Starting phenix.real_space_refine on Sat May 17 22:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr3_19455/05_2025/8rr3_19455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr3_19455/05_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_19455/05_2025/8rr3_19455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr3_19455/05_2025/8rr3_19455.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr3_19455/05_2025/8rr3_19455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr3_19455/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.81, per 1000 atoms: 0.66 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: 4.59 Conformation dependent library (CDL) restraints added in 2.3 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: 5.81 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: 5.88 Time building geometry restraints manager: 5.19 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.830 Find NCS groups from input model: 0.390 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.630 ------------------------------------------------------------------------------- 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 : 2.087 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: 0.3215 time to fit residues: 103.0980 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 : 1.827 ------------------------------------------------------------------------------- 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 = 0.112941 restraints weight = 35262.709| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.49 r_work: 0.3599 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.6880 (mtm110) cc_final: 0.6544 (mtp85) REVERT: B 52 LYS cc_start: 0.8523 (tptp) cc_final: 0.7799 (mtmt) REVERT: B 233 TYR cc_start: 0.8079 (t80) cc_final: 0.7836 (t80) REVERT: C 142 ASP cc_start: 0.6498 (t0) cc_final: 0.6269 (t0) REVERT: C 160 GLU cc_start: 0.7694 (pt0) cc_final: 0.7492 (pt0) REVERT: C 189 ILE cc_start: 0.8730 (mm) cc_final: 0.8357 (tt) REVERT: D 60 PHE cc_start: 0.7462 (t80) cc_final: 0.7186 (t80) REVERT: E 151 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7869 (mm) REVERT: E 301 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7134 (p0) REVERT: E 776 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8338 (tp30) REVERT: F 188 ASP cc_start: 0.7871 (m-30) cc_final: 0.7479 (m-30) outliers start: 33 outliers final: 8 residues processed: 220 average time/residue: 0.3120 time to fit residues: 102.1727 Evaluate side-chains 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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: 7.9990 chunk 51 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 178 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 ASN E 107 ASN E 117 ASN F 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.135951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108859 restraints weight = 34967.465| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.43 r_work: 0.3529 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16757 Z= 0.175 Angle : 0.627 8.909 23077 Z= 0.319 Chirality : 0.043 0.186 2714 Planarity : 0.005 0.055 2693 Dihedral : 17.393 175.663 3315 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.72 % Allowed : 14.12 % Favored : 83.16 % 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: 1.64 (0.18), residues: 805 sheet: 0.12 (0.29), residues: 334 loop : -0.18 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 115 HIS 0.005 0.001 HIS F 381 PHE 0.016 0.002 PHE F 241 TYR 0.019 0.002 TYR D 101 ARG 0.005 0.001 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 754) hydrogen bonds : angle 5.09920 ( 2115) metal coordination : bond 0.00377 ( 5) covalent geometry : bond 0.00390 (16752) covalent geometry : angle 0.62658 (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 226 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.7606 (tttt) cc_final: 0.7388 (tttt) REVERT: B 112 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6939 (mp0) REVERT: B 257 ILE cc_start: 0.7642 (tp) cc_final: 0.7131 (pt) REVERT: C 142 ASP cc_start: 0.6437 (t0) cc_final: 0.6161 (t0) REVERT: C 189 ILE cc_start: 0.8755 (mm) cc_final: 0.8405 (tt) REVERT: D 28 GLU cc_start: 0.8604 (pt0) cc_final: 0.8377 (pt0) REVERT: E 151 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7810 (mm) REVERT: F 184 ASP cc_start: 0.7753 (t0) cc_final: 0.7180 (t0) REVERT: F 188 ASP cc_start: 0.7904 (m-30) cc_final: 0.7332 (m-30) outliers start: 42 outliers final: 18 residues processed: 208 average time/residue: 0.3158 time to fit residues: 97.2044 Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 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 525 CYS Chi-restraints excluded: chain E residue 642 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 178 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 647 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 = 0.4033 r_free = 0.4033 target = 0.133398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105935 restraints weight = 34951.341| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.50 r_work: 0.3457 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16757 Z= 0.172 Angle : 0.604 8.563 23077 Z= 0.306 Chirality : 0.043 0.194 2714 Planarity : 0.005 0.057 2693 Dihedral : 17.351 177.556 3315 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.20 % Allowed : 14.64 % Favored : 83.16 % 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: 0.77 (0.20), residues: 1888 helix: 1.63 (0.18), residues: 806 sheet: -0.11 (0.28), residues: 330 loop : -0.34 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 115 HIS 0.004 0.001 HIS F 381 PHE 0.020 0.002 PHE A 245 TYR 0.018 0.002 TYR E 59 ARG 0.009 0.001 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 754) hydrogen bonds : angle 5.03952 ( 2115) metal coordination : bond 0.00253 ( 5) covalent geometry : bond 0.00385 (16752) covalent geometry : angle 0.60363 (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 212 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASN cc_start: 0.8246 (t0) cc_final: 0.7798 (p0) REVERT: B 52 LYS cc_start: 0.8514 (tptp) cc_final: 0.7794 (mtmt) REVERT: B 257 ILE cc_start: 0.7769 (tp) cc_final: 0.7377 (pt) REVERT: C 142 ASP cc_start: 0.6496 (t0) cc_final: 0.6221 (t0) REVERT: C 189 ILE cc_start: 0.8726 (mm) cc_final: 0.8373 (tt) REVERT: D 28 GLU cc_start: 0.8588 (pt0) cc_final: 0.8339 (pt0) REVERT: E 151 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7856 (mm) REVERT: F 184 ASP cc_start: 0.7617 (t0) cc_final: 0.7014 (t70) REVERT: F 188 ASP cc_start: 0.7911 (m-30) cc_final: 0.7238 (m-30) outliers start: 34 outliers final: 21 residues processed: 201 average time/residue: 0.2935 time to fit residues: 87.4943 Evaluate side-chains 178 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 120 VAL 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 488 THR 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: 7.9990 chunk 45 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.134700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107215 restraints weight = 35095.839| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.54 r_work: 0.3477 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16757 Z= 0.122 Angle : 0.577 9.999 23077 Z= 0.290 Chirality : 0.041 0.179 2714 Planarity : 0.004 0.052 2693 Dihedral : 17.275 179.756 3315 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.81 % Allowed : 16.39 % 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: 0.81 (0.20), residues: 1888 helix: 1.66 (0.18), residues: 812 sheet: -0.22 (0.28), residues: 342 loop : -0.27 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 115 HIS 0.003 0.001 HIS F 381 PHE 0.015 0.001 PHE A 245 TYR 0.021 0.001 TYR D 101 ARG 0.007 0.000 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 754) hydrogen bonds : angle 4.85492 ( 2115) metal coordination : bond 0.00146 ( 5) covalent geometry : bond 0.00267 (16752) covalent geometry : angle 0.57700 (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 209 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8527 (tptp) cc_final: 0.7801 (mtmt) REVERT: B 112 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6743 (mp0) REVERT: B 168 TYR cc_start: 0.6969 (t80) cc_final: 0.6303 (t80) REVERT: B 257 ILE cc_start: 0.7757 (tp) cc_final: 0.7300 (pt) REVERT: C 142 ASP cc_start: 0.6440 (t0) cc_final: 0.6189 (t0) REVERT: C 189 ILE cc_start: 0.8671 (mm) cc_final: 0.8350 (tt) REVERT: D 28 GLU cc_start: 0.8570 (pt0) cc_final: 0.8289 (pt0) REVERT: E 151 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7884 (mm) REVERT: E 358 MET cc_start: 0.7241 (mmt) cc_final: 0.6964 (mmt) REVERT: F 188 ASP cc_start: 0.7883 (m-30) cc_final: 0.7358 (m-30) outliers start: 28 outliers final: 19 residues processed: 199 average time/residue: 0.2944 time to fit residues: 86.9481 Evaluate side-chains 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 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 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 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 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: 0.5980 chunk 85 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.131605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103762 restraints weight = 35074.456| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.57 r_work: 0.3418 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16757 Z= 0.212 Angle : 0.640 8.940 23077 Z= 0.327 Chirality : 0.044 0.199 2714 Planarity : 0.005 0.061 2693 Dihedral : 17.328 177.490 3315 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.59 % Allowed : 16.32 % Favored : 81.09 % 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: 0.54 (0.20), residues: 1888 helix: 1.50 (0.18), residues: 807 sheet: -0.41 (0.28), residues: 328 loop : -0.44 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 115 HIS 0.007 0.001 HIS F 381 PHE 0.019 0.002 PHE F 241 TYR 0.021 0.002 TYR D 101 ARG 0.005 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 754) hydrogen bonds : angle 5.12418 ( 2115) metal coordination : bond 0.00385 ( 5) covalent geometry : bond 0.00481 (16752) covalent geometry : angle 0.64048 (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 206 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6873 (mp0) REVERT: B 168 TYR cc_start: 0.7038 (t80) cc_final: 0.6315 (t80) REVERT: B 233 TYR cc_start: 0.8141 (t80) cc_final: 0.7852 (t80) REVERT: B 257 ILE cc_start: 0.7926 (tp) cc_final: 0.7437 (pt) REVERT: C 189 ILE cc_start: 0.8679 (mm) cc_final: 0.8303 (tt) REVERT: E 151 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7864 (mm) REVERT: F 356 MET cc_start: 0.8896 (mmm) cc_final: 0.8665 (mmm) outliers start: 40 outliers final: 23 residues processed: 192 average time/residue: 0.2726 time to fit residues: 79.2193 Evaluate side-chains 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 91 CYS 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 175 ILE Chi-restraints excluded: chain E residue 114 HIS 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 488 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 548 HIS 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 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: 0.4980 chunk 66 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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** ** E 647 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 = 0.4054 r_free = 0.4054 target = 0.134933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107431 restraints weight = 34598.961| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.59 r_work: 0.3483 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16757 Z= 0.108 Angle : 0.583 11.719 23077 Z= 0.291 Chirality : 0.041 0.171 2714 Planarity : 0.004 0.050 2693 Dihedral : 17.213 173.637 3315 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.62 % Allowed : 17.29 % Favored : 81.09 % 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: 0.77 (0.20), residues: 1888 helix: 1.70 (0.18), residues: 805 sheet: -0.36 (0.28), residues: 341 loop : -0.28 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 115 HIS 0.023 0.001 HIS E 114 PHE 0.013 0.001 PHE A 245 TYR 0.023 0.001 TYR D 101 ARG 0.010 0.000 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 754) hydrogen bonds : angle 4.78114 ( 2115) metal coordination : bond 0.00130 ( 5) covalent geometry : bond 0.00230 (16752) covalent geometry : angle 0.58340 (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 205 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8153 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8482 (tptp) cc_final: 0.7793 (mtmt) REVERT: B 112 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6896 (mp0) REVERT: B 257 ILE cc_start: 0.7881 (tp) cc_final: 0.7532 (pt) REVERT: C 189 ILE cc_start: 0.8633 (mm) cc_final: 0.8313 (tt) REVERT: D 28 GLU cc_start: 0.8560 (pt0) cc_final: 0.8301 (pt0) REVERT: E 183 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.7877 (tp) REVERT: E 358 MET cc_start: 0.7453 (mmt) cc_final: 0.6973 (mmt) REVERT: F 97 PHE cc_start: 0.8286 (t80) cc_final: 0.7970 (t80) REVERT: F 188 ASP cc_start: 0.7861 (m-30) cc_final: 0.7349 (m-30) outliers start: 25 outliers final: 17 residues processed: 194 average time/residue: 0.2985 time to fit residues: 85.5658 Evaluate side-chains 178 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 LEU 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 518 GLU Chi-restraints excluded: chain E residue 548 HIS 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 346 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 150 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4047 r_free = 0.4047 target = 0.134492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.106820 restraints weight = 34682.741| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.63 r_work: 0.3478 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16757 Z= 0.122 Angle : 0.586 11.755 23077 Z= 0.292 Chirality : 0.041 0.180 2714 Planarity : 0.004 0.050 2693 Dihedral : 17.165 173.659 3315 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.68 % Allowed : 17.29 % Favored : 81.02 % 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: 0.81 (0.20), residues: 1888 helix: 1.75 (0.18), residues: 805 sheet: -0.38 (0.28), residues: 341 loop : -0.27 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 115 HIS 0.003 0.001 HIS E 749 PHE 0.013 0.001 PHE A 159 TYR 0.030 0.002 TYR D 101 ARG 0.006 0.000 ARG E 623 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 754) hydrogen bonds : angle 4.78227 ( 2115) metal coordination : bond 0.00137 ( 5) covalent geometry : bond 0.00272 (16752) covalent geometry : angle 0.58637 (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 193 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8096 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8480 (tptp) cc_final: 0.7779 (mtmt) REVERT: B 112 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6924 (mp0) REVERT: B 257 ILE cc_start: 0.7898 (tp) cc_final: 0.7575 (pt) REVERT: C 189 ILE cc_start: 0.8621 (mm) cc_final: 0.8325 (tt) REVERT: D 28 GLU cc_start: 0.8545 (pt0) cc_final: 0.8303 (pt0) REVERT: F 97 PHE cc_start: 0.8264 (t80) cc_final: 0.7957 (t80) REVERT: F 188 ASP cc_start: 0.7964 (m-30) cc_final: 0.7437 (m-30) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.2762 time to fit residues: 76.0506 Evaluate side-chains 178 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 LEU 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 518 GLU 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 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 122 optimal weight: 0.0570 chunk 182 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.135577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.108115 restraints weight = 34698.485| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.67 r_work: 0.3489 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3078 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= 0.111 Angle : 0.592 11.635 23077 Z= 0.293 Chirality : 0.041 0.173 2714 Planarity : 0.004 0.048 2693 Dihedral : 17.099 174.296 3315 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.55 % Allowed : 17.75 % Favored : 80.70 % 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: 0.88 (0.20), residues: 1888 helix: 1.82 (0.19), residues: 802 sheet: -0.28 (0.28), residues: 349 loop : -0.29 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 115 HIS 0.002 0.001 HIS E 749 PHE 0.013 0.001 PHE A 159 TYR 0.029 0.001 TYR D 101 ARG 0.008 0.000 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 754) hydrogen bonds : angle 4.71639 ( 2115) metal coordination : bond 0.00135 ( 5) covalent geometry : bond 0.00244 (16752) covalent geometry : angle 0.59178 (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 202 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.7955 (Cg_exo) cc_final: 0.7694 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8456 (tptp) cc_final: 0.7746 (mtmt) REVERT: B 112 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6954 (mp0) REVERT: B 257 ILE cc_start: 0.7898 (tp) cc_final: 0.7594 (pt) REVERT: C 41 ASP cc_start: 0.7860 (t70) cc_final: 0.7572 (t70) REVERT: C 189 ILE cc_start: 0.8535 (mm) cc_final: 0.8250 (tt) REVERT: C 242 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8109 (mt-10) REVERT: D 28 GLU cc_start: 0.8631 (pt0) cc_final: 0.8363 (pt0) REVERT: E 183 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7873 (tp) REVERT: F 97 PHE cc_start: 0.8265 (t80) cc_final: 0.7967 (t80) REVERT: F 188 ASP cc_start: 0.7894 (m-30) cc_final: 0.7370 (m-30) REVERT: F 191 MET cc_start: 0.8261 (mtp) cc_final: 0.8057 (mtt) outliers start: 24 outliers final: 19 residues processed: 194 average time/residue: 0.2756 time to fit residues: 79.8032 Evaluate side-chains 185 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 113 ASP 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 114 HIS 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 483 ILE Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 518 GLU 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 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 166 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.135023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108078 restraints weight = 34291.256| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.61 r_work: 0.3491 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3143 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= 0.116 Angle : 0.600 11.858 23077 Z= 0.296 Chirality : 0.041 0.177 2714 Planarity : 0.004 0.048 2693 Dihedral : 17.064 174.662 3313 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.23 % Allowed : 18.52 % Favored : 80.25 % 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: 0.92 (0.20), residues: 1888 helix: 1.88 (0.18), residues: 800 sheet: -0.36 (0.28), residues: 334 loop : -0.24 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 357 HIS 0.006 0.001 HIS E 114 PHE 0.014 0.001 PHE A 159 TYR 0.029 0.001 TYR D 101 ARG 0.008 0.000 ARG E 112 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 754) hydrogen bonds : angle 4.70686 ( 2115) metal coordination : bond 0.00101 ( 5) covalent geometry : bond 0.00257 (16752) covalent geometry : angle 0.59978 (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 192 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.7955 (Cg_exo) cc_final: 0.7710 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8463 (tptp) cc_final: 0.7744 (mtmt) REVERT: B 112 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6934 (mp0) REVERT: B 257 ILE cc_start: 0.7959 (tp) cc_final: 0.7683 (pt) REVERT: C 41 ASP cc_start: 0.7844 (t70) cc_final: 0.7460 (t70) REVERT: C 189 ILE cc_start: 0.8582 (mm) cc_final: 0.8303 (tt) REVERT: C 242 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8138 (mt-10) REVERT: D 28 GLU cc_start: 0.8619 (pt0) cc_final: 0.8353 (pt0) REVERT: E 183 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.7885 (tp) REVERT: E 358 MET cc_start: 0.7377 (mmt) cc_final: 0.6808 (mmm) REVERT: F 97 PHE cc_start: 0.8271 (t80) cc_final: 0.7986 (t80) REVERT: F 188 ASP cc_start: 0.7918 (m-30) cc_final: 0.7360 (m-30) outliers start: 19 outliers final: 18 residues processed: 186 average time/residue: 0.3074 time to fit residues: 86.8129 Evaluate side-chains 184 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR 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 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 483 ILE Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 518 GLU 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 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 317 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 106 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4026 r_free = 0.4026 target = 0.132905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106018 restraints weight = 34338.901| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.40 r_work: 0.3471 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16757 Z= 0.155 Angle : 0.629 12.323 23077 Z= 0.311 Chirality : 0.042 0.187 2714 Planarity : 0.005 0.053 2693 Dihedral : 17.075 175.085 3313 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.30 % Allowed : 18.26 % Favored : 80.44 % 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: 0.83 (0.20), residues: 1888 helix: 1.78 (0.19), residues: 804 sheet: -0.16 (0.28), residues: 330 loop : -0.41 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 115 HIS 0.004 0.001 HIS F 381 PHE 0.018 0.001 PHE A 159 TYR 0.029 0.002 TYR D 101 ARG 0.006 0.000 ARG E 623 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 754) hydrogen bonds : angle 4.85330 ( 2115) metal coordination : bond 0.00190 ( 5) covalent geometry : bond 0.00349 (16752) covalent geometry : angle 0.62925 (23077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7191.80 seconds wall clock time: 125 minutes 53.92 seconds (7553.92 seconds total)