Starting phenix.real_space_refine on Sun Aug 24 02:09:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rr3_19455/08_2025/8rr3_19455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rr3_19455/08_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_19455/08_2025/8rr3_19455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2025/8rr3_19455.map" model { file = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2025/8rr3_19455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rr3_19455/08_2025/8rr3_19455.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.35, per 1000 atoms: 0.21 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: 1.25 Conformation dependent library (CDL) restraints added in 613.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 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: 1.98 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: 2.21 Time building geometry restraints manager: 1.61 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: 5.400 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.011 0.001 ARG C 130 TYR 0.039 0.003 TYR B 233 PHE 0.058 0.002 PHE E 77 TRP 0.014 0.002 TRP E 433 HIS 0.008 0.001 HIS E 644 Details of bonding type rmsd covalent geometry : bond 0.00359 (16752) covalent geometry : angle 0.87994 (23077) hydrogen bonds : bond 0.17599 ( 754) hydrogen bonds : angle 7.24120 ( 2115) metal coordination : bond 0.18120 ( 5) *********************** 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 : 0.375 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 518 GLU cc_start: 0.7655 (pt0) cc_final: 0.6947 (pp20) 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: 0.1277 time to fit residues: 40.7333 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 : 0.494 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.0070 overall best weight: 0.4608 ------------------------------------------------------------------------------- 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** 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 = 0.4155 r_free = 0.4155 target = 0.140744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.114476 restraints weight = 35170.043| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.58 r_work: 0.3622 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1241 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= 0.126 Angle : 0.619 8.247 23077 Z= 0.315 Chirality : 0.043 0.244 2714 Planarity : 0.005 0.053 2693 Dihedral : 17.412 173.272 3319 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 13.54 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.20), residues: 1888 helix: 1.79 (0.18), residues: 794 sheet: 0.14 (0.29), residues: 325 loop : -0.01 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 130 TYR 0.014 0.002 TYR E 528 PHE 0.018 0.001 PHE E 456 TRP 0.009 0.001 TRP E 357 HIS 0.007 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00264 (16752) covalent geometry : angle 0.61874 (23077) hydrogen bonds : bond 0.04595 ( 754) hydrogen bonds : angle 5.23751 ( 2115) metal coordination : bond 0.00858 ( 5) *********************** 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 235 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8504 (tptp) cc_final: 0.7765 (mtmt) REVERT: B 111 LEU cc_start: 0.8482 (tp) cc_final: 0.8263 (tp) REVERT: B 233 TYR cc_start: 0.8084 (t80) cc_final: 0.7847 (t80) REVERT: C 142 ASP cc_start: 0.6493 (t0) cc_final: 0.6279 (t0) REVERT: C 160 GLU cc_start: 0.7672 (pt0) cc_final: 0.7465 (pt0) REVERT: C 189 ILE cc_start: 0.8712 (mm) cc_final: 0.8349 (tt) REVERT: D 60 PHE cc_start: 0.7459 (t80) cc_final: 0.7205 (t80) REVERT: E 151 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7854 (mm) REVERT: F 188 ASP cc_start: 0.7900 (m-30) cc_final: 0.7516 (m-30) outliers start: 31 outliers final: 7 residues processed: 225 average time/residue: 0.1178 time to fit residues: 39.6501 Evaluate side-chains 179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 31 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 107 ASN ** E 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.135769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.108245 restraints weight = 35417.932| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.50 r_work: 0.3500 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1887 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= 0.151 Angle : 0.598 8.602 23077 Z= 0.305 Chirality : 0.043 0.183 2714 Planarity : 0.004 0.050 2693 Dihedral : 17.347 175.624 3315 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.53 % Allowed : 13.73 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1888 helix: 1.75 (0.18), residues: 803 sheet: 0.24 (0.29), residues: 336 loop : -0.10 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 82 TYR 0.019 0.002 TYR D 101 PHE 0.014 0.002 PHE F 97 TRP 0.011 0.001 TRP E 115 HIS 0.004 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00327 (16752) covalent geometry : angle 0.59848 (23077) hydrogen bonds : bond 0.04176 ( 754) hydrogen bonds : angle 4.99164 ( 2115) metal coordination : bond 0.00289 ( 5) *********************** 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 218 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7601 (t) REVERT: B 112 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7090 (mp0) REVERT: B 257 ILE cc_start: 0.7460 (tp) cc_final: 0.6971 (pt) REVERT: C 142 ASP cc_start: 0.6351 (t0) cc_final: 0.6073 (t0) REVERT: C 160 GLU cc_start: 0.7803 (pt0) cc_final: 0.7569 (pt0) REVERT: C 189 ILE cc_start: 0.8723 (mm) cc_final: 0.8383 (tt) REVERT: D 28 GLU cc_start: 0.8564 (pt0) cc_final: 0.8321 (pt0) REVERT: D 60 PHE cc_start: 0.7554 (t80) cc_final: 0.7287 (t80) REVERT: E 151 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7818 (mm) REVERT: E 301 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7164 (p0) REVERT: F 97 PHE cc_start: 0.8534 (t80) cc_final: 0.8306 (t80) REVERT: F 184 ASP cc_start: 0.7687 (t0) cc_final: 0.7076 (t0) REVERT: F 188 ASP cc_start: 0.7930 (m-30) cc_final: 0.7353 (m-30) outliers start: 39 outliers final: 16 residues processed: 205 average time/residue: 0.1108 time to fit residues: 33.7887 Evaluate side-chains 182 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR 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 301 ASP 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 E residue 780 GLU 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 195 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.133569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.106762 restraints weight = 35360.911| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.44 r_work: 0.3461 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16757 Z= 0.173 Angle : 0.602 9.615 23077 Z= 0.306 Chirality : 0.043 0.195 2714 Planarity : 0.005 0.056 2693 Dihedral : 17.329 177.928 3315 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.53 % Allowed : 14.38 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.20), residues: 1888 helix: 1.67 (0.18), residues: 804 sheet: -0.03 (0.29), residues: 328 loop : -0.29 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 82 TYR 0.020 0.002 TYR D 101 PHE 0.021 0.002 PHE A 245 TRP 0.008 0.001 TRP E 115 HIS 0.005 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00388 (16752) covalent geometry : angle 0.60249 (23077) hydrogen bonds : bond 0.04129 ( 754) hydrogen bonds : angle 4.99524 ( 2115) metal coordination : bond 0.00277 ( 5) *********************** 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 221 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ASN cc_start: 0.8289 (t0) cc_final: 0.7850 (p0) REVERT: B 52 LYS cc_start: 0.8527 (tptp) cc_final: 0.7812 (mtmt) REVERT: B 168 TYR cc_start: 0.7027 (t80) cc_final: 0.6348 (t80) REVERT: B 257 ILE cc_start: 0.7735 (tp) cc_final: 0.7373 (pt) REVERT: C 142 ASP cc_start: 0.6494 (t0) cc_final: 0.6235 (t0) REVERT: C 189 ILE cc_start: 0.8723 (mm) cc_final: 0.8373 (tt) REVERT: D 28 GLU cc_start: 0.8581 (pt0) cc_final: 0.8335 (pt0) REVERT: E 151 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7844 (mm) REVERT: E 301 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7095 (p0) REVERT: F 97 PHE cc_start: 0.8501 (t80) cc_final: 0.8182 (t80) REVERT: F 184 ASP cc_start: 0.7658 (t0) cc_final: 0.7054 (t70) REVERT: F 188 ASP cc_start: 0.7901 (m-30) cc_final: 0.7211 (m-30) outliers start: 39 outliers final: 20 residues processed: 210 average time/residue: 0.1142 time to fit residues: 35.9956 Evaluate side-chains 179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 301 ASP 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 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 123 CYS 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 71 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4050 r_free = 0.4050 target = 0.134519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.107273 restraints weight = 35008.499| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.44 r_work: 0.3481 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2481 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= 0.133 Angle : 0.583 9.697 23077 Z= 0.292 Chirality : 0.042 0.182 2714 Planarity : 0.004 0.054 2693 Dihedral : 17.277 179.617 3315 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.94 % Allowed : 15.80 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1888 helix: 1.66 (0.18), residues: 812 sheet: -0.18 (0.28), residues: 340 loop : -0.26 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 84 TYR 0.021 0.002 TYR D 101 PHE 0.013 0.001 PHE A 245 TRP 0.008 0.001 TRP E 115 HIS 0.003 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00295 (16752) covalent geometry : angle 0.58309 (23077) hydrogen bonds : bond 0.03771 ( 754) hydrogen bonds : angle 4.86213 ( 2115) metal coordination : bond 0.00158 ( 5) *********************** 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 205 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8575 (tptp) cc_final: 0.7849 (mtmt) REVERT: B 168 TYR cc_start: 0.6949 (t80) cc_final: 0.6305 (t80) REVERT: B 257 ILE cc_start: 0.7780 (tp) cc_final: 0.7427 (pt) REVERT: C 142 ASP cc_start: 0.6456 (t70) cc_final: 0.6219 (t0) REVERT: C 189 ILE cc_start: 0.8674 (mm) cc_final: 0.8339 (tt) REVERT: D 28 GLU cc_start: 0.8567 (pt0) cc_final: 0.8285 (pt0) REVERT: E 114 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7345 (t-90) REVERT: E 151 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7877 (mm) REVERT: E 183 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.7857 (tp) REVERT: E 301 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7116 (p0) REVERT: E 358 MET cc_start: 0.7288 (mmt) cc_final: 0.7030 (mmt) REVERT: F 97 PHE cc_start: 0.8448 (t80) cc_final: 0.8127 (t80) REVERT: F 188 ASP cc_start: 0.7875 (m-30) cc_final: 0.7345 (m-30) outliers start: 30 outliers final: 20 residues processed: 196 average time/residue: 0.1194 time to fit residues: 35.3327 Evaluate side-chains 179 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain 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 301 ASP Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 689 LEU Chi-restraints excluded: chain E residue 780 GLU 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 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 162 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.134874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107236 restraints weight = 34744.230| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.60 r_work: 0.3475 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16757 Z= 0.121 Angle : 0.573 10.362 23077 Z= 0.287 Chirality : 0.041 0.180 2714 Planarity : 0.004 0.053 2693 Dihedral : 17.214 176.513 3315 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.68 % Allowed : 16.32 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.20), residues: 1888 helix: 1.73 (0.18), residues: 806 sheet: -0.21 (0.28), residues: 342 loop : -0.20 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 84 TYR 0.023 0.002 TYR D 101 PHE 0.011 0.001 PHE A 245 TRP 0.007 0.001 TRP E 115 HIS 0.004 0.001 HIS E 342 Details of bonding type rmsd covalent geometry : bond 0.00269 (16752) covalent geometry : angle 0.57330 (23077) hydrogen bonds : bond 0.03580 ( 754) hydrogen bonds : angle 4.78539 ( 2115) metal coordination : bond 0.00140 ( 5) *********************** 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 204 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8275 (Cg_exo) cc_final: 0.8018 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8574 (tptp) cc_final: 0.7853 (mtmt) REVERT: B 112 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6800 (mp0) REVERT: B 257 ILE cc_start: 0.7759 (tp) cc_final: 0.7377 (pt) REVERT: C 29 ARG cc_start: 0.7290 (ttt180) cc_final: 0.6818 (ttt180) REVERT: C 189 ILE cc_start: 0.8680 (mm) cc_final: 0.8374 (tt) REVERT: D 28 GLU cc_start: 0.8578 (pt0) cc_final: 0.8294 (pt0) REVERT: D 84 ARG cc_start: 0.7181 (ptp-110) cc_final: 0.6934 (ptp-110) REVERT: E 183 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7866 (tp) REVERT: F 97 PHE cc_start: 0.8417 (t80) cc_final: 0.8104 (t80) REVERT: F 188 ASP cc_start: 0.7919 (m-30) cc_final: 0.7385 (m-30) outliers start: 26 outliers final: 20 residues processed: 195 average time/residue: 0.1198 time to fit residues: 34.4317 Evaluate side-chains 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 432 GLU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 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 780 GLU Chi-restraints excluded: chain F residue 123 CYS Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 180 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 738 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.130207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102254 restraints weight = 35086.125| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.64 r_work: 0.3393 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16757 Z= 0.263 Angle : 0.695 10.480 23077 Z= 0.355 Chirality : 0.045 0.209 2714 Planarity : 0.005 0.066 2693 Dihedral : 17.356 174.289 3315 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.59 % Allowed : 16.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1888 helix: 1.37 (0.18), residues: 807 sheet: -0.35 (0.29), residues: 306 loop : -0.55 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 84 TYR 0.022 0.002 TYR E 59 PHE 0.023 0.002 PHE F 241 TRP 0.010 0.001 TRP F 183 HIS 0.007 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00594 (16752) covalent geometry : angle 0.69550 (23077) hydrogen bonds : bond 0.04673 ( 754) hydrogen bonds : angle 5.27425 ( 2115) metal coordination : bond 0.00529 ( 5) *********************** 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 213 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6864 (mp0) REVERT: B 168 TYR cc_start: 0.7048 (t80) cc_final: 0.6347 (t80) REVERT: B 257 ILE cc_start: 0.7995 (tp) cc_final: 0.7526 (pt) REVERT: C 189 ILE cc_start: 0.8667 (mm) cc_final: 0.8292 (tt) REVERT: D 254 ASP cc_start: 0.7348 (t70) cc_final: 0.6963 (p0) REVERT: F 97 PHE cc_start: 0.8519 (t80) cc_final: 0.8238 (t80) outliers start: 40 outliers final: 25 residues processed: 198 average time/residue: 0.1165 time to fit residues: 35.0852 Evaluate side-chains 184 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain D residue 175 ILE 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 513 LEU Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU 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 56 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 116 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.133904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106312 restraints weight = 34840.592| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.59 r_work: 0.3465 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16757 Z= 0.115 Angle : 0.600 12.287 23077 Z= 0.300 Chirality : 0.042 0.176 2714 Planarity : 0.004 0.053 2693 Dihedral : 17.220 173.606 3315 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.42 % Allowed : 17.68 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 1888 helix: 1.61 (0.18), residues: 805 sheet: -0.37 (0.28), residues: 332 loop : -0.38 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 82 TYR 0.027 0.002 TYR C 101 PHE 0.014 0.001 PHE C 114 TRP 0.011 0.001 TRP E 115 HIS 0.003 0.001 HIS E 527 Details of bonding type rmsd covalent geometry : bond 0.00254 (16752) covalent geometry : angle 0.60000 (23077) hydrogen bonds : bond 0.03595 ( 754) hydrogen bonds : angle 4.86633 ( 2115) metal coordination : bond 0.00170 ( 5) *********************** 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 208 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8129 (Cg_exo) cc_final: 0.7855 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8486 (tptp) cc_final: 0.7777 (mtmt) REVERT: B 112 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6854 (mp0) REVERT: B 257 ILE cc_start: 0.7896 (tp) cc_final: 0.7528 (pt) REVERT: C 189 ILE cc_start: 0.8632 (mm) cc_final: 0.8314 (tt) REVERT: D 28 GLU cc_start: 0.8564 (pt0) cc_final: 0.8313 (pt0) REVERT: E 183 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.7877 (tp) REVERT: F 97 PHE cc_start: 0.8437 (t80) cc_final: 0.8178 (t80) REVERT: F 188 ASP cc_start: 0.7915 (m-30) cc_final: 0.7439 (m-30) outliers start: 22 outliers final: 16 residues processed: 200 average time/residue: 0.1237 time to fit residues: 36.6337 Evaluate side-chains 183 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 113 ASP 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 E residue 122 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU 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 13 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.133843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.106264 restraints weight = 34846.797| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.63 r_work: 0.3462 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16757 Z= 0.128 Angle : 0.615 11.186 23077 Z= 0.304 Chirality : 0.042 0.181 2714 Planarity : 0.004 0.053 2693 Dihedral : 17.159 174.329 3315 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.23 % Allowed : 18.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 1888 helix: 1.66 (0.18), residues: 805 sheet: -0.32 (0.28), residues: 327 loop : -0.36 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 623 TYR 0.033 0.002 TYR D 101 PHE 0.017 0.001 PHE D 223 TRP 0.012 0.001 TRP E 115 HIS 0.002 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00287 (16752) covalent geometry : angle 0.61543 (23077) hydrogen bonds : bond 0.03597 ( 754) hydrogen bonds : angle 4.83399 ( 2115) metal coordination : bond 0.00114 ( 5) *********************** 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 200 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8073 (Cg_exo) cc_final: 0.7810 (Cg_endo) REVERT: B 52 LYS cc_start: 0.8486 (tptp) cc_final: 0.7765 (mtmt) REVERT: B 112 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6875 (mp0) REVERT: B 252 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8184 (mtm110) REVERT: B 257 ILE cc_start: 0.7927 (tp) cc_final: 0.7589 (pt) REVERT: C 189 ILE cc_start: 0.8623 (mm) cc_final: 0.8321 (tt) REVERT: D 28 GLU cc_start: 0.8592 (pt0) cc_final: 0.8324 (pt0) REVERT: D 254 ASP cc_start: 0.7294 (t70) cc_final: 0.6914 (p0) REVERT: E 183 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7894 (tp) REVERT: F 97 PHE cc_start: 0.8425 (t80) cc_final: 0.8172 (t80) REVERT: F 188 ASP cc_start: 0.7958 (m-30) cc_final: 0.7441 (m-30) outliers start: 19 outliers final: 17 residues processed: 193 average time/residue: 0.1182 time to fit residues: 34.0003 Evaluate side-chains 183 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 289 ARG Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.130765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102904 restraints weight = 35036.113| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.62 r_work: 0.3406 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16757 Z= 0.223 Angle : 0.689 13.410 23077 Z= 0.346 Chirality : 0.045 0.202 2714 Planarity : 0.005 0.061 2693 Dihedral : 17.224 174.267 3315 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.36 % Allowed : 18.13 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.20), residues: 1888 helix: 1.41 (0.18), residues: 807 sheet: -0.35 (0.28), residues: 307 loop : -0.57 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 781 TYR 0.033 0.002 TYR D 101 PHE 0.019 0.002 PHE A 159 TRP 0.011 0.001 TRP F 183 HIS 0.006 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00509 (16752) covalent geometry : angle 0.68934 (23077) hydrogen bonds : bond 0.04281 ( 754) hydrogen bonds : angle 5.14047 ( 2115) metal coordination : bond 0.00330 ( 5) ********************** 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 193 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 PRO cc_start: 0.8073 (Cg_exo) cc_final: 0.7801 (Cg_endo) REVERT: B 112 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6973 (mp0) REVERT: B 252 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8299 (mtm110) REVERT: C 189 ILE cc_start: 0.8669 (mm) cc_final: 0.8330 (tt) REVERT: D 254 ASP cc_start: 0.7419 (t70) cc_final: 0.7007 (p0) REVERT: F 97 PHE cc_start: 0.8487 (t80) cc_final: 0.8220 (t80) outliers start: 21 outliers final: 20 residues processed: 184 average time/residue: 0.1239 time to fit residues: 33.8996 Evaluate side-chains 190 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 122 LEU 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 289 ARG 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 542 VAL Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 69 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 148 optimal weight: 0.0370 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0470 chunk 113 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.133961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106549 restraints weight = 34752.458| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.61 r_work: 0.3466 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16757 Z= 0.116 Angle : 0.621 12.991 23077 Z= 0.307 Chirality : 0.042 0.177 2714 Planarity : 0.004 0.051 2693 Dihedral : 17.117 175.557 3315 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.10 % Allowed : 18.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1888 helix: 1.62 (0.18), residues: 805 sheet: -0.39 (0.29), residues: 307 loop : -0.40 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.030 0.002 TYR D 101 PHE 0.014 0.001 PHE A 159 TRP 0.014 0.001 TRP E 115 HIS 0.004 0.001 HIS E 342 Details of bonding type rmsd covalent geometry : bond 0.00257 (16752) covalent geometry : angle 0.62114 (23077) hydrogen bonds : bond 0.03506 ( 754) hydrogen bonds : angle 4.84097 ( 2115) metal coordination : bond 0.00140 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.12 seconds wall clock time: 53 minutes 30.66 seconds (3210.66 seconds total)