Starting phenix.real_space_refine on Sun Aug 24 01:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr1_19453/08_2025/8rr1_19453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr1_19453/08_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_19453/08_2025/8rr1_19453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr1_19453/08_2025/8rr1_19453.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr1_19453/08_2025/8rr1_19453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr1_19453/08_2025/8rr1_19453.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.82, per 1000 atoms: 0.17 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: 1.19 Conformation dependent library (CDL) restraints added in 520.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.38 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: 2.73 Time building geometry restraints manager: 1.53 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: 2.940 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.630 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- 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 : 5.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG E 435 TYR 0.006 0.001 TYR F 137 PHE 0.009 0.001 PHE F 97 TRP 0.011 0.001 TRP E 659 HIS 0.008 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00268 (16712) covalent geometry : angle 0.58652 (22999) hydrogen bonds : bond 0.17083 ( 748) hydrogen bonds : angle 6.78954 ( 2082) metal coordination : bond 0.00660 ( 5) *********************** 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 : 0.542 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: 0.4830 time to fit residues: 53.4938 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 : 0.478 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.071044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049221 restraints weight = 45678.938| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.83 r_work: 0.2650 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16717 Z= 0.149 Angle : 0.530 7.781 22999 Z= 0.271 Chirality : 0.041 0.188 2700 Planarity : 0.004 0.051 2709 Dihedral : 15.782 130.747 3211 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 1.54 % Allowed : 12.82 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1898 helix: 2.12 (0.18), residues: 835 sheet: 0.21 (0.29), residues: 339 loop : -0.38 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 630 TYR 0.014 0.001 TYR F 137 PHE 0.010 0.001 PHE C 114 TRP 0.009 0.001 TRP E 115 HIS 0.007 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00329 (16712) covalent geometry : angle 0.53010 (22999) hydrogen bonds : bond 0.04496 ( 748) hydrogen bonds : angle 4.83645 ( 2082) metal coordination : bond 0.00254 ( 5) *********************** 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 116 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 715 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8935 (ttm) REVERT: F 100 MET cc_start: 0.9022 (ppp) cc_final: 0.8671 (ppp) outliers start: 24 outliers final: 6 residues processed: 110 average time/residue: 0.4398 time to fit residues: 55.0006 Evaluate side-chains 95 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 CYS 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 550 ASN Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 715 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 434 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 = 0.3359 r_free = 0.3359 target = 0.070341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048506 restraints weight = 46256.551| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.82 r_work: 0.2629 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16717 Z= 0.199 Angle : 0.541 8.479 22999 Z= 0.272 Chirality : 0.042 0.204 2700 Planarity : 0.004 0.053 2709 Dihedral : 15.707 129.478 3211 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 2.18 % Allowed : 12.76 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1898 helix: 2.14 (0.18), residues: 834 sheet: 0.17 (0.28), residues: 341 loop : -0.33 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 431 TYR 0.008 0.001 TYR F 135 PHE 0.012 0.001 PHE E 521 TRP 0.008 0.001 TRP E 115 HIS 0.007 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00457 (16712) covalent geometry : angle 0.54093 (22999) hydrogen bonds : bond 0.04451 ( 748) hydrogen bonds : angle 4.60840 ( 2082) metal coordination : bond 0.00356 ( 5) *********************** 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 125 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: C 64 ASP cc_start: 0.8456 (t0) cc_final: 0.8206 (t0) REVERT: D 70 ASP cc_start: 0.8781 (m-30) cc_final: 0.8580 (m-30) REVERT: D 160 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: E 715 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9019 (ttm) REVERT: F 96 GLU cc_start: 0.9581 (mp0) cc_final: 0.9355 (pm20) REVERT: F 100 MET cc_start: 0.9154 (ppp) cc_final: 0.8813 (ppp) outliers start: 34 outliers final: 16 residues processed: 117 average time/residue: 0.3978 time to fit residues: 53.5756 Evaluate side-chains 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 125 THR 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 118 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 206 LEU 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 587 TRP Chi-restraints excluded: chain E residue 651 CYS 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 Chi-restraints excluded: chain F residue 108 VAL 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 87 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 162 optimal weight: 0.0060 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 GLN E 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.071980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050226 restraints weight = 45599.285| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.83 r_work: 0.2687 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 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 = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16717 Z= 0.097 Angle : 0.494 8.942 22999 Z= 0.246 Chirality : 0.040 0.183 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.600 126.447 3211 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 1.54 % Allowed : 13.78 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.20), residues: 1898 helix: 2.11 (0.18), residues: 860 sheet: 0.20 (0.29), residues: 333 loop : -0.43 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 788 TYR 0.014 0.001 TYR F 137 PHE 0.013 0.001 PHE E 521 TRP 0.008 0.001 TRP E 659 HIS 0.006 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00211 (16712) covalent geometry : angle 0.49431 (22999) hydrogen bonds : bond 0.03566 ( 748) hydrogen bonds : angle 4.31280 ( 2082) metal coordination : bond 0.00262 ( 5) *********************** 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 114 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: C 64 ASP cc_start: 0.8390 (t0) cc_final: 0.8148 (t0) REVERT: D 70 ASP cc_start: 0.8750 (m-30) cc_final: 0.8511 (m-30) REVERT: D 113 ASP cc_start: 0.8378 (t0) cc_final: 0.8139 (t0) REVERT: E 453 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8921 (mm) REVERT: E 715 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.9007 (ttm) outliers start: 24 outliers final: 8 residues processed: 109 average time/residue: 0.4246 time to fit residues: 52.6689 Evaluate side-chains 97 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.072136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.050435 restraints weight = 45483.546| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.82 r_work: 0.2695 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 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 = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16717 Z= 0.100 Angle : 0.482 9.720 22999 Z= 0.238 Chirality : 0.040 0.182 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.480 123.265 3211 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.20), residues: 1898 helix: 2.25 (0.18), residues: 854 sheet: 0.27 (0.29), residues: 337 loop : -0.37 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 93 TYR 0.006 0.001 TYR E 463 PHE 0.012 0.001 PHE E 735 TRP 0.007 0.001 TRP E 659 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00223 (16712) covalent geometry : angle 0.48162 (22999) hydrogen bonds : bond 0.03411 ( 748) hydrogen bonds : angle 4.19702 ( 2082) metal coordination : bond 0.00092 ( 5) *********************** 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 113 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.582 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: 0.8680 (t0) REVERT: A 160 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: D 70 ASP cc_start: 0.8772 (m-30) cc_final: 0.8522 (m-30) REVERT: D 160 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: E 453 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8850 (mm) REVERT: E 715 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.9002 (ttm) REVERT: F 100 MET cc_start: 0.8829 (ppp) cc_final: 0.8573 (ppp) outliers start: 24 outliers final: 10 residues processed: 105 average time/residue: 0.4480 time to fit residues: 53.6360 Evaluate side-chains 100 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 715 MET Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 157 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.072309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050480 restraints weight = 45748.565| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.84 r_work: 0.2689 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 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 = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1506 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= 0.099 Angle : 0.487 10.868 22999 Z= 0.240 Chirality : 0.040 0.176 2700 Planarity : 0.004 0.053 2709 Dihedral : 15.407 120.839 3211 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.16 % Favored : 97.79 % Rotamer: Outliers : 1.54 % Allowed : 14.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.20), residues: 1898 helix: 2.31 (0.18), residues: 854 sheet: 0.24 (0.28), residues: 342 loop : -0.35 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 431 TYR 0.006 0.001 TYR E 59 PHE 0.012 0.001 PHE E 735 TRP 0.007 0.001 TRP E 115 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00223 (16712) covalent geometry : angle 0.48742 (22999) hydrogen bonds : bond 0.03282 ( 748) hydrogen bonds : angle 4.12452 ( 2082) metal coordination : bond 0.00108 ( 5) *********************** 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 115 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8928 (t0) cc_final: 0.8707 (t0) REVERT: A 160 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: D 70 ASP cc_start: 0.8802 (m-30) cc_final: 0.8538 (m-30) REVERT: D 160 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: E 99 LYS cc_start: 0.9608 (mmmt) cc_final: 0.9381 (mmmm) REVERT: E 453 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8820 (mm) REVERT: E 494 MET cc_start: 0.8864 (mtp) cc_final: 0.8634 (mpp) REVERT: F 96 GLU cc_start: 0.9597 (mp0) cc_final: 0.9377 (pm20) REVERT: F 100 MET cc_start: 0.8906 (ppp) cc_final: 0.8601 (ppp) outliers start: 24 outliers final: 11 residues processed: 109 average time/residue: 0.4595 time to fit residues: 57.1079 Evaluate side-chains 101 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 178 MET Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 0.2980 chunk 108 optimal weight: 0.0570 chunk 164 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 142 optimal weight: 0.0670 chunk 83 optimal weight: 6.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3420 r_free = 0.3420 target = 0.073056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051420 restraints weight = 45096.065| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.82 r_work: 0.2721 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 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 = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1660 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= 0.086 Angle : 0.487 10.724 22999 Z= 0.237 Chirality : 0.040 0.182 2700 Planarity : 0.004 0.053 2709 Dihedral : 15.261 117.118 3211 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 1.15 % Allowed : 14.87 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.20), residues: 1898 helix: 2.40 (0.18), residues: 848 sheet: 0.33 (0.28), residues: 351 loop : -0.34 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.009 0.001 TYR E 59 PHE 0.012 0.001 PHE F 97 TRP 0.007 0.001 TRP E 659 HIS 0.005 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00186 (16712) covalent geometry : angle 0.48678 (22999) hydrogen bonds : bond 0.03022 ( 748) hydrogen bonds : angle 4.04879 ( 2082) metal coordination : bond 0.00468 ( 5) *********************** 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 106 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8932 (t0) cc_final: 0.8704 (t0) REVERT: A 160 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: D 70 ASP cc_start: 0.8768 (m-30) cc_final: 0.8511 (m-30) REVERT: D 160 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: E 99 LYS cc_start: 0.9598 (mmmt) cc_final: 0.9367 (mmmm) REVERT: E 453 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8805 (mm) REVERT: E 494 MET cc_start: 0.8836 (mtp) cc_final: 0.8610 (mpp) REVERT: F 96 GLU cc_start: 0.9617 (mp0) cc_final: 0.9386 (pm20) REVERT: F 100 MET cc_start: 0.9048 (ppp) cc_final: 0.8762 (ppp) outliers start: 18 outliers final: 7 residues processed: 100 average time/residue: 0.4854 time to fit residues: 54.8304 Evaluate side-chains 97 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU 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 178 MET Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 150 optimal weight: 0.0870 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.072171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.050215 restraints weight = 45730.925| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.89 r_work: 0.2686 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 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 = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16717 Z= 0.121 Angle : 0.502 11.722 22999 Z= 0.244 Chirality : 0.040 0.175 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.196 115.257 3211 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 1.28 % Allowed : 15.00 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1898 helix: 2.42 (0.18), residues: 848 sheet: 0.28 (0.28), residues: 354 loop : -0.34 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 431 TYR 0.017 0.001 TYR F 137 PHE 0.014 0.001 PHE E 735 TRP 0.007 0.001 TRP E 115 HIS 0.006 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00277 (16712) covalent geometry : angle 0.50220 (22999) hydrogen bonds : bond 0.03295 ( 748) hydrogen bonds : angle 4.09013 ( 2082) metal coordination : bond 0.00176 ( 5) *********************** 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 107 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8939 (t0) cc_final: 0.8721 (t0) REVERT: A 160 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: D 70 ASP cc_start: 0.8771 (m-30) cc_final: 0.8533 (m-30) REVERT: D 79 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8646 (ttpp) REVERT: D 160 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: E 99 LYS cc_start: 0.9608 (mmmt) cc_final: 0.9378 (mmmm) REVERT: E 453 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8798 (mm) REVERT: E 494 MET cc_start: 0.8858 (mtp) cc_final: 0.8611 (mpp) REVERT: F 96 GLU cc_start: 0.9618 (mp0) cc_final: 0.9395 (pm20) REVERT: F 100 MET cc_start: 0.9074 (ppp) cc_final: 0.8806 (ppp) REVERT: F 285 ASP cc_start: 0.9283 (m-30) cc_final: 0.9064 (t0) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.4731 time to fit residues: 55.8685 Evaluate side-chains 102 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 178 MET 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 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 83 optimal weight: 0.0970 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 48 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 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 = 0.3420 r_free = 0.3420 target = 0.073036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.051377 restraints weight = 45418.359| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.82 r_work: 0.2714 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 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 = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1755 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= 0.087 Angle : 0.488 11.907 22999 Z= 0.236 Chirality : 0.039 0.167 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.112 112.155 3207 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.16 % Favored : 97.79 % Rotamer: Outliers : 0.90 % Allowed : 15.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.20), residues: 1898 helix: 2.43 (0.18), residues: 848 sheet: 0.34 (0.28), residues: 351 loop : -0.34 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.007 0.001 TYR E 59 PHE 0.011 0.001 PHE F 97 TRP 0.007 0.001 TRP E 659 HIS 0.005 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00190 (16712) covalent geometry : angle 0.48834 (22999) hydrogen bonds : bond 0.02956 ( 748) hydrogen bonds : angle 4.00228 ( 2082) metal coordination : bond 0.00073 ( 5) *********************** 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 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.8874 (mtt) cc_final: 0.8618 (mtt) REVERT: A 160 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: D 70 ASP cc_start: 0.8804 (m-30) cc_final: 0.8567 (m-30) REVERT: D 79 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8663 (ttpp) REVERT: E 99 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9375 (mmmm) REVERT: E 494 MET cc_start: 0.8860 (mtp) cc_final: 0.8646 (mpp) REVERT: F 96 GLU cc_start: 0.9615 (mp0) cc_final: 0.9395 (pm20) REVERT: F 100 MET cc_start: 0.9066 (ppp) cc_final: 0.8786 (ppp) REVERT: F 121 MET cc_start: 0.8901 (ptp) cc_final: 0.8657 (pmm) REVERT: F 285 ASP cc_start: 0.9248 (m-30) cc_final: 0.9048 (t0) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.4714 time to fit residues: 54.3309 Evaluate side-chains 99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 178 MET Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 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 = 0.3411 r_free = 0.3411 target = 0.072624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.050647 restraints weight = 45423.696| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.89 r_work: 0.2691 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 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 = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1770 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 : 0.492 12.546 22999 Z= 0.239 Chirality : 0.039 0.171 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.071 109.774 3207 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.03 % Allowed : 15.38 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.20), residues: 1898 helix: 2.45 (0.18), residues: 847 sheet: 0.29 (0.28), residues: 355 loop : -0.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.018 0.001 TYR F 137 PHE 0.015 0.001 PHE E 735 TRP 0.007 0.001 TRP E 115 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00235 (16712) covalent geometry : angle 0.49204 (22999) hydrogen bonds : bond 0.03105 ( 748) hydrogen bonds : angle 4.01317 ( 2082) metal coordination : bond 0.00128 ( 5) ********************** 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 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8858 (t0) cc_final: 0.8645 (t0) REVERT: A 160 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: D 70 ASP cc_start: 0.8816 (m-30) cc_final: 0.8540 (m-30) REVERT: D 79 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8717 (ttpp) REVERT: D 160 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: E 99 LYS cc_start: 0.9607 (mmmt) cc_final: 0.9388 (mmmm) REVERT: E 494 MET cc_start: 0.8888 (mtp) cc_final: 0.8670 (mpp) REVERT: F 96 GLU cc_start: 0.9617 (mp0) cc_final: 0.9400 (pm20) REVERT: F 100 MET cc_start: 0.9094 (ppp) cc_final: 0.8821 (ppp) REVERT: F 285 ASP cc_start: 0.9262 (m-30) cc_final: 0.9049 (t0) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.4818 time to fit residues: 55.6742 Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 MET Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 TRP Chi-restraints excluded: chain E residue 651 CYS Chi-restraints excluded: chain E residue 740 SER Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 162 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 434 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 = 0.3395 r_free = 0.3395 target = 0.071896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.050066 restraints weight = 45465.114| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.82 r_work: 0.2681 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16717 Z= 0.135 Angle : 0.528 11.936 22999 Z= 0.257 Chirality : 0.040 0.174 2700 Planarity : 0.004 0.052 2709 Dihedral : 15.074 108.235 3207 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.03 % Allowed : 15.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.20), residues: 1898 helix: 2.40 (0.18), residues: 845 sheet: 0.25 (0.28), residues: 355 loop : -0.34 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 714 TYR 0.007 0.001 TYR E 59 PHE 0.011 0.001 PHE F 97 TRP 0.005 0.001 TRP E 115 HIS 0.006 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00309 (16712) covalent geometry : angle 0.52766 (22999) hydrogen bonds : bond 0.03361 ( 748) hydrogen bonds : angle 4.09031 ( 2082) metal coordination : bond 0.00197 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.20 seconds wall clock time: 68 minutes 9.34 seconds (4089.34 seconds total)