Starting phenix.real_space_refine on Sun Aug 24 02:44:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr4_19457/08_2025/8rr4_19457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr4_19457/08_2025/8rr4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rr4_19457/08_2025/8rr4_19457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr4_19457/08_2025/8rr4_19457.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr4_19457/08_2025/8rr4_19457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr4_19457/08_2025/8rr4_19457.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.21, per 1000 atoms: 0.25 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: 1.54 Conformation dependent library (CDL) restraints added in 674.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 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: 2.11 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: 3.27 Time building geometry restraints manager: 2.01 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=" N SER C 208 " pdb=" CA SER C 208 " pdb=" C SER C 208 " ideal model delta sigma weight residual 114.39 108.70 5.69 1.45e+00 4.76e-01 1.54e+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: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.300 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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= 0.228 Angle : 0.571 9.124 23377 Z= 0.336 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 aren 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 covalent geometry : bond 0.00284 (16993) covalent geometry : angle 0.57135 (23377) hydrogen bonds : bond 0.22300 ( 773) hydrogen bonds : angle 7.01491 ( 2133) metal coordination : bond 0.25447 ( 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 : 0.631 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: 0.7914 (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: 0.1595 time to fit residues: 45.4343 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 : 0.598 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 8.9990 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3426 r_free = 0.3426 target = 0.068811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049674 restraints weight = 56725.070| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.90 r_work: 0.2737 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 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 = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1557 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= 0.127 Angle : 0.530 6.930 23377 Z= 0.273 Chirality : 0.041 0.199 2747 Planarity : 0.004 0.049 2756 Dihedral : 15.630 121.311 3256 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Rotamer: Outliers : 1.20 % Allowed : 12.60 % Favored : 86.20 % 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 aren not related in a simple way. whole: 1.36 (0.20), residues: 1936 helix: 2.03 (0.18), residues: 847 sheet: 0.48 (0.29), residues: 364 loop : -0.16 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 431 TYR 0.012 0.001 TYR E 463 PHE 0.013 0.001 PHE E 521 TRP 0.011 0.001 TRP E 587 HIS 0.007 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00267 (16993) covalent geometry : angle 0.53005 (23377) hydrogen bonds : bond 0.04713 ( 773) hydrogen bonds : angle 4.81803 ( 2133) metal coordination : bond 0.01109 ( 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 138 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.9137 (mmm) cc_final: 0.8937 (mmt) REVERT: B 41 ASP cc_start: 0.7998 (t70) cc_final: 0.7677 (t0) REVERT: B 135 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8586 (tp30) REVERT: B 160 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 259 MET cc_start: 0.9213 (mmm) cc_final: 0.8834 (mmp) REVERT: D 160 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: E 668 MET cc_start: 0.8762 (mtp) cc_final: 0.8539 (mtp) REVERT: F 129 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8369 (mttt) outliers start: 19 outliers final: 7 residues processed: 135 average time/residue: 0.1262 time to fit residues: 27.3744 Evaluate side-chains 113 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR 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 492 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 653 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 184 optimal weight: 0.0000 chunk 141 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 197 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 HIS ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049172 restraints weight = 57322.051| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.93 r_work: 0.2724 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16998 Z= 0.112 Angle : 0.492 7.310 23377 Z= 0.249 Chirality : 0.040 0.199 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.497 118.294 3246 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Rotamer: Outliers : 1.39 % Allowed : 12.73 % Favored : 85.89 % 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 aren not related in a simple way. whole: 1.43 (0.20), residues: 1936 helix: 2.17 (0.18), residues: 848 sheet: 0.48 (0.29), residues: 359 loop : -0.23 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 675 TYR 0.008 0.001 TYR E 463 PHE 0.013 0.001 PHE E 521 TRP 0.007 0.001 TRP E 587 HIS 0.006 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00243 (16993) covalent geometry : angle 0.49230 (23377) hydrogen bonds : bond 0.04152 ( 773) hydrogen bonds : angle 4.46582 ( 2133) metal coordination : bond 0.00129 ( 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 134 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.9196 (mmm) cc_final: 0.8978 (mmm) REVERT: B 160 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 259 MET cc_start: 0.9275 (mmm) cc_final: 0.8954 (mmp) REVERT: C 259 MET cc_start: 0.9189 (mmm) cc_final: 0.8872 (mmm) REVERT: E 668 MET cc_start: 0.8757 (mtp) cc_final: 0.8521 (mtp) REVERT: F 129 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8336 (mttt) outliers start: 22 outliers final: 11 residues processed: 131 average time/residue: 0.1267 time to fit residues: 26.4678 Evaluate side-chains 115 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 160 GLU 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 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 693 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 11 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 124 optimal weight: 0.0270 chunk 111 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 159 optimal weight: 0.6980 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.066775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.047318 restraints weight = 56914.929| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.88 r_work: 0.2666 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2319 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= 0.174 Angle : 0.536 14.637 23377 Z= 0.267 Chirality : 0.041 0.146 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.470 116.717 3246 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 1.64 % Allowed : 13.74 % Favored : 84.63 % 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 aren not related in a simple way. whole: 1.36 (0.20), residues: 1936 helix: 2.16 (0.18), residues: 853 sheet: 0.34 (0.29), residues: 369 loop : -0.29 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 675 TYR 0.009 0.001 TYR F 214 PHE 0.016 0.001 PHE F 97 TRP 0.007 0.001 TRP E 115 HIS 0.005 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00392 (16993) covalent geometry : angle 0.53567 (23377) hydrogen bonds : bond 0.04182 ( 773) hydrogen bonds : angle 4.40952 ( 2133) metal coordination : bond 0.00321 ( 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: 26 poor density : 111 time to evaluate : 0.653 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: 0.9055 (t70) cc_final: 0.8668 (t0) REVERT: B 259 MET cc_start: 0.9295 (mmm) cc_final: 0.9048 (mmp) REVERT: C 64 ASP cc_start: 0.8464 (t0) cc_final: 0.8190 (t0) REVERT: C 259 MET cc_start: 0.9238 (mmm) cc_final: 0.9009 (mmm) REVERT: D 160 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: E 416 MET cc_start: 0.9093 (ppp) cc_final: 0.8463 (ppp) REVERT: E 668 MET cc_start: 0.8749 (mtp) cc_final: 0.8519 (mtp) REVERT: F 97 PHE cc_start: 0.9066 (m-10) cc_final: 0.8802 (m-10) REVERT: F 129 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8322 (mttt) outliers start: 26 outliers final: 16 residues processed: 132 average time/residue: 0.1181 time to fit residues: 25.0933 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C 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 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 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 763 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: 4.9990 chunk 174 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.048143 restraints weight = 56761.916| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.92 r_work: 0.2691 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2484 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 : 0.491 11.205 23377 Z= 0.246 Chirality : 0.040 0.146 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.406 113.961 3246 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % 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 aren not related in a simple way. whole: 1.35 (0.20), residues: 1936 helix: 2.20 (0.18), residues: 856 sheet: 0.30 (0.29), residues: 364 loop : -0.33 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 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 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00250 (16993) covalent geometry : angle 0.49054 (23377) hydrogen bonds : bond 0.03536 ( 773) hydrogen bonds : angle 4.19946 ( 2133) metal coordination : bond 0.00126 ( 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: 23 poor density : 115 time to evaluate : 0.632 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: 0.9053 (t70) cc_final: 0.8681 (t0) REVERT: B 70 ASP cc_start: 0.9241 (m-30) cc_final: 0.8919 (m-30) REVERT: B 160 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8436 (mt-10) REVERT: B 259 MET cc_start: 0.9261 (mmm) cc_final: 0.9057 (mmp) REVERT: C 194 MET cc_start: 0.9238 (mmm) cc_final: 0.8893 (mmt) REVERT: C 259 MET cc_start: 0.9279 (mmm) cc_final: 0.9009 (mmm) REVERT: E 416 MET cc_start: 0.9104 (ppp) cc_final: 0.8425 (ppp) REVERT: E 668 MET cc_start: 0.8700 (mtp) cc_final: 0.8467 (mtp) REVERT: F 129 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8335 (mttt) outliers start: 23 outliers final: 17 residues processed: 134 average time/residue: 0.1239 time to fit residues: 26.4463 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 160 GLU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 40 LEU 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 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 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: 20.0000 chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3393 r_free = 0.3393 target = 0.067335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047903 restraints weight = 57008.018| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.89 r_work: 0.2685 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16998 Z= 0.123 Angle : 0.498 11.984 23377 Z= 0.248 Chirality : 0.040 0.139 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.309 111.163 3246 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 1.39 % Allowed : 15.12 % Favored : 83.49 % 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 aren not related in a simple way. whole: 1.38 (0.20), residues: 1936 helix: 2.24 (0.18), residues: 856 sheet: 0.27 (0.29), residues: 364 loop : -0.34 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.009 0.001 TYR E 729 PHE 0.011 0.001 PHE E 521 TRP 0.009 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00276 (16993) covalent geometry : angle 0.49819 (23377) hydrogen bonds : bond 0.03565 ( 773) hydrogen bonds : angle 4.15815 ( 2133) metal coordination : bond 0.00159 ( 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 128 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.678 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: 0.9038 (t70) cc_final: 0.8651 (t0) REVERT: B 70 ASP cc_start: 0.9264 (m-30) cc_final: 0.8961 (m-30) REVERT: B 160 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8442 (mt-10) REVERT: C 64 ASP cc_start: 0.8463 (t0) cc_final: 0.8240 (t0) REVERT: C 259 MET cc_start: 0.9275 (mmm) cc_final: 0.9059 (mmm) REVERT: D 160 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: E 416 MET cc_start: 0.9102 (ppp) cc_final: 0.8396 (ppp) REVERT: E 668 MET cc_start: 0.8712 (mtp) cc_final: 0.8460 (mtp) REVERT: F 129 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8370 (mttt) outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.1194 time to fit residues: 23.9738 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 40 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 111 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3410 r_free = 0.3410 target = 0.068129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048640 restraints weight = 56459.914| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.90 r_work: 0.2705 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16998 Z= 0.096 Angle : 0.494 13.066 23377 Z= 0.244 Chirality : 0.039 0.140 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.213 107.673 3246 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.24 % Rotamer: Outliers : 0.95 % Allowed : 15.82 % Favored : 83.24 % 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 aren not related in a simple way. whole: 1.45 (0.20), residues: 1936 helix: 2.30 (0.18), residues: 856 sheet: 0.41 (0.29), residues: 355 loop : -0.34 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.007 0.001 TYR E 729 PHE 0.011 0.001 PHE E 521 TRP 0.010 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00212 (16993) covalent geometry : angle 0.49389 (23377) hydrogen bonds : bond 0.03229 ( 773) hydrogen bonds : angle 4.03730 ( 2133) metal coordination : bond 0.00101 ( 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 122 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.383 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: 0.9017 (t70) cc_final: 0.8630 (t0) REVERT: B 70 ASP cc_start: 0.9248 (m-30) cc_final: 0.8942 (m-30) REVERT: C 41 ASP cc_start: 0.8550 (t0) cc_final: 0.8304 (t0) REVERT: C 160 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: C 194 MET cc_start: 0.9209 (mmm) cc_final: 0.8826 (mmm) REVERT: C 259 MET cc_start: 0.9273 (mmm) cc_final: 0.8924 (mmm) REVERT: E 416 MET cc_start: 0.9117 (ppp) cc_final: 0.8399 (ppp) REVERT: F 129 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8354 (mttt) outliers start: 15 outliers final: 12 residues processed: 119 average time/residue: 0.1140 time to fit residues: 21.7828 Evaluate side-chains 115 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 160 GLU 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 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 763 LEU Chi-restraints excluded: chain F residue 111 HIS 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: 2.9990 chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 134 optimal weight: 0.0060 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.048228 restraints weight = 56777.485| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.89 r_work: 0.2692 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2850 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= 0.114 Angle : 0.506 12.853 23377 Z= 0.250 Chirality : 0.039 0.137 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.156 105.630 3246 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 1.32 % Allowed : 15.88 % Favored : 82.80 % 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 aren not related in a simple way. whole: 1.48 (0.20), residues: 1936 helix: 2.34 (0.18), residues: 856 sheet: 0.42 (0.29), residues: 361 loop : -0.36 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 82 TYR 0.007 0.001 TYR E 83 PHE 0.011 0.001 PHE E 521 TRP 0.010 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00258 (16993) covalent geometry : angle 0.50573 (23377) hydrogen bonds : bond 0.03387 ( 773) hydrogen bonds : angle 4.03795 ( 2133) metal coordination : bond 0.00134 ( 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 127 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9010 (t70) cc_final: 0.8613 (t0) REVERT: B 70 ASP cc_start: 0.9249 (m-30) cc_final: 0.8961 (m-30) REVERT: C 259 MET cc_start: 0.9294 (mmm) cc_final: 0.8968 (mmm) REVERT: D 160 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: E 416 MET cc_start: 0.9130 (ppp) cc_final: 0.8469 (ppp) REVERT: F 129 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8361 (mttt) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.1187 time to fit residues: 24.1734 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 40 LEU 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 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 763 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 122 GLU 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: 1.9990 chunk 166 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 154 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048188 restraints weight = 56962.252| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.90 r_work: 0.2696 rms_B_bonded: 3.87 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 = 0.65 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 = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16998 Z= 0.116 Angle : 0.528 14.122 23377 Z= 0.259 Chirality : 0.040 0.134 2747 Planarity : 0.004 0.048 2756 Dihedral : 15.102 106.095 3246 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.81 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 aren not related in a simple way. whole: 1.49 (0.20), residues: 1936 helix: 2.32 (0.18), residues: 856 sheet: 0.51 (0.29), residues: 352 loop : -0.35 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.012 0.001 TYR E 83 PHE 0.026 0.001 PHE F 97 TRP 0.010 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00259 (16993) covalent geometry : angle 0.52755 (23377) hydrogen bonds : bond 0.03352 ( 773) hydrogen bonds : angle 4.05196 ( 2133) metal coordination : bond 0.00128 ( 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 134 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.845 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: 0.9011 (t70) cc_final: 0.8609 (t0) REVERT: B 70 ASP cc_start: 0.9268 (m-30) cc_final: 0.8981 (m-30) REVERT: C 68 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 259 MET cc_start: 0.9291 (mmm) cc_final: 0.9060 (mmm) REVERT: E 416 MET cc_start: 0.9121 (ppp) cc_final: 0.8452 (ppp) REVERT: F 129 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8362 (mttt) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.1239 time to fit residues: 26.6857 Evaluate side-chains 121 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 40 LEU 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 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 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: 6.9990 chunk 172 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 21 optimal weight: 0.0030 chunk 96 optimal weight: 0.0370 chunk 194 optimal weight: 10.0000 chunk 177 optimal weight: 0.0020 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 overall best weight: 1.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.048165 restraints weight = 56837.226| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.91 r_work: 0.2691 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3012 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= 0.117 Angle : 0.544 14.308 23377 Z= 0.268 Chirality : 0.040 0.149 2747 Planarity : 0.004 0.048 2756 Dihedral : 15.070 106.581 3246 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % Rotamer: Outliers : 1.20 % Allowed : 16.01 % Favored : 82.80 % 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 aren not related in a simple way. whole: 1.49 (0.20), residues: 1936 helix: 2.30 (0.18), residues: 856 sheet: 0.52 (0.30), residues: 352 loop : -0.34 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.012 0.001 TYR E 83 PHE 0.027 0.001 PHE F 97 TRP 0.011 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00263 (16993) covalent geometry : angle 0.54370 (23377) hydrogen bonds : bond 0.03362 ( 773) hydrogen bonds : angle 4.06422 ( 2133) metal coordination : bond 0.00123 ( 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 124 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.672 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: 0.9022 (t70) cc_final: 0.8619 (t0) REVERT: B 70 ASP cc_start: 0.9281 (m-30) cc_final: 0.9001 (m-30) REVERT: C 259 MET cc_start: 0.9284 (mmm) cc_final: 0.9076 (mmm) REVERT: D 160 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: E 416 MET cc_start: 0.9129 (ppp) cc_final: 0.8490 (ppp) REVERT: E 668 MET cc_start: 0.8338 (mtp) cc_final: 0.8128 (mmm) REVERT: F 129 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8348 (mttt) outliers start: 19 outliers final: 17 residues processed: 121 average time/residue: 0.1232 time to fit residues: 24.2023 Evaluate side-chains 123 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 40 LEU 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 163 LEU 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 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: 3.9990 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 88 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.048618 restraints weight = 56319.884| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.91 r_work: 0.2705 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16998 Z= 0.101 Angle : 0.531 14.375 23377 Z= 0.262 Chirality : 0.039 0.139 2747 Planarity : 0.004 0.048 2756 Dihedral : 15.024 107.047 3246 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 1.13 % Allowed : 15.94 % Favored : 82.92 % 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 aren not related in a simple way. whole: 1.52 (0.20), residues: 1936 helix: 2.33 (0.18), residues: 856 sheet: 0.56 (0.30), residues: 354 loop : -0.35 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.008 0.001 TYR E 83 PHE 0.025 0.001 PHE F 97 TRP 0.011 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00226 (16993) covalent geometry : angle 0.53113 (23377) hydrogen bonds : bond 0.03177 ( 773) hydrogen bonds : angle 4.00426 ( 2133) metal coordination : bond 0.00089 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.45 seconds wall clock time: 69 minutes 25.85 seconds (4165.85 seconds total)