18), residues: 858 sheet: 0.15 (0.28), residues: 338 loop : -0.47 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 659 HIS 0.007 0.001 HIS E 546 PHE 0.013 0.001 PHE E 521 TYR 0.014 0.001 TYR F 137 ARG 0.002 0.000 ARG E 788 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 748) hydrogen bonds : angle 4.33465 ( 2082) metal coordination : bond 0.00139 ( 5) covalent geometry : bond 0.00250 (16712) covalent geometry : angle 0.49922 (22999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: C 64 ASP cc_start: 0.8470 (t0) cc_final: 0.8218 (t0) REVERT: D 70 ASP cc_start: 0.8763 (m-30) cc_final: 0.8504 (m-30) REVERT: D 113 ASP cc_start: 0.8378 (t0) cc_final: 0.8158 (t0) REVERT: D 160 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: E 416 MET cc_start: 0.8692 (pp-130) cc_final: 0.8476 (ppp) REVERT: E 453 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8896 (mm) REVERT: E 683 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8937 (tm) REVERT: E 715 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8938 (ttm) REVERT: F 100 MET cc_start: 0.9214 (ppp) cc_final: 0.8894 (ppp) outliers start: 24 outliers final: 8 residues processed: 109 average time/residue: 1.1097 time to fit residues: 138.2397 Evaluate side-chains 96 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.049857 restraints weight = 45999.008| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.83 r_work: 0.2678 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16717 Z= 0.108 Angle : 0.490 9.841 22999 Z= 0.244 Chirality : 0.040 0.185 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.534 124.520 3211 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Rotamer: Outliers : 1.92 % Allowed : 13.53 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1898 helix: 2.23 (0.18), residues: 854 sheet: 0.11 (0.28), residues: 340 loop : -0.42 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 659 HIS 0.006 0.001 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.017 0.001 TYR E 83 ARG 0.002 0.000 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 748) hydrogen bonds : angle 4.22130 ( 2082) metal coordination : bond 0.00369 ( 5) covalent geometry : bond 0.00240 (16712) covalent geometry : angle 0.49040 (22999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8926 (t0) cc_final: 0.8712 (t0) REVERT: A 160 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: C 64 ASP cc_start: 0.8446 (t0) cc_final: 0.8177 (t0) REVERT: D 70 ASP cc_start: 0.8789 (m-30) cc_final: 0.8539 (m-30) REVERT: D 160 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: E 416 MET cc_start: 0.8736 (pp-130) cc_final: 0.8522 (ppp) REVERT: E 453 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8852 (mm) REVERT: E 547 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8964 (tp) REVERT: E 683 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8951 (tm) REVERT: E 715 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8931 (ttm) REVERT: F 100 MET cc_start: 0.9244 (ppp) cc_final: 0.8946 (ppp) outliers start: 30 outliers final: 12 residues processed: 111 average time/residue: 1.0924 time to fit residues: 138.7094 Evaluate side-chains 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 195 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.072135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050219 restraints weight = 45974.013| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.90 r_work: 0.2687 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16717 Z= 0.097 Angle : 0.485 10.841 22999 Z= 0.239 Chirality : 0.040 0.179 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.426 121.165 3211 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 14.23 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1898 helix: 2.29 (0.18), residues: 854 sheet: 0.21 (0.28), residues: 351 loop : -0.41 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 659 HIS 0.004 0.000 HIS E 546 PHE 0.011 0.001 PHE E 521 TYR 0.017 0.001 TYR F 137 ARG 0.002 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 748) hydrogen bonds : angle 4.13163 ( 2082) metal coordination : bond 0.00128 ( 5) covalent geometry : bond 0.00214 (16712) covalent geometry : angle 0.48489 (22999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: C 64 ASP cc_start: 0.8408 (t0) cc_final: 0.8133 (t0) REVERT: D 70 ASP cc_start: 0.8738 (m-30) cc_final: 0.8482 (m-30) REVERT: D 79 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: D 160 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: E 178 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.8862 (pmt) REVERT: E 416 MET cc_start: 0.8777 (pp-130) cc_final: 0.8534 (ppp) REVERT: E 453 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8819 (mm) REVERT: E 547 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8983 (tp) REVERT: E 683 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8851 (tm) REVERT: E 715 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8979 (ttm) REVERT: F 100 MET cc_start: 0.9258 (ppp) cc_final: 0.8963 (ppp) outliers start: 25 outliers final: 11 residues processed: 110 average time/residue: 1.1295 time to fit residues: 141.3194 Evaluate side-chains 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 82 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 0.0980 chunk 135 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 68 optimal weight: 0.0070 chunk 147 optimal weight: 1.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 GLN ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050598 restraints weight = 45648.436| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.83 r_work: 0.2700 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16717 Z= 0.098 Angle : 0.481 10.927 22999 Z= 0.238 Chirality : 0.039 0.177 2700 Planarity : 0.004 0.053 2709 Dihedral : 15.306 118.233 3211 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 1.79 % Allowed : 14.42 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1898 helix: 2.34 (0.18), residues: 855 sheet: 0.23 (0.28), residues: 351 loop : -0.40 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 659 HIS 0.005 0.001 HIS E 546 PHE 0.010 0.001 PHE E 521 TYR 0.009 0.001 TYR E 83 ARG 0.003 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 748) hydrogen bonds : angle 4.07914 ( 2082) metal coordination : bond 0.00127 ( 5) covalent geometry : bond 0.00219 (16712) covalent geometry : angle 0.48094 (22999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8877 (t0) cc_final: 0.8655 (t0) REVERT: A 160 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: C 64 ASP cc_start: 0.8409 (t0) cc_final: 0.8149 (t0) REVERT: D 70 ASP cc_start: 0.8777 (m-30) cc_final: 0.8540 (m-30) REVERT: D 79 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (ttpp) REVERT: D 160 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: E 99 LYS cc_start: 0.9609 (mmmt) cc_final: 0.9382 (mmmm) REVERT: E 178 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8845 (pmt) REVERT: E 416 MET cc_start: 0.8761 (pp-130) cc_final: 0.8524 (ppp) REVERT: E 453 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8825 (mm) REVERT: E 547 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.9006 (tp) REVERT: E 683 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8928 (tm) REVERT: E 715 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8954 (ttm) REVERT: E 729 TYR cc_start: 0.8096 (m-80) cc_final: 0.7891 (m-80) REVERT: F 100 MET cc_start: 0.9264 (ppp) cc_final: 0.8984 (ppp) outliers start: 28 outliers final: 13 residues processed: 110 average time/residue: 1.1211 time to fit residues: 140.3402 Evaluate side-chains 109 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 101 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 86 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.070993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049270 restraints weight = 45601.938| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.80 r_work: 0.2652 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16717 Z= 0.171 Angle : 0.526 11.681 22999 Z= 0.258 Chirality : 0.041 0.185 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.278 117.647 3211 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Rotamer: Outliers : 1.60 % Allowed : 14.87 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1898 helix: 2.30 (0.18), residues: 853 sheet: 0.15 (0.28), residues: 353 loop : -0.42 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 115 HIS 0.006 0.001 HIS E 546 PHE 0.015 0.001 PHE E 735 TYR 0.015 0.001 TYR F 137 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 748) hydrogen bonds : angle 4.21143 ( 2082) metal coordination : bond 0.00250 ( 5) covalent geometry : bond 0.00394 (16712) covalent geometry : angle 0.52574 (22999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8913 (t0) cc_final: 0.8707 (t0) REVERT: A 160 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: C 64 ASP cc_start: 0.8472 (t0) cc_final: 0.8196 (t0) REVERT: D 70 ASP cc_start: 0.8783 (m-30) cc_final: 0.8551 (m-30) REVERT: D 79 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8679 (ttpp) REVERT: D 160 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: E 99 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9392 (mmmm) REVERT: E 416 MET cc_start: 0.8775 (pp-130) cc_final: 0.8555 (ppp) REVERT: E 453 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8847 (mm) REVERT: E 547 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8951 (tt) REVERT: E 683 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8994 (tm) REVERT: E 715 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8950 (ttm) REVERT: F 100 MET cc_start: 0.9280 (ppp) cc_final: 0.9015 (ppp) REVERT: F 285 ASP cc_start: 0.9263 (m-30) cc_final: 0.9060 (t0) outliers start: 25 outliers final: 13 residues processed: 110 average time/residue: 1.0591 time to fit residues: 133.5317 Evaluate side-chains 106 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 683 LEU Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 101 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 137 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050340 restraints weight = 45686.442| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.82 r_work: 0.2691 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16717 Z= 0.103 Angle : 0.494 11.769 22999 Z= 0.243 Chirality : 0.040 0.174 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.193 115.250 3207 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.89 % Rotamer: Outliers : 1.47 % Allowed : 14.87 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1898 helix: 2.34 (0.18), residues: 853 sheet: 0.17 (0.28), residues: 351 loop : -0.38 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 659 HIS 0.006 0.001 HIS E 546 PHE 0.011 0.001 PHE E 521 TYR 0.008 0.001 TYR E 83 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 748) hydrogen bonds : angle 4.09999 ( 2082) metal coordination : bond 0.00616 ( 5) covalent geometry : bond 0.00231 (16712) covalent geometry : angle 0.49386 (22999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: C 64 ASP cc_start: 0.8438 (t0) cc_final: 0.8162 (t0) REVERT: D 70 ASP cc_start: 0.8790 (m-30) cc_final: 0.8562 (m-30) REVERT: D 79 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8669 (ttpp) REVERT: D 160 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: E 99 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9394 (mmmm) REVERT: E 178 MET cc_start: 0.9352 (pmm) cc_final: 0.8964 (pmt) REVERT: E 416 MET cc_start: 0.8758 (pp-130) cc_final: 0.8527 (ppp) REVERT: E 453 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8824 (mm) REVERT: E 547 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8964 (tp) REVERT: F 100 MET cc_start: 0.9275 (ppp) cc_final: 0.9006 (ppp) REVERT: F 285 ASP cc_start: 0.9253 (m-30) cc_final: 0.9041 (t0) outliers start: 23 outliers final: 13 residues processed: 107 average time/residue: 1.1708 time to fit residues: 142.5448 Evaluate side-chains 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 101 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050475 restraints weight = 45546.035| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.81 r_work: 0.2697 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16717 Z= 0.104 Angle : 0.509 12.337 22999 Z= 0.246 Chirality : 0.040 0.175 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.130 112.716 3207 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.35 % Allowed : 15.19 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1898 helix: 2.39 (0.18), residues: 850 sheet: 0.14 (0.28), residues: 355 loop : -0.34 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 659 HIS 0.005 0.001 HIS E 546 PHE 0.010 0.001 PHE E 521 TYR 0.008 0.001 TYR E 83 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 748) hydrogen bonds : angle 4.08299 ( 2082) metal coordination : bond 0.00113 ( 5) covalent geometry : bond 0.00236 (16712) covalent geometry : angle 0.50945 (22999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.8821 (mtt) cc_final: 0.8618 (mtt) REVERT: A 160 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: C 64 ASP cc_start: 0.8428 (t0) cc_final: 0.8166 (t0) REVERT: D 70 ASP cc_start: 0.8800 (m-30) cc_final: 0.8513 (m-30) REVERT: D 79 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8677 (ttpp) REVERT: D 160 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: E 99 LYS cc_start: 0.9612 (mmmt) cc_final: 0.9392 (mmmm) REVERT: E 178 MET cc_start: 0.9363 (pmm) cc_final: 0.8969 (pmt) REVERT: E 416 MET cc_start: 0.8750 (pp-130) cc_final: 0.8522 (ppp) REVERT: E 453 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (mm) REVERT: F 100 MET cc_start: 0.9275 (ppp) cc_final: 0.9006 (ppp) REVERT: F 121 MET cc_start: 0.8990 (ptp) cc_final: 0.8754 (pmm) REVERT: F 285 ASP cc_start: 0.9255 (m-30) cc_final: 0.9036 (t0) outliers start: 21 outliers final: 14 residues processed: 104 average time/residue: 1.1416 time to fit residues: 134.8662 Evaluate side-chains 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 101 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050875 restraints weight = 45444.724| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.82 r_work: 0.2706 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16717 Z= 0.095 Angle : 0.511 12.928 22999 Z= 0.246 Chirality : 0.040 0.170 2700 Planarity : 0.004 0.053 2709 Dihedral : 15.081 109.780 3207 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.16 % Favored : 97.79 % Rotamer: Outliers : 1.28 % Allowed : 15.26 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1898 helix: 2.39 (0.18), residues: 852 sheet: 0.16 (0.28), residues: 355 loop : -0.34 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 115 HIS 0.005 0.001 HIS E 546 PHE 0.013 0.001 PHE E 735 TYR 0.017 0.001 TYR F 137 ARG 0.002 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 748) hydrogen bonds : angle 4.02502 ( 2082) metal coordination : bond 0.00116 ( 5) covalent geometry : bond 0.00212 (16712) covalent geometry : angle 0.51110 (22999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10208.45 seconds wall clock time: 178 minutes 23.77 seconds (10703.77 seconds total)