Starting phenix.real_space_refine on Sat Jun 14 18:13:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr4_19457/06_2025/8rr4_19457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr4_19457/06_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_19457/06_2025/8rr4_19457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr4_19457/06_2025/8rr4_19457.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr4_19457/06_2025/8rr4_19457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr4_19457/06_2025/8rr4_19457.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.123 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.17, per 1000 atoms: 0.61 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: 3.96 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.30 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: 6.13 Time building geometry restraints manager: 4.61 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: 2.120 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.790 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 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 TRP 0.020 0.001 TRP F 344 HIS 0.015 0.001 HIS F 381 PHE 0.013 0.001 PHE F 179 TYR 0.009 0.001 TYR F 341 ARG 0.003 0.000 ARG E 630 Details of bonding type rmsd hydrogen bonds : bond 0.22300 ( 773) hydrogen bonds : angle 7.01491 ( 2133) metal coordination : bond 0.25447 ( 5) covalent geometry : bond 0.00284 (16993) covalent geometry : angle 0.57135 (23377) *********************** 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 : 1.906 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 668 MET cc_start: 0.7935 (mtp) cc_final: 0.7428 (mtp) REVERT: E 715 MET cc_start: 0.8417 (ttp) cc_final: 0.8066 (ttm) outliers start: 8 outliers final: 3 residues processed: 196 average time/residue: 0.3351 time to fit residues: 95.1017 Evaluate side-chains 112 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 169 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 182 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 ASN E 418 GLN F 111 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.066764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047493 restraints weight = 57207.235| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.89 r_work: 0.2672 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16998 Z= 0.219 Angle : 0.578 7.850 23377 Z= 0.298 Chirality : 0.042 0.180 2747 Planarity : 0.004 0.050 2756 Dihedral : 15.694 123.745 3256 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 1.83 % Allowed : 12.60 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1936 helix: 2.00 (0.18), residues: 845 sheet: 0.42 (0.29), residues: 360 loop : -0.20 (0.25), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 587 HIS 0.010 0.001 HIS E 546 PHE 0.012 0.001 PHE E 521 TYR 0.011 0.001 TYR E 463 ARG 0.005 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 773) hydrogen bonds : angle 4.95398 ( 2133) metal coordination : bond 0.00983 ( 5) covalent geometry : bond 0.00486 (16993) covalent geometry : angle 0.57770 (23377) *********************** 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 140 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 ASP cc_start: 0.8060 (t70) cc_final: 0.7747 (t0) REVERT: B 135 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8758 (tp30) REVERT: B 259 MET cc_start: 0.9252 (mmm) cc_final: 0.8892 (mmp) REVERT: C 64 ASP cc_start: 0.8427 (t0) cc_final: 0.8092 (t0) REVERT: C 259 MET cc_start: 0.9239 (mmm) cc_final: 0.8922 (mmm) REVERT: D 160 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: E 422 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9396 (mm) REVERT: E 668 MET cc_start: 0.8742 (mtp) cc_final: 0.8511 (mtp) REVERT: F 129 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8381 (mttt) outliers start: 29 outliers final: 13 residues processed: 133 average time/residue: 0.2624 time to fit residues: 55.2541 Evaluate side-chains 117 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 422 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 693 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 343 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 115 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 95 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 GLN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.067434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048302 restraints weight = 56520.221| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.84 r_work: 0.2698 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 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 = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2020 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= 0.122 Angle : 0.498 7.413 23377 Z= 0.252 Chirality : 0.040 0.152 2747 Planarity : 0.004 0.049 2756 Dihedral : 15.580 121.457 3246 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 1.39 % Allowed : 12.98 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1936 helix: 2.15 (0.18), residues: 846 sheet: 0.30 (0.29), residues: 374 loop : -0.28 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 587 HIS 0.016 0.001 HIS F 111 PHE 0.014 0.001 PHE E 521 TYR 0.009 0.001 TYR E 463 ARG 0.004 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 773) hydrogen bonds : angle 4.53705 ( 2133) metal coordination : bond 0.00222 ( 5) covalent geometry : bond 0.00264 (16993) covalent geometry : angle 0.49834 (23377) *********************** 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 131 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ASP cc_start: 0.8367 (t0) cc_final: 0.8155 (t0) REVERT: B 135 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8785 (tp30) REVERT: B 160 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8396 (mt-10) REVERT: B 259 MET cc_start: 0.9235 (mmm) cc_final: 0.8962 (mmp) REVERT: C 64 ASP cc_start: 0.8464 (t0) cc_final: 0.8252 (t0) REVERT: C 194 MET cc_start: 0.9276 (mmm) cc_final: 0.9067 (mmm) REVERT: C 259 MET cc_start: 0.9225 (mmm) cc_final: 0.8939 (mmm) REVERT: E 416 MET cc_start: 0.9033 (ppp) cc_final: 0.8453 (ppp) REVERT: E 668 MET cc_start: 0.8721 (mtp) cc_final: 0.8509 (mtp) REVERT: F 129 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8335 (mttt) outliers start: 22 outliers final: 11 residues processed: 126 average time/residue: 0.2532 time to fit residues: 50.9685 Evaluate side-chains 112 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 D residue 214 CYS 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 547 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 159 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.067464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048293 restraints weight = 56727.906| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.84 r_work: 0.2697 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 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 = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16998 Z= 0.121 Angle : 0.487 6.856 23377 Z= 0.246 Chirality : 0.040 0.146 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.482 117.846 3246 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 1.76 % Allowed : 13.48 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1936 helix: 2.20 (0.18), residues: 854 sheet: 0.29 (0.29), residues: 364 loop : -0.28 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 115 HIS 0.004 0.000 HIS E 546 PHE 0.018 0.001 PHE F 97 TYR 0.008 0.001 TYR E 729 ARG 0.004 0.000 ARG E 675 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 773) hydrogen bonds : angle 4.30867 ( 2133) metal coordination : bond 0.00166 ( 5) covalent geometry : bond 0.00266 (16993) covalent geometry : angle 0.48651 (23377) *********************** 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 141 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.640 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: B 135 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8831 (tp30) REVERT: B 160 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 259 MET cc_start: 0.9252 (mmm) cc_final: 0.9049 (mmp) REVERT: C 64 ASP cc_start: 0.8466 (t0) cc_final: 0.8244 (t0) REVERT: C 259 MET cc_start: 0.9226 (mmm) cc_final: 0.8960 (mmm) REVERT: D 160 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: E 416 MET cc_start: 0.9083 (ppp) cc_final: 0.8471 (ppp) REVERT: E 668 MET cc_start: 0.8741 (mtp) cc_final: 0.8518 (mtp) REVERT: F 97 PHE cc_start: 0.9041 (m-10) cc_final: 0.8816 (m-10) REVERT: F 129 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8334 (mttt) outliers start: 28 outliers final: 18 residues processed: 135 average time/residue: 0.2502 time to fit residues: 54.4347 Evaluate side-chains 119 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 160 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS 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 Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 120 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.066595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047473 restraints weight = 57488.003| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.85 r_work: 0.2669 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16998 Z= 0.156 Angle : 0.507 7.089 23377 Z= 0.255 Chirality : 0.040 0.135 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.457 116.137 3246 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 1.51 % Allowed : 14.37 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1936 helix: 2.23 (0.18), residues: 855 sheet: 0.28 (0.28), residues: 369 loop : -0.33 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 115 HIS 0.005 0.001 HIS E 546 PHE 0.011 0.001 PHE E 521 TYR 0.010 0.001 TYR F 214 ARG 0.003 0.000 ARG E 431 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 773) hydrogen bonds : angle 4.31283 ( 2133) metal coordination : bond 0.00233 ( 5) covalent geometry : bond 0.00350 (16993) covalent geometry : angle 0.50729 (23377) *********************** 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 132 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.660 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: 0.9063 (t70) cc_final: 0.8692 (t0) REVERT: B 70 ASP cc_start: 0.9249 (m-30) cc_final: 0.8948 (m-30) REVERT: B 160 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8470 (mt-10) REVERT: C 64 ASP cc_start: 0.8503 (t0) cc_final: 0.8281 (t0) REVERT: C 259 MET cc_start: 0.9249 (mmm) cc_final: 0.9024 (mmm) REVERT: D 160 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: E 416 MET cc_start: 0.9132 (ppp) cc_final: 0.8458 (ppp) REVERT: E 668 MET cc_start: 0.8735 (mtp) cc_final: 0.8501 (mtp) REVERT: F 129 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8339 (mttt) outliers start: 24 outliers final: 15 residues processed: 125 average time/residue: 0.2525 time to fit residues: 51.1198 Evaluate side-chains 118 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS 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 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 50 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 170 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.065781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.046655 restraints weight = 57267.772| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.83 r_work: 0.2644 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16998 Z= 0.186 Angle : 0.538 7.624 23377 Z= 0.269 Chirality : 0.041 0.140 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.454 115.596 3246 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 2.02 % Allowed : 14.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1936 helix: 2.20 (0.18), residues: 855 sheet: 0.16 (0.28), residues: 369 loop : -0.41 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 433 HIS 0.005 0.001 HIS E 546 PHE 0.015 0.001 PHE E 735 TYR 0.011 0.001 TYR F 214 ARG 0.002 0.000 ARG E 675 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 773) hydrogen bonds : angle 4.37198 ( 2133) metal coordination : bond 0.00294 ( 5) covalent geometry : bond 0.00421 (16993) covalent geometry : angle 0.53848 (23377) *********************** 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 144 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9061 (t70) cc_final: 0.8688 (t0) REVERT: B 70 ASP cc_start: 0.9263 (m-30) cc_final: 0.8969 (m-30) REVERT: B 160 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 64 ASP cc_start: 0.8553 (t0) cc_final: 0.8324 (t0) REVERT: C 259 MET cc_start: 0.9273 (mmm) cc_final: 0.9055 (mmm) REVERT: D 160 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: E 262 MET cc_start: 0.8842 (ppp) cc_final: 0.8189 (ppp) REVERT: E 416 MET cc_start: 0.9117 (ppp) cc_final: 0.8490 (ppp) REVERT: F 129 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8398 (mttt) outliers start: 32 outliers final: 19 residues processed: 137 average time/residue: 0.2948 time to fit residues: 64.7276 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN 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 D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS 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 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 117 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 167 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 GLN ** E 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047536 restraints weight = 56865.590| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.87 r_work: 0.2670 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16998 Z= 0.119 Angle : 0.517 7.811 23377 Z= 0.257 Chirality : 0.040 0.142 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.374 113.487 3246 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.45 % Allowed : 15.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1936 helix: 2.24 (0.18), residues: 856 sheet: 0.23 (0.28), residues: 369 loop : -0.39 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 PHE 0.019 0.001 PHE F 97 TYR 0.007 0.001 TYR E 729 ARG 0.003 0.000 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 773) hydrogen bonds : angle 4.23292 ( 2133) metal coordination : bond 0.00150 ( 5) covalent geometry : bond 0.00266 (16993) covalent geometry : angle 0.51664 (23377) *********************** 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 132 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 2.436 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: 0.9042 (t70) cc_final: 0.8672 (t0) REVERT: B 70 ASP cc_start: 0.9274 (m-30) cc_final: 0.8969 (m-30) REVERT: B 160 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8437 (mt-10) REVERT: C 64 ASP cc_start: 0.8533 (t0) cc_final: 0.8288 (t0) REVERT: D 160 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: E 416 MET cc_start: 0.9129 (ppp) cc_final: 0.8490 (ppp) REVERT: F 129 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8367 (mttt) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.2472 time to fit residues: 50.9968 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 : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS 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 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 139 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 13 optimal weight: 0.0020 chunk 92 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.066928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047778 restraints weight = 56859.448| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.83 r_work: 0.2680 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16998 Z= 0.116 Angle : 0.521 8.937 23377 Z= 0.260 Chirality : 0.040 0.140 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.308 110.974 3246 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % Rotamer: Outliers : 1.26 % Allowed : 16.19 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1936 helix: 2.28 (0.18), residues: 856 sheet: 0.28 (0.28), residues: 369 loop : -0.38 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 PHE 0.016 0.001 PHE F 97 TYR 0.007 0.001 TYR E 729 ARG 0.002 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 773) hydrogen bonds : angle 4.21003 ( 2133) metal coordination : bond 0.00129 ( 5) covalent geometry : bond 0.00258 (16993) covalent geometry : angle 0.52130 (23377) *********************** 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 128 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.651 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: 0.9015 (t70) cc_final: 0.8628 (t0) REVERT: B 70 ASP cc_start: 0.9256 (m-30) cc_final: 0.8959 (m-30) REVERT: B 160 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8431 (mt-10) REVERT: C 64 ASP cc_start: 0.8524 (t0) cc_final: 0.8269 (t0) REVERT: D 160 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: E 416 MET cc_start: 0.9103 (ppp) cc_final: 0.8511 (ppp) REVERT: F 129 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8388 (mttt) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.2536 time to fit residues: 50.5672 Evaluate side-chains 124 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 214 CYS 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 628 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain F residue 117 LEU 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 9 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 chunk 197 optimal weight: 8.9990 chunk 94 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.068050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048886 restraints weight = 57043.898| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.89 r_work: 0.2710 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 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 = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3073 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= 0.092 Angle : 0.511 9.607 23377 Z= 0.253 Chirality : 0.040 0.147 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.199 105.943 3246 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.09 % Rotamer: Outliers : 1.07 % Allowed : 16.38 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1936 helix: 2.34 (0.18), residues: 855 sheet: 0.45 (0.29), residues: 364 loop : -0.35 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 433 HIS 0.003 0.000 HIS E 546 PHE 0.018 0.001 PHE F 97 TYR 0.007 0.001 TYR E 83 ARG 0.002 0.000 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 773) hydrogen bonds : angle 4.05916 ( 2133) metal coordination : bond 0.00079 ( 5) covalent geometry : bond 0.00202 (16993) covalent geometry : angle 0.51076 (23377) *********************** 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 135 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8987 (t70) cc_final: 0.8605 (t0) REVERT: A 211 GLU cc_start: 0.8487 (mp0) cc_final: 0.8232 (tm-30) REVERT: B 70 ASP cc_start: 0.9262 (m-30) cc_final: 0.8954 (m-30) REVERT: C 64 ASP cc_start: 0.8484 (t0) cc_final: 0.8205 (t0) REVERT: C 70 ASP cc_start: 0.9141 (m-30) cc_final: 0.8804 (m-30) REVERT: C 194 MET cc_start: 0.9229 (mmm) cc_final: 0.8844 (mmm) REVERT: E 262 MET cc_start: 0.8921 (ppp) cc_final: 0.8144 (ppp) REVERT: E 416 MET cc_start: 0.9136 (ppp) cc_final: 0.8495 (ppp) REVERT: F 129 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8358 (mttt) outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 0.2692 time to fit residues: 55.7597 Evaluate side-chains 120 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 214 CYS 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 507 SER Chi-restraints excluded: chain E residue 546 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 108 optimal weight: 0.0370 chunk 36 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 179 optimal weight: 0.0270 chunk 45 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.067935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048805 restraints weight = 56951.043| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.85 r_work: 0.2713 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16998 Z= 0.100 Angle : 0.551 20.146 23377 Z= 0.269 Chirality : 0.040 0.137 2747 Planarity : 0.004 0.047 2756 Dihedral : 15.162 106.254 3246 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 0.76 % Allowed : 16.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.20), residues: 1936 helix: 2.36 (0.18), residues: 855 sheet: 0.48 (0.29), residues: 364 loop : -0.36 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 PHE 0.016 0.001 PHE F 97 TYR 0.023 0.001 TYR E 83 ARG 0.003 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 773) hydrogen bonds : angle 4.02932 ( 2133) metal coordination : bond 0.00082 ( 5) covalent geometry : bond 0.00221 (16993) covalent geometry : angle 0.55071 (23377) ********************** 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 125 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8969 (t70) cc_final: 0.8573 (t0) REVERT: A 211 GLU cc_start: 0.8456 (mp0) cc_final: 0.8229 (tm-30) REVERT: B 70 ASP cc_start: 0.9244 (m-30) cc_final: 0.8942 (m-30) REVERT: C 64 ASP cc_start: 0.8492 (t0) cc_final: 0.8201 (t0) REVERT: C 70 ASP cc_start: 0.9129 (m-30) cc_final: 0.8788 (m-30) REVERT: E 262 MET cc_start: 0.8910 (ppp) cc_final: 0.8176 (ppp) REVERT: E 416 MET cc_start: 0.9100 (ppp) cc_final: 0.8509 (ppp) REVERT: F 129 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8364 (mttt) REVERT: F 132 TYR cc_start: 0.9133 (t80) cc_final: 0.8909 (t80) outliers start: 12 outliers final: 10 residues processed: 122 average time/residue: 0.2537 time to fit residues: 50.5144 Evaluate side-chains 119 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 763 LEU 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 168 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048684 restraints weight = 56933.123| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.91 r_work: 0.2708 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16998 Z= 0.104 Angle : 0.554 18.202 23377 Z= 0.272 Chirality : 0.040 0.141 2747 Planarity : 0.004 0.046 2756 Dihedral : 15.145 106.762 3246 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Rotamer: Outliers : 0.82 % Allowed : 16.57 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1936 helix: 2.35 (0.18), residues: 855 sheet: 0.52 (0.29), residues: 364 loop : -0.34 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 433 HIS 0.004 0.000 HIS E 546 PHE 0.015 0.001 PHE F 97 TYR 0.009 0.001 TYR E 83 ARG 0.002 0.000 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 773) hydrogen bonds : angle 4.01674 ( 2133) metal coordination : bond 0.00090 ( 5) covalent geometry : bond 0.00233 (16993) covalent geometry : angle 0.55386 (23377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9102.50 seconds wall clock time: 161 minutes 43.16 seconds (9703.16 seconds total)