Starting phenix.real_space_refine on Sat Jun 14 14:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr3_19455/06_2025/8rr3_19455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr3_19455/06_2025/8rr3_19455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rr3_19455/06_2025/8rr3_19455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr3_19455/06_2025/8rr3_19455.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr3_19455/06_2025/8rr3_19455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr3_19455/06_2025/8rr3_19455.cif" } resolution = 3.4 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= 0.007 sd= 1.089 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 81 5.49 5 S 81 5.16 5 C 9991 2.51 5 N 2869 2.21 5 O 3270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 16294 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: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1622 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain breaks: 2 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: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1663 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} 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: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2278 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 1 Chain: "T" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1742 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 20, 'rna3p': 60} 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: 10.95, per 1000 atoms: 0.67 Number of scatterers: 16294 At special positions: 0 Unit cell: (104.25, 116.76, 166.8, 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 81 16.00 P 81 15.00 O 3270 8.00 N 2869 7.00 C 9991 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: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 724 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 551 " 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 " 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3482 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 10 sheets defined 48.2% alpha, 12.9% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.503A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.557A 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 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.590A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 209' Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.574A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.898A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 removed outlier: 3.657A pdb=" N VAL B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 137 removed outlier: 3.626A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.419A 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 229 through 243 removed outlier: 3.573A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.879A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.588A pdb=" N VAL C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 137 removed outlier: 3.739A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 131 " --> pdb=" O ASN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.482A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.594A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.004A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.588A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.961A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 110 through 137 removed outlier: 3.521A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.700A 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: 4.448A 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 229 through 243 removed outlier: 3.734A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) 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: 3.618A pdb=" N LYS E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 4.132A pdb=" N MET E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 4.374A pdb=" N ILE E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) 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: 3.806A pdb=" N GLN E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 removed outlier: 3.529A pdb=" N LEU E 349 " --> pdb=" O PRO E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 360 removed outlier: 3.503A pdb=" N GLU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 391 removed outlier: 3.743A pdb=" N LEU E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 removed outlier: 3.564A pdb=" N PHE E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 467 removed outlier: 3.713A pdb=" N SER E 459 " --> pdb=" O ASN E 455 " (cutoff:3.500A) removed outlier: 4.074A 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 removed outlier: 3.513A pdb=" N ILE E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 595 removed outlier: 4.055A pdb=" N ALA E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 3.792A 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 632 Processing helix chain 'E' and resid 670 through 677 removed outlier: 3.813A 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 759 through 762 Processing helix chain 'E' and resid 763 through 771 Processing helix chain 'E' and resid 771 through 792 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 125 through 154 Processing helix chain 'F' and resid 183 through 202 removed outlier: 3.596A pdb=" N MET F 187 " --> pdb=" O TRP F 183 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 215 removed outlier: 4.258A pdb=" N ASN F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET F 215 " --> pdb=" O GLU F 212 " (cutoff:3.500A) 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 269 removed outlier: 3.837A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 320 through 329 removed outlier: 3.613A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) 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 helix chain 'F' and resid 377 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.750A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.584A 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: 6.343A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU B 249 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.850A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.621A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 153 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 162 through 167 removed outlier: 6.477A pdb=" N ARG E 82 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE E 109 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU E 84 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA E 73 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU E 423 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS E 424 " --> pdb=" O GLN E 434 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN E 434 " --> pdb=" O LYS E 424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 173 through 174 removed outlier: 6.187A pdb=" N VAL E 241 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU E 310 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 602 through 606 removed outlier: 6.476A pdb=" N LEU E 576 " --> pdb=" O SER E 603 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE E 605 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL E 578 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA E 540 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL E 579 " --> pdb=" O ALA E 540 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL E 542 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 511 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N PHE E 543 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU E 513 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR E 510 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 506 " --> pdb=" O THR E 510 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR E 502 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA E 501 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 486 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET E 750 " --> pdb=" O PHE E 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 636 through 638 removed outlier: 3.530A pdb=" N GLU E 636 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 654 " --> pdb=" O GLU E 636 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS E 660 " --> pdb=" O LEU E 682 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE E 684 " --> pdb=" O LYS E 660 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 662 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N GLU E 686 " --> pdb=" O VAL E 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.515A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 288 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY F 310 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LEU F 290 " --> pdb=" O GLY F 310 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3258 1.33 - 1.45: 4023 1.45 - 1.57: 9183 1.57 - 1.69: 159 1.69 - 1.81: 129 Bond restraints: 16752 Sorted by residual: bond pdb=" C2 SAH F 501 " pdb=" N3 SAH F 501 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" N ILE F 98 " pdb=" CA ILE F 98 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.88e+00 bond pdb=" N LEU F 342 " pdb=" CA LEU F 342 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.16e-02 7.43e+03 6.84e+00 bond pdb=" N LEU F 351 " pdb=" CA LEU F 351 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.21e-02 6.83e+03 6.78e+00 bond pdb=" C8 SAH F 501 " pdb=" N7 SAH F 501 " ideal model delta sigma weight residual 1.299 1.350 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 16747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 22569 2.67 - 5.35: 442 5.35 - 8.02: 48 8.02 - 10.69: 16 10.69 - 13.36: 2 Bond angle restraints: 23077 Sorted by residual: angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 111.71 106.10 5.61 1.15e+00 7.56e-01 2.38e+01 angle pdb=" CB MET E 721 " pdb=" CG MET E 721 " pdb=" SD MET E 721 " ideal model delta sigma weight residual 112.70 126.06 -13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 111.07 106.41 4.66 1.07e+00 8.73e-01 1.90e+01 angle pdb=" CA GLU A 140 " pdb=" CB GLU A 140 " pdb=" CG GLU A 140 " ideal model delta sigma weight residual 114.10 122.53 -8.43 2.00e+00 2.50e-01 1.78e+01 angle pdb=" CA MET F 121 " pdb=" CB MET F 121 " pdb=" CG MET F 121 " ideal model delta sigma weight residual 114.10 122.50 -8.40 2.00e+00 2.50e-01 1.76e+01 ... (remaining 23072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 9777 35.47 - 70.94: 404 70.94 - 106.40: 40 106.40 - 141.87: 3 141.87 - 177.34: 3 Dihedral angle restraints: 10227 sinusoidal: 4807 harmonic: 5420 Sorted by residual: dihedral pdb=" CA SER F 316 " pdb=" C SER F 316 " pdb=" N MET F 317 " pdb=" CA MET F 317 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C4' U T 1 " pdb=" C3' U T 1 " pdb=" O3' U T 1 " pdb=" P A T 2 " ideal model delta sinusoidal sigma weight residual 220.00 42.66 177.34 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' A T 15 " pdb=" C3' A T 15 " pdb=" O3' A T 15 " pdb=" P U T 16 " ideal model delta sinusoidal sigma weight residual -110.00 66.47 -176.47 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 10224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1936 0.044 - 0.089: 523 0.089 - 0.133: 208 0.133 - 0.177: 35 0.177 - 0.222: 12 Chirality restraints: 2714 Sorted by residual: chirality pdb=" CA ILE F 346 " pdb=" N ILE F 346 " pdb=" C ILE F 346 " pdb=" CB ILE F 346 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' U T 6 " pdb=" O4' U T 6 " pdb=" C2' U T 6 " pdb=" N1 U T 6 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE A 201 " pdb=" N PHE A 201 " pdb=" C PHE A 201 " pdb=" CB PHE A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2711 not shown) Planarity restraints: 2693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 77 " 0.023 2.00e-02 2.50e+03 2.48e-02 1.07e+01 pdb=" CG PHE E 77 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE E 77 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 77 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 77 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 77 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 77 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 113 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASP C 113 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP C 113 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 114 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 130 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C ARG C 130 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG C 130 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU C 131 " -0.014 2.00e-02 2.50e+03 ... (remaining 2690 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 211 2.61 - 3.19: 14342 3.19 - 3.76: 26171 3.76 - 4.33: 35674 4.33 - 4.90: 57508 Nonbonded interactions: 133906 Sorted by model distance: nonbonded pdb=" OD1 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.042 2.230 nonbonded pdb=" OD1 ASP E 691 " pdb=" OG SER E 706 " model vdw 2.088 3.040 nonbonded pdb=" OD2 ASP E 666 " pdb="ZN ZN E 901 " model vdw 2.115 2.230 nonbonded pdb=" OD1 ASN F 222 " pdb=" O2' G T 9 " model vdw 2.136 3.040 nonbonded pdb=" O LEU F 290 " pdb=" O2' SAH F 501 " model vdw 2.152 3.040 ... (remaining 133901 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 8 through 103 or resid 107 through 202 or resid 225 throug \ h 257)) selection = (chain 'B' and resid 8 through 257) selection = (chain 'C' and (resid 8 through 103 or resid 107 through 202 or resid 225 throug \ h 257)) selection = (chain 'D' and (resid 8 through 103 or resid 107 through 202 or resid 225 throug \ h 257)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.87 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.360 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.246 16757 Z= 0.211 Angle : 0.880 13.363 23077 Z= 0.481 Chirality : 0.049 0.222 2714 Planarity : 0.005 0.040 2693 Dihedral : 18.124 177.340 6745 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.93 % Rotamer: Outliers : 0.58 % Allowed : 15.16 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1888 helix: 1.18 (0.18), residues: 777 sheet: 0.16 (0.29), residues: 330 loop : -0.31 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 433 HIS 0.008 0.001 HIS E 644 PHE 0.058 0.002 PHE E 77 TYR 0.039 0.003 TYR B 233 ARG 0.011 0.001 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.17599 ( 754) hydrogen bonds : angle 7.24120 ( 2115) metal coordination : bond 0.18120 ( 5) covalent geometry : bond 0.00359 (16752) covalent geometry : angle 0.87994 (23077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 ILE cc_start: 0.7136 (tp) cc_final: 0.6558 (pt) REVERT: E 552 HIS cc_start: 0.8454 (p-80) cc_final: 0.8170 (p-80) REVERT: F 187 MET cc_start: 0.7512 (mtt) cc_final: 0.7272 (mtt) REVERT: F 188 ASP cc_start: 0.7389 (m-30) cc_final: 0.6902 (m-30) outliers start: 9 outliers final: 3 residues processed: 220 average time/residue: 0.3099 time to fit residues: 99.0159 Evaluate side-chains 179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 178 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 115 GLN A 139 ASN C 107 GLN D 115 GLN E 107 ASN ** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.139558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112945 restraints weight = 35262.711| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.48 r_work: 0.3601 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3609 r_free = 0.3609 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16757 Z= 0.139 Angle : 0.623 8.064 23077 Z= 0.319 Chirality : 0.043 0.246 2714 Planarity : 0.005 0.052 2693 Dihedral : 17.422 173.279 3319 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.14 % Allowed : 13.54 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.10 (0.20), residues: 1888 helix: 1.79 (0.18), residues: 794 sheet: 0.12 (0.29), residues: 325 loop : -0.02 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 587 HIS 0.004 0.001 HIS F 381 PHE 0.017 0.001 PHE E 456 TYR 0.012 0.002 TYR B 168 ARG 0.006 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 754) hydrogen bonds : angle 5.25231 ( 2115) metal coordination : bond 0.00299 ( 5) covalent geometry : bond 0.00298 (16752) covalent geometry : angle 0.62259 (23077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.6835 (mtm110) cc_final: 0.6487 (mtp85) REVERT: B 52 LYS cc_start: 0.8519 (tptp) cc_final: 0.7792 (mtmt) REVERT: B 233 TYR cc_start: 0.8080 (t80) cc_final: 0.7837 (t80) REVERT: C 142 ASP cc_start: 0.6473 (t0) cc_final: 0.6247 (t0) REVERT: C 189 ILE cc_start: 0.8725 (mm) cc_final: 0.8346 (tt) REVERT: D 60 PHE cc_start: 0.7486 (t80) cc_final: 0.7202 (t80) REVERT: E 83 TYR cc_start: 0.8052 (m-80) cc_final: 0.7845 (m-80) REVERT: E 151 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7873 (mm) REVERT: E 301 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7152 (p0) REVERT: E 776 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: F 188 ASP cc_start: 0.7866 (m-30) cc_final: 0.7452 (m-30) outliers start: 33 outliers final: 8 residues processed: 220 average time/residue: 0.2966 time to fit residues: 96.0755 Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 776 GLU Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 0.0470 chunk 178 optimal weight: 0.2980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 ASN E 117 ASN ** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.140568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113852 restraints weight = 34770.604| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.60 r_work: 0.3608 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16757 Z= 0.111 Angle : 0.579 10.296 23077 Z= 0.291 Chirality : 0.042 0.186 2714 Planarity : 0.004 0.042 2693 Dihedral : 17.297 175.630 3315 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.14 % Allowed : 14.18 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.19 (0.20), residues: 1888 helix: 1.83 (0.18), residues: 802 sheet: 0.22 (0.29), residues: 329 loop : 0.03 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 115 HIS 0.004 0.001 HIS E 342 PHE 0.013 0.001 PHE A 245 TYR 0.019 0.001 TYR D 101 ARG 0.005 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 754) hydrogen bonds : angle 4.88316 ( 2115) metal coordination : bond 0.00166 ( 5) covalent geometry : bond 0.00232 (16752) covalent geometry : angle 0.57883 (23077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6944 (mp0) REVERT: B 168 TYR cc_start: 0.6898 (t80) cc_final: 0.6324 (t80) REVERT: B 233 TYR cc_start: 0.8100 (t80) cc_final: 0.7791 (t80) REVERT: C 142 ASP cc_start: 0.6364 (t0) cc_final: 0.6110 (t0) REVERT: C 189 ILE cc_start: 0.8680 (mm) cc_final: 0.8357 (tt) REVERT: D 28 GLU cc_start: 0.8572 (pt0) cc_final: 0.8320 (pt0) REVERT: D 60 PHE cc_start: 0.7476 (t80) cc_final: 0.7174 (t80) REVERT: E 151 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7804 (mm) REVERT: F 121 MET cc_start: 0.7862 (mmm) cc_final: 0.7642 (mmm) outliers start: 33 outliers final: 16 residues processed: 209 average time/residue: 0.3088 time to fit residues: 94.9082 Evaluate side-chains 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 621 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 178 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN E 61 GLN E 107 ASN E 117 ASN ** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.135225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108220 restraints weight = 35274.495| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.44 r_work: 0.3513 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16757 Z= 0.192 Angle : 0.620 8.347 23077 Z= 0.316 Chirality : 0.043 0.196 2714 Planarity : 0.005 0.056 2693 Dihedral : 17.341 177.378 3315 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.40 % Allowed : 14.51 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1888 helix: 1.70 (0.18), residues: 804 sheet: 0.05 (0.28), residues: 334 loop : -0.27 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 115 HIS 0.006 0.001 HIS F 381 PHE 0.018 0.002 PHE A 245 TYR 0.020 0.002 TYR E 59 ARG 0.009 0.001 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 754) hydrogen bonds : angle 5.04429 ( 2115) metal coordination : bond 0.00359 ( 5) covalent geometry : bond 0.00431 (16752) covalent geometry : angle 0.62010 (23077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6929 (mp0) REVERT: B 168 TYR cc_start: 0.7030 (t80) cc_final: 0.6376 (t80) REVERT: B 257 ILE cc_start: 0.7648 (tp) cc_final: 0.7318 (pt) REVERT: C 142 ASP cc_start: 0.6482 (t0) cc_final: 0.6225 (t0) REVERT: C 160 GLU cc_start: 0.7727 (pt0) cc_final: 0.7488 (pt0) REVERT: C 189 ILE cc_start: 0.8743 (mm) cc_final: 0.8409 (tt) REVERT: D 28 GLU cc_start: 0.8597 (pt0) cc_final: 0.8362 (pt0) REVERT: E 151 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7850 (mm) REVERT: F 184 ASP cc_start: 0.7807 (t0) cc_final: 0.7189 (t0) REVERT: F 188 ASP cc_start: 0.7916 (m-30) cc_final: 0.7283 (m-30) outliers start: 37 outliers final: 20 residues processed: 202 average time/residue: 0.3003 time to fit residues: 90.2429 Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.136299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109254 restraints weight = 35558.664| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.55 r_work: 0.3533 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16757 Z= 0.131 Angle : 0.576 10.092 23077 Z= 0.291 Chirality : 0.042 0.180 2714 Planarity : 0.004 0.053 2693 Dihedral : 17.279 179.861 3315 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.55 % Allowed : 15.61 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1888 helix: 1.71 (0.18), residues: 811 sheet: -0.12 (0.28), residues: 338 loop : -0.27 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 115 HIS 0.007 0.001 HIS E 551 PHE 0.015 0.001 PHE A 245 TYR 0.019 0.002 TYR D 101 ARG 0.006 0.000 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 754) hydrogen bonds : angle 4.87120 ( 2115) metal coordination : bond 0.00167 ( 5) covalent geometry : bond 0.00290 (16752) covalent geometry : angle 0.57576 (23077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8481 (tptp) cc_final: 0.7770 (mtmt) REVERT: B 112 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6936 (mp0) REVERT: B 168 TYR cc_start: 0.7013 (t80) cc_final: 0.6340 (t80) REVERT: B 257 ILE cc_start: 0.7677 (tp) cc_final: 0.7360 (pt) REVERT: C 142 ASP cc_start: 0.6474 (t70) cc_final: 0.6265 (t0) REVERT: C 160 GLU cc_start: 0.7629 (pt0) cc_final: 0.7424 (pt0) REVERT: C 189 ILE cc_start: 0.8693 (mm) cc_final: 0.8386 (tt) REVERT: D 28 GLU cc_start: 0.8587 (pt0) cc_final: 0.8345 (pt0) REVERT: D 159 PHE cc_start: 0.7664 (m-80) cc_final: 0.7460 (m-10) REVERT: E 151 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7875 (mm) REVERT: E 183 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.7868 (tp) REVERT: F 188 ASP cc_start: 0.7897 (m-30) cc_final: 0.7415 (m-30) outliers start: 24 outliers final: 15 residues processed: 193 average time/residue: 0.2943 time to fit residues: 85.4299 Evaluate side-chains 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 101 optimal weight: 0.6980 chunk 85 optimal weight: 0.0030 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110060 restraints weight = 35232.558| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.49 r_work: 0.3547 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16757 Z= 0.115 Angle : 0.570 9.014 23077 Z= 0.286 Chirality : 0.041 0.176 2714 Planarity : 0.004 0.050 2693 Dihedral : 17.215 177.468 3315 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.88 % Allowed : 16.06 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1888 helix: 1.76 (0.18), residues: 805 sheet: -0.12 (0.28), residues: 344 loop : -0.19 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 115 HIS 0.006 0.001 HIS E 551 PHE 0.012 0.001 PHE A 245 TYR 0.022 0.001 TYR D 101 ARG 0.005 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 754) hydrogen bonds : angle 4.77414 ( 2115) metal coordination : bond 0.00099 ( 5) covalent geometry : bond 0.00253 (16752) covalent geometry : angle 0.56971 (23077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8307 (Cg_exo) cc_final: 0.8048 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8535 (tptp) cc_final: 0.7816 (mtmt) REVERT: B 112 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6897 (mp0) REVERT: B 257 ILE cc_start: 0.7705 (tp) cc_final: 0.7287 (pt) REVERT: C 189 ILE cc_start: 0.8690 (mm) cc_final: 0.8406 (tt) REVERT: D 28 GLU cc_start: 0.8577 (pt0) cc_final: 0.8304 (pt0) REVERT: E 183 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.7879 (tp) REVERT: F 188 ASP cc_start: 0.7864 (m-30) cc_final: 0.7365 (m-30) outliers start: 29 outliers final: 20 residues processed: 187 average time/residue: 0.3132 time to fit residues: 88.6204 Evaluate side-chains 178 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 79 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.137682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.110871 restraints weight = 35069.612| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.48 r_work: 0.3553 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16757 Z= 0.109 Angle : 0.565 10.069 23077 Z= 0.283 Chirality : 0.041 0.174 2714 Planarity : 0.004 0.049 2693 Dihedral : 17.148 174.125 3315 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.94 % Allowed : 16.19 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.00 (0.20), residues: 1888 helix: 1.85 (0.18), residues: 804 sheet: -0.12 (0.28), residues: 344 loop : -0.18 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 357 HIS 0.005 0.001 HIS E 551 PHE 0.011 0.001 PHE C 114 TYR 0.024 0.001 TYR D 101 ARG 0.004 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 754) hydrogen bonds : angle 4.68662 ( 2115) metal coordination : bond 0.00103 ( 5) covalent geometry : bond 0.00239 (16752) covalent geometry : angle 0.56469 (23077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8196 (t0) cc_final: 0.7935 (t0) REVERT: A 204 PRO cc_start: 0.8150 (Cg_exo) cc_final: 0.7897 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8538 (tptp) cc_final: 0.7830 (mtmt) REVERT: B 112 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6926 (mp0) REVERT: B 233 TYR cc_start: 0.7969 (t80) cc_final: 0.7665 (t80) REVERT: B 257 ILE cc_start: 0.7679 (tp) cc_final: 0.7364 (pt) REVERT: C 189 ILE cc_start: 0.8610 (mm) cc_final: 0.8345 (tt) REVERT: D 28 GLU cc_start: 0.8560 (pt0) cc_final: 0.8283 (pt0) REVERT: E 183 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.7912 (tp) REVERT: F 188 ASP cc_start: 0.7855 (m-30) cc_final: 0.7348 (m-30) outliers start: 30 outliers final: 23 residues processed: 191 average time/residue: 0.2861 time to fit residues: 81.4303 Evaluate side-chains 187 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 150 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 644 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 = 0.4089 r_free = 0.4089 target = 0.136503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.109694 restraints weight = 35049.743| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.62 r_work: 0.3524 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16757 Z= 0.132 Angle : 0.577 10.136 23077 Z= 0.290 Chirality : 0.042 0.181 2714 Planarity : 0.004 0.052 2693 Dihedral : 17.127 174.532 3313 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.68 % Allowed : 16.52 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1888 helix: 1.82 (0.18), residues: 803 sheet: -0.18 (0.28), residues: 342 loop : -0.20 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 115 HIS 0.005 0.001 HIS E 551 PHE 0.012 0.001 PHE F 241 TYR 0.029 0.002 TYR D 101 ARG 0.005 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 754) hydrogen bonds : angle 4.75924 ( 2115) metal coordination : bond 0.00161 ( 5) covalent geometry : bond 0.00296 (16752) covalent geometry : angle 0.57744 (23077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8125 (Cg_exo) cc_final: 0.7869 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8520 (tptp) cc_final: 0.7848 (mtmt) REVERT: B 233 TYR cc_start: 0.8091 (t80) cc_final: 0.7763 (t80) REVERT: B 257 ILE cc_start: 0.7758 (tp) cc_final: 0.7478 (pt) REVERT: C 189 ILE cc_start: 0.8620 (mm) cc_final: 0.8333 (tt) REVERT: D 28 GLU cc_start: 0.8586 (pt0) cc_final: 0.8311 (pt0) REVERT: E 183 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7849 (tp) REVERT: F 97 PHE cc_start: 0.8306 (t80) cc_final: 0.7997 (t80) REVERT: F 188 ASP cc_start: 0.7908 (m-30) cc_final: 0.7436 (m-30) outliers start: 26 outliers final: 20 residues processed: 187 average time/residue: 0.2878 time to fit residues: 79.8846 Evaluate side-chains 184 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 122 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 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 = 0.4060 r_free = 0.4060 target = 0.135431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107744 restraints weight = 34869.417| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.64 r_work: 0.3483 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16757 Z= 0.121 Angle : 0.584 11.049 23077 Z= 0.291 Chirality : 0.041 0.171 2714 Planarity : 0.004 0.053 2693 Dihedral : 17.081 175.082 3313 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.62 % Allowed : 16.84 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1888 helix: 1.80 (0.18), residues: 804 sheet: -0.19 (0.28), residues: 336 loop : -0.21 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 115 HIS 0.005 0.001 HIS E 551 PHE 0.011 0.001 PHE F 241 TYR 0.029 0.001 TYR D 101 ARG 0.005 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 754) hydrogen bonds : angle 4.72758 ( 2115) metal coordination : bond 0.00142 ( 5) covalent geometry : bond 0.00270 (16752) covalent geometry : angle 0.58400 (23077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 204 PRO cc_start: 0.7993 (Cg_exo) cc_final: 0.7746 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8554 (tptp) cc_final: 0.7845 (mtmt) REVERT: B 257 ILE cc_start: 0.7782 (tp) cc_final: 0.7498 (pt) REVERT: C 160 GLU cc_start: 0.7700 (pt0) cc_final: 0.7497 (pt0) REVERT: C 189 ILE cc_start: 0.8609 (mm) cc_final: 0.8331 (tt) REVERT: C 242 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8181 (mt-10) REVERT: D 28 GLU cc_start: 0.8592 (pt0) cc_final: 0.8304 (pt0) REVERT: D 178 MET cc_start: 0.7710 (ttm) cc_final: 0.7507 (ttm) REVERT: E 183 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.7864 (tp) REVERT: F 97 PHE cc_start: 0.8290 (t80) cc_final: 0.7965 (t80) REVERT: F 188 ASP cc_start: 0.7906 (m-30) cc_final: 0.7411 (m-30) outliers start: 25 outliers final: 23 residues processed: 182 average time/residue: 0.2846 time to fit residues: 78.2770 Evaluate side-chains 186 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 99 optimal weight: 0.0270 chunk 28 optimal weight: 0.0070 chunk 166 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 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 = 0.4071 r_free = 0.4071 target = 0.136138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109637 restraints weight = 34166.924| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.57 r_work: 0.3516 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16757 Z= 0.105 Angle : 0.579 11.627 23077 Z= 0.287 Chirality : 0.041 0.168 2714 Planarity : 0.004 0.049 2693 Dihedral : 16.994 176.397 3313 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 17.36 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.03 (0.20), residues: 1888 helix: 1.93 (0.18), residues: 800 sheet: -0.20 (0.29), residues: 326 loop : -0.18 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 115 HIS 0.004 0.001 HIS E 551 PHE 0.009 0.001 PHE A 159 TYR 0.027 0.001 TYR D 101 ARG 0.006 0.000 ARG E 623 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 754) hydrogen bonds : angle 4.64146 ( 2115) metal coordination : bond 0.00066 ( 5) covalent geometry : bond 0.00229 (16752) covalent geometry : angle 0.57856 (23077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: A 204 PRO cc_start: 0.7925 (Cg_exo) cc_final: 0.7673 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8487 (tptp) cc_final: 0.7781 (mtmt) REVERT: B 112 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6857 (mp0) REVERT: C 41 ASP cc_start: 0.7812 (t70) cc_final: 0.7452 (t70) REVERT: C 189 ILE cc_start: 0.8517 (mm) cc_final: 0.8263 (tt) REVERT: C 242 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8230 (mt-10) REVERT: D 28 GLU cc_start: 0.8590 (pt0) cc_final: 0.8303 (pt0) REVERT: E 183 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7910 (tp) REVERT: F 97 PHE cc_start: 0.8232 (t80) cc_final: 0.7932 (t80) REVERT: F 188 ASP cc_start: 0.7767 (m-30) cc_final: 0.7295 (m-30) outliers start: 22 outliers final: 17 residues processed: 192 average time/residue: 0.2968 time to fit residues: 84.9342 Evaluate side-chains 182 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 106 optimal weight: 8.9990 chunk 1 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 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 = 0.4074 r_free = 0.4074 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108659 restraints weight = 34687.806| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.66 r_work: 0.3501 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16757 Z= 0.115 Angle : 0.591 11.690 23077 Z= 0.294 Chirality : 0.042 0.359 2714 Planarity : 0.004 0.050 2693 Dihedral : 16.974 177.492 3313 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.42 % Allowed : 17.94 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % 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: 1.04 (0.20), residues: 1888 helix: 1.96 (0.18), residues: 800 sheet: -0.19 (0.29), residues: 324 loop : -0.20 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 115 HIS 0.005 0.001 HIS E 551 PHE 0.010 0.001 PHE F 241 TYR 0.026 0.001 TYR D 101 ARG 0.006 0.000 ARG E 623 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 754) hydrogen bonds : angle 4.66875 ( 2115) metal coordination : bond 0.00105 ( 5) covalent geometry : bond 0.00259 (16752) covalent geometry : angle 0.59066 (23077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7401.39 seconds wall clock time: 128 minutes 35.39 seconds (7715.39 seconds total)