Starting phenix.real_space_refine on Fri Jul 3 21:42:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr4_19457/07_2026/8rr4_19457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr4_19457/07_2026/8rr4_19457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rr4_19457/07_2026/8rr4_19457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr4_19457/07_2026/8rr4_19457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rr4_19457/07_2026/8rr4_19457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr4_19457/07_2026/8rr4_19457.map" } resolution = 3.2 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= 1.123 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 85 5.16 5 C 10175 2.51 5 N 2911 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16539 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: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1811 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 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: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5265 Classifications: {'peptide': 672} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 631} Chain breaks: 3 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: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16539 At special positions: 0 Unit cell: (126.768, 108.42, 175.14, 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 85 16.00 P 76 15.00 O 3290 8.00 N 2911 7.00 C 10175 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: 1.00 Conformation dependent library (CDL) restraints added in 704.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 551 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 724 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 546 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 644 " pdb="ZN ZN E 902 " - pdb=" ND1 HIS E 548 " 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 49.1% alpha, 13.8% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.527A pdb=" N ALA A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.086A 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 122 Processing helix chain 'A' and resid 122 through 137 removed outlier: 4.057A 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 187 removed outlier: 4.575A 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 203 through 208 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.644A pdb=" N VAL A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.526A pdb=" N ALA B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.087A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 122 through 137 removed outlier: 4.057A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.575A 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 213 through 221 removed outlier: 3.644A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.526A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 46 through 55 removed outlier: 4.086A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 122 through 137 removed outlier: 4.057A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.575A 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 205 through 209 removed outlier: 3.644A pdb=" N LEU C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.667A 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 34 removed outlier: 3.527A pdb=" N ALA D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.087A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 137 removed outlier: 4.057A 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: 4.574A 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 212 through 221 removed outlier: 3.644A 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: 3.531A pdb=" N LYS E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.690A pdb=" N ILE E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 288 Processing helix chain 'E' and resid 292 through 296 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: 3.721A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.915A 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: 3.532A pdb=" N PHE E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 467 removed outlier: 4.065A 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: 4.169A pdb=" N ALA E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 3.790A 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: 3.956A 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: 4.343A 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 removed outlier: 3.533A pdb=" N ILE E 775 " --> pdb=" O PHE E 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.588A pdb=" N TRP F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 154 removed outlier: 3.736A pdb=" N ILE F 148 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.522A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 213 removed outlier: 4.478A 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 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.577A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) 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: 3.676A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 removed outlier: 3.671A 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: 6.911A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.333A 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: 6.911A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (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: 6.911A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.333A 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: 6.910A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (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: 3.538A pdb=" N GLY E 140 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP E 106 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER E 139 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE E 108 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 8.030A 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: 3.626A pdb=" N PHE E 85 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER E 67 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA E 73 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA E 65 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TYR E 75 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL E 63 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 77 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN E 61 " --> pdb=" O PHE E 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.846A pdb=" N TYR E 173 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 339 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 602 through 606 removed outlier: 6.186A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 577 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER E 511 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.441A 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: 6.771A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 506 " --> pdb=" O THR E 510 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR E 502 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 634 through 638 removed outlier: 6.863A pdb=" N VAL E 654 " --> pdb=" O GLU E 635 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 637 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA E 652 " --> pdb=" O PHE E 637 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU E 683 " --> pdb=" O MET E 721 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN E 723 " --> pdb=" O LEU E 683 " (cutoff:3.500A) removed outlier: 6.519A 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: 6.508A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.806A 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: 4.436A pdb=" N GLY F 383 " --> pdb=" O GLN F 343 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2650 1.32 - 1.44: 4571 1.44 - 1.56: 9488 1.56 - 1.69: 149 1.69 - 1.81: 135 Bond restraints: 16993 Sorted by residual: bond pdb=" C PRO C 198 " pdb=" O PRO C 198 " ideal model delta sigma weight residual 1.234 1.193 0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" CA SER C 208 " pdb=" CB SER C 208 " ideal model delta sigma weight residual 1.536 1.488 0.049 1.46e-02 4.69e+03 1.11e+01 bond pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 1.466 1.432 0.034 1.19e-02 7.06e+03 8.18e+00 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 7.07e+00 bond pdb=" O5' A T 66 " pdb=" C5' A T 66 " ideal model delta sigma weight residual 1.420 1.459 -0.039 1.50e-02 4.44e+03 6.61e+00 ... (remaining 16988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 22927 1.82 - 3.65: 355 3.65 - 5.47: 75 5.47 - 7.30: 17 7.30 - 9.12: 3 Bond angle restraints: 23377 Sorted by residual: angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 112.38 103.26 9.12 1.22e+00 6.72e-01 5.59e+01 angle pdb=" CA HIS F 381 " pdb=" CB HIS F 381 " pdb=" CG HIS F 381 " ideal model delta sigma weight residual 113.80 120.30 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" N LYS F 380 " pdb=" CA LYS F 380 " pdb=" C LYS F 380 " ideal model delta sigma weight residual 114.62 109.07 5.55 1.14e+00 7.69e-01 2.37e+01 angle pdb=" C PRO F 337 " pdb=" CA PRO F 337 " pdb=" CB PRO F 337 " ideal model delta sigma weight residual 112.89 107.15 5.74 1.31e+00 5.83e-01 1.92e+01 angle pdb=" C1' C T 54 " pdb=" N1 C T 54 " pdb=" C2 C T 54 " ideal model delta sigma weight residual 118.80 123.21 -4.41 1.10e+00 8.26e-01 1.61e+01 ... (remaining 23372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 9524 24.65 - 49.31: 613 49.31 - 73.96: 182 73.96 - 98.61: 30 98.61 - 123.27: 2 Dihedral angle restraints: 10351 sinusoidal: 4794 harmonic: 5557 Sorted by residual: 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 -8.35 33.35 1 8.00e+00 1.56e-02 2.47e+01 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 147.00 113.88 33.12 1 8.00e+00 1.56e-02 2.44e+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 -28.22 31.22 1 8.00e+00 1.56e-02 2.17e+01 ... (remaining 10348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2549 0.093 - 0.186: 186 0.186 - 0.279: 4 0.279 - 0.373: 0 0.373 - 0.466: 8 Chirality restraints: 2747 Sorted by residual: chirality pdb=" P C T 65 " pdb=" OP1 C T 65 " pdb=" OP2 C T 65 " pdb=" O5' C T 65 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.42e+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 5.41e+00 chirality pdb=" P G T 67 " pdb=" OP1 G T 67 " pdb=" OP2 G T 67 " pdb=" O5' G T 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.20e+00 ... (remaining 2744 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 379 " 0.389 9.50e-02 1.11e+02 1.74e-01 1.86e+01 pdb=" NE ARG F 379 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 379 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 379 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 95 " -0.274 9.50e-02 1.11e+02 1.23e-01 9.25e+00 pdb=" NE ARG F 95 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 95 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 95 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 95 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 378 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C LYS F 378 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS F 378 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 379 " 0.018 2.00e-02 2.50e+03 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 122 2.55 - 3.14: 12727 3.14 - 3.73: 26990 3.73 - 4.31: 36648 4.31 - 4.90: 60379 Nonbonded interactions: 136866 Sorted by model distance: nonbonded pdb=" O ALA E 549 " pdb=" OD1 ASN E 550 " model vdw 1.967 3.040 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.083 2.230 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 902 " model vdw 2.089 2.230 nonbonded pdb=" OD1 ASP A 41 " pdb=" N LEU A 42 " model vdw 2.173 3.120 nonbonded pdb=" OD1 ASP D 41 " pdb=" N LEU D 42 " model vdw 2.174 3.120 ... (remaining 136861 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 206 or resid 212 through 261)) selection = chain 'B' selection = (chain 'C' and (resid 7 through 206 or resid 212 through 261)) selection = (chain 'D' and (resid 7 through 206 or resid 212 through 261)) } 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=0.87 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: 0.010 Normalize map: mean=0, sd=1: 3.850 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.470 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.005 0.261 16998 Z= 0.234 Angle : 0.571 9.124 23377 Z= 0.366 Chirality : 0.048 0.466 2747 Planarity : 0.005 0.174 2756 Dihedral : 17.639 123.267 6779 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 0.50 % Allowed : 12.22 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.22 (0.20), residues: 1936 helix: 1.78 (0.18), residues: 805 sheet: 0.72 (0.31), residues: 358 loop : -0.10 (0.24), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 630 TYR 0.009 0.001 TYR F 341 PHE 0.013 0.001 PHE F 179 TRP 0.020 0.001 TRP F 344 HIS 0.015 0.001 HIS F 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.18 (16993) covalent geometry : angle 0.57137 / 0.37 (23377) hydrogen bonds : bond 0.22300 / 15.12 ( 773) hydrogen bonds : angle 7.01491 / 5.08 ( 2133) metal coordination : bond 0.25447 / 15.08 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8452 (tttp) cc_final: 0.7392 (tttp) REVERT: B 259 MET cc_start: 0.8778 (mmm) cc_final: 0.8480 (mmp) REVERT: C 194 MET cc_start: 0.8172 (mmt) cc_final: 0.7913 (mmt) REVERT: E 145 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8849 (tm-30) REVERT: E 449 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9392 (pt0) REVERT: E 668 MET cc_start: 0.7935 (mtp) cc_final: 0.7428 (mtp) REVERT: E 715 MET cc_start: 0.8417 (ttp) cc_final: 0.8067 (ttm) REVERT: F 111 HIS cc_start: 0.8142 (m170) cc_final: 0.7853 (m-70) outliers start: 8 outliers final: 3 residues processed: 196 average time/residue: 0.1266 time to fit residues: 36.2709 Evaluate side-chains 113 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain F residue 278 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 61 GLN E 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049572 restraints weight = 56813.912| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.90 r_work: 0.2736 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16998 Z= 0.139 Angle : 0.541 6.934 23377 Z= 0.288 Chirality : 0.041 0.272 2747 Planarity : 0.004 0.050 2756 Dihedral : 15.693 121.759 3256 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Rotamer: Outliers : 1.26 % Allowed : 12.41 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.39 (0.20), residues: 1936 helix: 2.10 (0.18), residues: 832 sheet: 0.53 (0.29), residues: 373 loop : -0.20 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 788 TYR 0.011 0.001 TYR E 463 PHE 0.012 0.001 PHE E 521 TRP 0.010 0.001 TRP E 587 HIS 0.007 0.001 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16993) covalent geometry : angle 0.54135 / 0.29 (23377) hydrogen bonds : bond 0.06091 / 4.05 ( 773) hydrogen bonds : angle 5.10637 / 3.67 ( 2133) metal coordination : bond 0.01174 / 0.74 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASP cc_start: 0.7998 (t70) cc_final: 0.7725 (t0) REVERT: B 259 MET cc_start: 0.9186 (mmm) cc_final: 0.8746 (mmp) REVERT: D 160 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: E 668 MET cc_start: 0.8751 (mtp) cc_final: 0.8498 (mtp) REVERT: F 121 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8497 (ttt) REVERT: F 129 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8382 (mttt) outliers start: 20 outliers final: 5 residues processed: 134 average time/residue: 0.1044 time to fit residues: 22.2940 Evaluate side-chains 111 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain F residue 121 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 184 optimal weight: 0.0570 chunk 141 optimal weight: 0.0060 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 98 HIS ** 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 = 0.3416 r_free = 0.3416 target = 0.068334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049023 restraints weight = 57339.263| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.92 r_work: 0.2719 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16998 Z= 0.126 Angle : 0.494 7.918 23377 Z= 0.259 Chirality : 0.041 0.273 2747 Planarity : 0.004 0.048 2756 Dihedral : 15.574 119.789 3246 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.26 % Allowed : 12.73 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.34 (0.20), residues: 1936 helix: 2.10 (0.18), residues: 841 sheet: 0.45 (0.29), residues: 371 loop : -0.28 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 675 TYR 0.009 0.001 TYR E 463 PHE 0.014 0.001 PHE F 97 TRP 0.008 0.001 TRP E 587 HIS 0.009 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16993) covalent geometry : angle 0.49401 / 0.26 (23377) hydrogen bonds : bond 0.04844 / 3.17 ( 773) hydrogen bonds : angle 4.66572 / 3.35 ( 2133) metal coordination : bond 0.00198 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 GLU cc_start: 0.8983 (tp30) cc_final: 0.8760 (tp30) REVERT: B 160 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8452 (mt-10) REVERT: B 259 MET cc_start: 0.9262 (mmm) cc_final: 0.8907 (mmp) REVERT: E 668 MET cc_start: 0.8768 (mtp) cc_final: 0.8544 (mtp) REVERT: F 129 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8374 (mttt) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.1103 time to fit residues: 21.2515 Evaluate side-chains 112 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 11 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 0.0040 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 120 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.068827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049524 restraints weight = 56787.724| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.92 r_work: 0.2733 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16998 Z= 0.099 Angle : 0.481 11.329 23377 Z= 0.248 Chirality : 0.040 0.146 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.500 117.306 3246 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % Rotamer: Outliers : 1.58 % Allowed : 13.04 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.37 (0.20), residues: 1936 helix: 2.15 (0.18), residues: 848 sheet: 0.42 (0.29), residues: 359 loop : -0.28 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 431 TYR 0.008 0.001 TYR E 463 PHE 0.014 0.001 PHE E 521 TRP 0.008 0.001 TRP E 433 HIS 0.006 0.001 HIS F 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (16993) covalent geometry : angle 0.48125 / 0.25 (23377) hydrogen bonds : bond 0.04077 / 2.65 ( 773) hydrogen bonds : angle 4.40111 / 3.16 ( 2133) metal coordination : bond 0.00100 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASP cc_start: 0.8151 (t70) cc_final: 0.7883 (t0) REVERT: B 160 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 259 MET cc_start: 0.9279 (mmm) cc_final: 0.8952 (mmp) REVERT: C 194 MET cc_start: 0.9271 (mmm) cc_final: 0.9002 (mmm) REVERT: C 259 MET cc_start: 0.9167 (mmm) cc_final: 0.8840 (mmm) REVERT: D 160 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: E 668 MET cc_start: 0.8778 (mtp) cc_final: 0.8546 (mtp) REVERT: F 129 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8359 (mttt) outliers start: 25 outliers final: 13 residues processed: 133 average time/residue: 0.0970 time to fit residues: 20.8324 Evaluate side-chains 119 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 693 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 195 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 98 HIS E 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.066874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.047483 restraints weight = 57111.727| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.88 r_work: 0.2674 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16998 Z= 0.180 Angle : 0.528 9.083 23377 Z= 0.270 Chirality : 0.041 0.147 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.465 116.367 3246 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 1.58 % Allowed : 14.11 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.29 (0.20), residues: 1936 helix: 2.13 (0.18), residues: 852 sheet: 0.23 (0.28), residues: 364 loop : -0.32 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 431 TYR 0.007 0.001 TYR E 463 PHE 0.013 0.001 PHE E 521 TRP 0.007 0.001 TRP E 115 HIS 0.006 0.001 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (16993) covalent geometry : angle 0.52776 / 0.27 (23377) hydrogen bonds : bond 0.04407 / 2.88 ( 773) hydrogen bonds : angle 4.43718 / 3.20 ( 2133) metal coordination : bond 0.00318 / 0.16 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9024 (t70) cc_final: 0.8633 (t0) REVERT: B 259 MET cc_start: 0.9308 (mmm) cc_final: 0.8981 (mmp) REVERT: C 64 ASP cc_start: 0.8385 (t0) cc_final: 0.8067 (t0) REVERT: C 259 MET cc_start: 0.9251 (mmm) cc_final: 0.8906 (mmm) REVERT: D 160 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: E 416 MET cc_start: 0.9076 (ppp) cc_final: 0.8498 (ppp) REVERT: E 668 MET cc_start: 0.8777 (mtp) cc_final: 0.8555 (mtp) REVERT: F 129 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8338 (mttt) outliers start: 25 outliers final: 13 residues processed: 133 average time/residue: 0.0952 time to fit residues: 20.5263 Evaluate side-chains 121 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 154 optimal weight: 9.9990 chunk 200 optimal weight: 30.0000 chunk 176 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 111 optimal weight: 0.0040 chunk 44 optimal weight: 0.7980 overall best weight: 2.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.047073 restraints weight = 57376.426| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.88 r_work: 0.2661 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16998 Z= 0.186 Angle : 0.533 10.997 23377 Z= 0.272 Chirality : 0.041 0.144 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.482 116.130 3246 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Rotamer: Outliers : 1.45 % Allowed : 15.00 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.19 (0.20), residues: 1936 helix: 2.10 (0.18), residues: 852 sheet: 0.14 (0.28), residues: 364 loop : -0.41 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.009 0.001 TYR F 214 PHE 0.012 0.001 PHE E 521 TRP 0.008 0.001 TRP E 433 HIS 0.006 0.001 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (16993) covalent geometry : angle 0.53283 / 0.27 (23377) hydrogen bonds : bond 0.04253 / 2.78 ( 773) hydrogen bonds : angle 4.38862 / 3.16 ( 2133) metal coordination : bond 0.00339 / 0.18 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9067 (t70) cc_final: 0.8677 (t0) REVERT: B 160 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8552 (mt-10) REVERT: B 259 MET cc_start: 0.9299 (mmm) cc_final: 0.9029 (mmp) REVERT: C 136 MET cc_start: 0.9129 (mtt) cc_final: 0.8813 (mtt) REVERT: C 259 MET cc_start: 0.9245 (mmm) cc_final: 0.9009 (mmm) REVERT: D 160 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: E 416 MET cc_start: 0.9083 (ppp) cc_final: 0.8426 (ppp) REVERT: E 668 MET cc_start: 0.8774 (mtp) cc_final: 0.8546 (mtp) REVERT: F 129 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8344 (mttt) outliers start: 23 outliers final: 16 residues processed: 128 average time/residue: 0.1125 time to fit residues: 23.2759 Evaluate side-chains 116 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.047348 restraints weight = 56631.136| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.88 r_work: 0.2669 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16998 Z= 0.147 Angle : 0.518 11.111 23377 Z= 0.264 Chirality : 0.041 0.144 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.471 115.240 3246 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 1.26 % Allowed : 15.19 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.21 (0.20), residues: 1936 helix: 2.13 (0.18), residues: 854 sheet: 0.15 (0.28), residues: 364 loop : -0.42 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 431 TYR 0.007 0.001 TYR E 463 PHE 0.023 0.001 PHE F 97 TRP 0.008 0.001 TRP E 433 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16993) covalent geometry : angle 0.51811 / 0.26 (23377) hydrogen bonds : bond 0.04021 / 2.63 ( 773) hydrogen bonds : angle 4.31490 / 3.11 ( 2133) metal coordination : bond 0.00262 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9060 (t70) cc_final: 0.8681 (t0) REVERT: B 70 ASP cc_start: 0.9240 (m-30) cc_final: 0.8946 (m-30) REVERT: B 160 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8567 (mt-10) REVERT: B 259 MET cc_start: 0.9291 (mmm) cc_final: 0.9057 (mmp) REVERT: C 64 ASP cc_start: 0.8420 (t0) cc_final: 0.8177 (t0) REVERT: C 136 MET cc_start: 0.9124 (mtt) cc_final: 0.8786 (mtt) REVERT: C 259 MET cc_start: 0.9233 (mmm) cc_final: 0.9014 (mmm) REVERT: D 160 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: E 416 MET cc_start: 0.9079 (ppp) cc_final: 0.8392 (ppp) REVERT: F 129 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8360 (mttt) outliers start: 20 outliers final: 19 residues processed: 125 average time/residue: 0.0948 time to fit residues: 19.2668 Evaluate side-chains 119 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 151 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 0.0050 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.047872 restraints weight = 56905.658| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.88 r_work: 0.2683 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16998 Z= 0.113 Angle : 0.508 13.222 23377 Z= 0.256 Chirality : 0.040 0.146 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.400 112.927 3246 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 15.12 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.30 (0.20), residues: 1936 helix: 2.16 (0.18), residues: 856 sheet: 0.24 (0.29), residues: 362 loop : -0.35 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.007 0.001 TYR E 729 PHE 0.020 0.001 PHE F 97 TRP 0.013 0.001 TRP E 433 HIS 0.005 0.000 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (16993) covalent geometry : angle 0.50778 / 0.26 (23377) hydrogen bonds : bond 0.03668 / 2.40 ( 773) hydrogen bonds : angle 4.18329 / 3.01 ( 2133) metal coordination : bond 0.00168 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9052 (t70) cc_final: 0.8666 (t0) REVERT: B 70 ASP cc_start: 0.9253 (m-30) cc_final: 0.8946 (m-30) REVERT: B 160 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8504 (mt-10) REVERT: C 64 ASP cc_start: 0.8441 (t0) cc_final: 0.8173 (t0) REVERT: C 70 ASP cc_start: 0.9142 (m-30) cc_final: 0.8881 (m-30) REVERT: D 160 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: E 262 MET cc_start: 0.8700 (ppp) cc_final: 0.7991 (ppp) REVERT: E 416 MET cc_start: 0.9078 (ppp) cc_final: 0.8433 (ppp) REVERT: F 129 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8348 (mttt) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.1057 time to fit residues: 21.2935 Evaluate side-chains 118 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 64 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 527 HIS ** 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 = 0.3382 r_free = 0.3382 target = 0.066961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.047541 restraints weight = 57104.846| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.88 r_work: 0.2673 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16998 Z= 0.136 Angle : 0.523 13.606 23377 Z= 0.264 Chirality : 0.040 0.149 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.370 111.807 3246 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 1.39 % Allowed : 15.31 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.33 (0.20), residues: 1936 helix: 2.19 (0.18), residues: 855 sheet: 0.35 (0.29), residues: 366 loop : -0.41 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 217 TYR 0.006 0.001 TYR E 463 PHE 0.014 0.001 PHE F 97 TRP 0.010 0.001 TRP E 433 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16993) covalent geometry : angle 0.52253 / 0.26 (23377) hydrogen bonds : bond 0.03834 / 2.50 ( 773) hydrogen bonds : angle 4.20013 / 3.03 ( 2133) metal coordination : bond 0.00200 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9032 (t70) cc_final: 0.8632 (t0) REVERT: B 70 ASP cc_start: 0.9270 (m-30) cc_final: 0.8991 (m-30) REVERT: B 160 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8550 (mt-10) REVERT: C 64 ASP cc_start: 0.8481 (t0) cc_final: 0.8205 (t0) REVERT: C 70 ASP cc_start: 0.9142 (m-30) cc_final: 0.8883 (m-30) REVERT: D 160 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: E 416 MET cc_start: 0.9089 (ppp) cc_final: 0.8438 (ppp) REVERT: F 129 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8350 (mttt) outliers start: 22 outliers final: 21 residues processed: 121 average time/residue: 0.1081 time to fit residues: 21.1263 Evaluate side-chains 123 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 492 ILE Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 104 optimal weight: 0.0000 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 21 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 527 HIS ** 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 = 0.3386 r_free = 0.3386 target = 0.067152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047661 restraints weight = 57038.384| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.90 r_work: 0.2676 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16998 Z= 0.125 Angle : 0.528 14.336 23377 Z= 0.264 Chirality : 0.040 0.151 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.332 110.225 3246 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Rotamer: Outliers : 1.51 % Allowed : 15.31 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.37 (0.20), residues: 1936 helix: 2.22 (0.18), residues: 855 sheet: 0.41 (0.29), residues: 361 loop : -0.40 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 431 TYR 0.006 0.001 TYR E 463 PHE 0.014 0.001 PHE F 97 TRP 0.011 0.001 TRP E 433 HIS 0.005 0.000 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16993) covalent geometry : angle 0.52780 / 0.26 (23377) hydrogen bonds : bond 0.03727 / 2.44 ( 773) hydrogen bonds : angle 4.15421 / 2.99 ( 2133) metal coordination : bond 0.00173 / 0.09 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9031 (t70) cc_final: 0.8630 (t0) REVERT: B 70 ASP cc_start: 0.9265 (m-30) cc_final: 0.8984 (m-30) REVERT: B 160 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8523 (mt-10) REVERT: C 70 ASP cc_start: 0.9130 (m-30) cc_final: 0.8854 (m-30) REVERT: C 194 MET cc_start: 0.9298 (mmm) cc_final: 0.9097 (mmm) REVERT: D 160 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: E 416 MET cc_start: 0.9095 (ppp) cc_final: 0.8472 (ppp) REVERT: F 129 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8343 (mttt) outliers start: 24 outliers final: 20 residues processed: 126 average time/residue: 0.0975 time to fit residues: 20.1325 Evaluate side-chains 125 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 67 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048312 restraints weight = 56391.460| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.89 r_work: 0.2696 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16998 Z= 0.100 Angle : 0.519 13.998 23377 Z= 0.258 Chirality : 0.040 0.153 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.273 107.932 3246 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 1.20 % Allowed : 15.94 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % 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 are not related in a simple way. whole: 1.41 (0.20), residues: 1936 helix: 2.25 (0.18), residues: 855 sheet: 0.45 (0.29), residues: 361 loop : -0.38 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 82 TYR 0.005 0.001 TYR E 729 PHE 0.014 0.001 PHE F 97 TRP 0.011 0.001 TRP E 433 HIS 0.005 0.000 HIS E 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (16993) covalent geometry : angle 0.51913 / 0.26 (23377) hydrogen bonds : bond 0.03493 / 2.30 ( 773) hydrogen bonds : angle 4.07590 / 2.94 ( 2133) metal coordination : bond 0.00103 / 0.05 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.22 seconds wall clock time: 56 minutes 23.82 seconds (3383.82 seconds total)