Starting phenix.real_space_refine on Fri Jul 3 09:32:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw9_41663/07_2026/8tw9_41663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw9_41663/07_2026/8tw9_41663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2026/8tw9_41663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2026/8tw9_41663.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2026/8tw9_41663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2026/8tw9_41663.cif" } resolution = 3.6 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= 0.009 sd= 0.060 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 Fe 4 7.16 5 P 23 5.49 5 S 66 5.16 5 C 8583 2.51 5 N 2287 2.21 5 O 2623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13586 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 8919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8919 Classifications: {'peptide': 1124} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 1071} Chain breaks: 3 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 4, 'ASP:plan': 5, 'GLU:plan': 5, 'HIS:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 126 Chain: "D" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2953 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5516 SG CYS E 665 57.782 51.541 16.459 1.00 81.51 S ATOM 5604 SG CYS E 677 63.716 52.975 18.203 1.00 87.54 S ATOM 6340 SG CYS E 763 60.281 55.831 21.407 1.00 94.87 S ATOM 5533 SG CYS E 668 60.127 57.610 15.605 1.00 78.76 S Time building chain proxies: 2.36, per 1000 atoms: 0.17 Number of scatterers: 13586 At special positions: 0 Unit cell: (103.5, 121.716, 127.512, 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) Fe 4 26.01 S 66 16.00 P 23 15.00 O 2623 8.00 N 2287 7.00 C 8583 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: 1.05 Conformation dependent library (CDL) restraints added in 545.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 E2301 " pdb="FE4 SF4 E2301 " - pdb=" SG CYS E 668 " pdb="FE1 SF4 E2301 " - pdb=" SG CYS E 665 " pdb="FE2 SF4 E2301 " - pdb=" SG CYS E 677 " pdb="FE3 SF4 E2301 " - pdb=" SG CYS E 763 " Number of angles added : 12 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 19 sheets defined 44.4% alpha, 17.6% beta 9 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'C' and resid 735 through 740 removed outlier: 3.647A pdb=" N LEU C 739 " --> pdb=" O THR C 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 50 removed outlier: 4.245A pdb=" N SER E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN E 29 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 removed outlier: 3.549A pdb=" N ILE E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 147 No H-bonds generated for 'chain 'E' and resid 145 through 147' Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 216 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 354 through 370 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 422 through 429 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O GLN E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 447 Processing helix chain 'E' and resid 455 through 466 removed outlier: 4.670A pdb=" N THR E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Proline residue: E 461 - end of helix removed outlier: 4.165A pdb=" N PHE E 464 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 466 through 488 Processing helix chain 'E' and resid 488 through 498 removed outlier: 3.517A pdb=" N PHE E 492 " --> pdb=" O TYR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 510 Processing helix chain 'E' and resid 511 through 527 Processing helix chain 'E' and resid 577 through 598 Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 603 through 607 Processing helix chain 'E' and resid 609 through 627 Processing helix chain 'E' and resid 643 through 653 Processing helix chain 'E' and resid 661 through 668 Processing helix chain 'E' and resid 693 through 706 removed outlier: 3.769A pdb=" N ASN E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 747 Processing helix chain 'E' and resid 769 through 798 removed outlier: 3.974A pdb=" N ILE E 798 " --> pdb=" O ASN E 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 806 through 834 removed outlier: 3.524A pdb=" N LYS E 810 " --> pdb=" O ARG E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 843 through 869 removed outlier: 3.633A pdb=" N ILE E 849 " --> pdb=" O GLU E 845 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG E 867 " --> pdb=" O ALA E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 919 removed outlier: 3.967A pdb=" N LEU E 910 " --> pdb=" O PRO E 906 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 913 " --> pdb=" O MET E 909 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 919 " --> pdb=" O HIS E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1006 removed outlier: 4.686A pdb=" N LYS E1004 " --> pdb=" O SER E1000 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL E1005 " --> pdb=" O ASP E1001 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E1006 " --> pdb=" O ILE E1002 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1032 removed outlier: 3.542A pdb=" N VAL E1022 " --> pdb=" O ALA E1018 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E1030 " --> pdb=" O TRP E1026 " (cutoff:3.500A) Processing helix chain 'E' and resid 1038 through 1047 Processing helix chain 'E' and resid 1055 through 1062 removed outlier: 3.501A pdb=" N GLN E1062 " --> pdb=" O GLU E1058 " (cutoff:3.500A) Processing helix chain 'E' and resid 1064 through 1077 Processing helix chain 'E' and resid 1101 through 1104 Processing helix chain 'E' and resid 1110 through 1112 No H-bonds generated for 'chain 'E' and resid 1110 through 1112' Processing helix chain 'E' and resid 1115 through 1128 Processing helix chain 'E' and resid 1136 through 1141 removed outlier: 3.521A pdb=" N ILE E1140 " --> pdb=" O ASP E1136 " (cutoff:3.500A) Processing helix chain 'E' and resid 1142 through 1158 Processing helix chain 'E' and resid 1158 through 1166 Processing helix chain 'E' and resid 1177 through 1189 Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 45 through 51 removed outlier: 3.759A pdb=" N ARG D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.945A pdb=" N LYS B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 181 through 199 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.597A pdb=" N THR B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 253 through 269 Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.986A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.600A pdb=" N GLN B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.824A pdb=" N PHE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 719 through 722 Processing sheet with id=AA2, first strand: chain 'C' and resid 728 through 733 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 728 through 733 current: chain 'D' and resid 65 through 76 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 88 through 96 current: chain 'D' and resid 112 through 118 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 112 through 118 current: chain 'B' and resid 49 through 52 removed outlier: 5.397A pdb=" N VAL B 49 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LYS B 61 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ARG B 111 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG B 63 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLU B 109 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N HIS B 65 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU B 107 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN B 67 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU B 105 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 69 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS B 103 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 71 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 97 " --> pdb=" O PHE B 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 75 through 78 removed outlier: 3.746A pdb=" N ARG E 75 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP E 264 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 81 through 87 removed outlier: 3.525A pdb=" N PHE E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 166 through 172 removed outlier: 6.889A pdb=" N THR E 187 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N CYS E 143 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 241 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.869A pdb=" N GLY E 319 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE E 350 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU E 321 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU E 352 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR E 323 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET E 309 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU E 292 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE E 311 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP E 290 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR E 313 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 288 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE E 315 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 286 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET E 287 " --> pdb=" O SER E 375 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE E 374 " --> pdb=" O MET E 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AA8, first strand: chain 'E' and resid 542 through 543 Processing sheet with id=AA9, first strand: chain 'E' and resid 558 through 560 removed outlier: 6.926A pdb=" N TRP E 880 " --> pdb=" O LEU E 872 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU E 874 " --> pdb=" O GLY E 878 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY E 878 " --> pdb=" O LEU E 874 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE E 636 " --> pdb=" O PRO E 949 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 564 through 567 removed outlier: 3.531A pdb=" N ALA E 952 " --> pdb=" O PHE E 972 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 572 through 575 Processing sheet with id=AB3, first strand: chain 'E' and resid 708 through 710 Processing sheet with id=AB4, first strand: chain 'E' and resid 890 through 894 Processing sheet with id=AB5, first strand: chain 'E' and resid 920 through 928 removed outlier: 4.044A pdb=" N GLN E 922 " --> pdb=" O HIS E 937 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS E 937 " --> pdb=" O GLN E 922 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN E 924 " --> pdb=" O GLU E 935 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU E 935 " --> pdb=" O GLN E 924 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU E 926 " --> pdb=" O ILE E 933 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE E 933 " --> pdb=" O LEU E 926 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 991 through 992 Processing sheet with id=AB7, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB8, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AB9, first strand: chain 'B' and resid 275 through 276 removed outlier: 3.509A pdb=" N MET B 275 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 368 through 370 608 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 5553 1.41 - 1.62: 8263 1.62 - 1.84: 104 1.84 - 2.06: 0 2.06 - 2.27: 12 Bond restraints: 13932 Sorted by residual: bond pdb=" C ARG B 354 " pdb=" N GLY B 355 " ideal model delta sigma weight residual 1.331 1.538 -0.207 1.46e-02 4.69e+03 2.01e+02 bond pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 1.331 1.556 -0.225 2.07e-02 2.33e+03 1.18e+02 bond pdb=" C1' DG P 2 " pdb=" N9 DG P 2 " ideal model delta sigma weight residual 1.468 1.344 0.124 1.40e-02 5.10e+03 7.86e+01 bond pdb=" C1' DG P 8 " pdb=" N9 DG P 8 " ideal model delta sigma weight residual 1.468 1.348 0.120 1.40e-02 5.10e+03 7.38e+01 bond pdb=" C ASP B 297 " pdb=" O ASP B 297 " ideal model delta sigma weight residual 1.235 1.324 -0.089 1.13e-02 7.83e+03 6.27e+01 ... (remaining 13927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 18428 3.94 - 7.87: 500 7.87 - 11.81: 28 11.81 - 15.74: 7 15.74 - 19.68: 2 Bond angle restraints: 18965 Sorted by residual: angle pdb=" O GLU E 766 " pdb=" C GLU E 766 " pdb=" N ASN E 767 " ideal model delta sigma weight residual 122.95 111.66 11.29 1.24e+00 6.50e-01 8.28e+01 angle pdb=" N GLU E1060 " pdb=" CA GLU E1060 " pdb=" C GLU E1060 " ideal model delta sigma weight residual 111.75 100.61 11.14 1.28e+00 6.10e-01 7.58e+01 angle pdb=" N LEU E 122 " pdb=" CA LEU E 122 " pdb=" C LEU E 122 " ideal model delta sigma weight residual 111.75 100.75 11.00 1.28e+00 6.10e-01 7.39e+01 angle pdb=" CA ASN B 352 " pdb=" C ASN B 352 " pdb=" N SER B 353 " ideal model delta sigma weight residual 116.57 104.58 11.99 1.40e+00 5.10e-01 7.33e+01 angle pdb=" C GLY B 355 " pdb=" N MET B 356 " pdb=" CA MET B 356 " ideal model delta sigma weight residual 123.27 108.23 15.04 1.85e+00 2.92e-01 6.61e+01 ... (remaining 18960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 7940 24.28 - 48.55: 347 48.55 - 72.83: 74 72.83 - 97.10: 7 97.10 - 121.38: 1 Dihedral angle restraints: 8369 sinusoidal: 3507 harmonic: 4862 Sorted by residual: dihedral pdb=" CA ARG E 672 " pdb=" C ARG E 672 " pdb=" N PRO E 673 " pdb=" CA PRO E 673 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO E 634 " pdb=" C PRO E 634 " pdb=" N LEU E 635 " pdb=" CA LEU E 635 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLY E 687 " pdb=" C GLY E 687 " pdb=" N GLU E 688 " pdb=" CA GLU E 688 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 8366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1396 0.082 - 0.165: 579 0.165 - 0.247: 94 0.247 - 0.329: 24 0.329 - 0.412: 5 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CA ASP E 258 " pdb=" N ASP E 258 " pdb=" C ASP E 258 " pdb=" CB ASP E 258 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA ASP E 316 " pdb=" N ASP E 316 " pdb=" C ASP E 316 " pdb=" CB ASP E 316 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB VAL B 270 " pdb=" CA VAL B 270 " pdb=" CG1 VAL B 270 " pdb=" CG2 VAL B 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2095 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 355 " 0.055 2.00e-02 2.50e+03 1.19e-01 1.42e+02 pdb=" C GLY B 355 " -0.206 2.00e-02 2.50e+03 pdb=" O GLY B 355 " 0.079 2.00e-02 2.50e+03 pdb=" N MET B 356 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 81 " 0.052 2.00e-02 2.50e+03 1.03e-01 1.07e+02 pdb=" C ASN E 81 " -0.179 2.00e-02 2.50e+03 pdb=" O ASN E 81 " 0.070 2.00e-02 2.50e+03 pdb=" N MET E 82 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 485 " 0.119 2.00e-02 2.50e+03 6.36e-02 8.08e+01 pdb=" CG TYR E 485 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 485 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR E 485 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR E 485 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR E 485 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR E 485 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 485 " 0.087 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 16 2.37 - 3.00: 6810 3.00 - 3.63: 20128 3.63 - 4.27: 31104 4.27 - 4.90: 51037 Nonbonded interactions: 109095 Sorted by model distance: nonbonded pdb=" SD MET E1052 " pdb=" CE2 TYR E1059 " model vdw 1.734 3.700 nonbonded pdb=" O GLU E 845 " pdb=" N ALA E 847 " model vdw 2.205 3.120 nonbonded pdb=" O LEU B 351 " pdb=" OD1 ASN B 352 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR B 261 " pdb=" O TRP B 284 " model vdw 2.219 3.040 nonbonded pdb=" O LEU E 815 " pdb=" OG SER E 818 " model vdw 2.283 3.040 ... (remaining 109090 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.270 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.014 0.534 13936 Z= 0.796 Angle : 1.744 38.408 18977 Z= 1.100 Chirality : 0.089 0.412 2098 Planarity : 0.015 0.177 2365 Dihedral : 14.137 121.377 5215 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.00 % Favored : 94.02 % Rotamer: Outliers : 0.64 % Allowed : 4.91 % Favored : 94.45 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: -1.53 (0.19), residues: 1640 helix: -0.80 (0.18), residues: 610 sheet: -0.49 (0.31), residues: 266 loop : -1.28 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 781 TYR 0.119 0.016 TYR E 485 PHE 0.071 0.010 PHE E 347 TRP 0.106 0.012 TRP E 384 HIS 0.021 0.004 HIS E 388 Details of bonding type rmsd/Z covalent geometry : bond 0.01268 / 0.78 (13932) covalent geometry : angle 1.66851 / 1.10 (18965) hydrogen bonds : bond 0.16596 / 15.04 ( 631) hydrogen bonds : angle 7.19588 / 7.43 ( 1771) metal coordination : bond 0.32325 / 15.85 ( 4) metal coordination : angle 20.25073 / 11.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8841 (mmm) cc_final: 0.8314 (mmm) REVERT: E 140 PHE cc_start: 0.7589 (m-80) cc_final: 0.7246 (m-80) REVERT: E 286 VAL cc_start: 0.8502 (t) cc_final: 0.8225 (p) REVERT: E 651 THR cc_start: 0.8696 (m) cc_final: 0.8426 (p) REVERT: E 1154 ILE cc_start: 0.8453 (mt) cc_final: 0.8245 (mt) REVERT: D 31 MET cc_start: 0.7833 (tpt) cc_final: 0.7398 (tpt) REVERT: D 38 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 96 LYS cc_start: 0.9275 (tttp) cc_final: 0.8629 (ttmm) REVERT: B 363 MET cc_start: 0.8925 (mmt) cc_final: 0.8440 (mmt) outliers start: 9 outliers final: 2 residues processed: 200 average time/residue: 0.1012 time to fit residues: 29.5845 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 ASN E 638 HIS E 705 GLN E 794 ASN B 6 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062617 restraints weight = 61969.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063976 restraints weight = 31669.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064847 restraints weight = 20179.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065383 restraints weight = 14996.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.065756 restraints weight = 12460.157| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13936 Z= 0.172 Angle : 0.798 36.237 18977 Z= 0.368 Chirality : 0.046 0.177 2098 Planarity : 0.005 0.047 2365 Dihedral : 12.537 123.613 2038 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 1.49 % Allowed : 8.89 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.10 (0.20), residues: 1640 helix: 0.85 (0.20), residues: 630 sheet: -0.09 (0.30), residues: 278 loop : -0.47 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 69 TYR 0.021 0.002 TYR B 269 PHE 0.030 0.002 PHE E 830 TRP 0.020 0.002 TRP E 683 HIS 0.008 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (13932) covalent geometry : angle 0.69328 / 0.37 (18965) hydrogen bonds : bond 0.05539 / 5.41 ( 631) hydrogen bonds : angle 5.47414 / 5.42 ( 1771) metal coordination : bond 0.01401 / 0.68 ( 4) metal coordination : angle 15.71174 / 8.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8855 (mmm) cc_final: 0.8472 (mmm) REVERT: E 741 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7733 (mt-10) REVERT: E 973 ASN cc_start: 0.7630 (m-40) cc_final: 0.7028 (t0) REVERT: E 1077 LEU cc_start: 0.8118 (tp) cc_final: 0.7720 (pp) REVERT: D 38 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 96 LYS cc_start: 0.9145 (tttp) cc_final: 0.8639 (ttmm) REVERT: B 63 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7146 (ttm-80) REVERT: B 180 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8213 (mm) REVERT: B 363 MET cc_start: 0.8623 (mmt) cc_final: 0.8179 (mmt) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 0.0938 time to fit residues: 19.8223 Evaluate side-chains 109 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS E 999 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.060019 restraints weight = 62337.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061287 restraints weight = 32441.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062149 restraints weight = 21026.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062705 restraints weight = 15698.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063025 restraints weight = 12979.221| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13936 Z= 0.166 Angle : 0.702 32.192 18977 Z= 0.326 Chirality : 0.044 0.219 2098 Planarity : 0.004 0.046 2365 Dihedral : 12.181 116.756 2035 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 9.46 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.46 (0.21), residues: 1640 helix: 1.25 (0.20), residues: 639 sheet: 0.21 (0.32), residues: 271 loop : -0.43 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 267 TYR 0.015 0.002 TYR E 313 PHE 0.038 0.002 PHE E 830 TRP 0.012 0.001 TRP E 683 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (13932) covalent geometry : angle 0.62180 / 0.32 (18965) hydrogen bonds : bond 0.04755 / 4.55 ( 631) hydrogen bonds : angle 5.16662 / 5.14 ( 1771) metal coordination : bond 0.01069 / 0.50 ( 4) metal coordination : angle 12.94937 / 7.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8894 (mmm) cc_final: 0.8548 (mmm) REVERT: E 287 MET cc_start: 0.8718 (ttp) cc_final: 0.8478 (ttm) REVERT: E 391 SER cc_start: 0.7566 (m) cc_final: 0.7248 (p) REVERT: E 694 MET cc_start: 0.7285 (tpt) cc_final: 0.6605 (tpt) REVERT: E 926 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8507 (tp) REVERT: E 973 ASN cc_start: 0.7936 (m-40) cc_final: 0.7296 (t0) REVERT: E 1077 LEU cc_start: 0.8225 (tp) cc_final: 0.7935 (pp) REVERT: D 38 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 96 LYS cc_start: 0.9147 (tttp) cc_final: 0.8740 (ttmm) REVERT: B 136 MET cc_start: 0.8301 (mtm) cc_final: 0.7926 (mtm) REVERT: B 282 ILE cc_start: 0.8746 (mm) cc_final: 0.8487 (mm) REVERT: B 363 MET cc_start: 0.8420 (mmt) cc_final: 0.7776 (mmt) outliers start: 29 outliers final: 13 residues processed: 129 average time/residue: 0.0927 time to fit residues: 18.6736 Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 926 LEU Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain B residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 43 optimal weight: 0.0980 chunk 163 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1033 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058338 restraints weight = 62288.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059601 restraints weight = 32779.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060423 restraints weight = 21188.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060948 restraints weight = 15903.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061254 restraints weight = 13231.944| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13936 Z= 0.185 Angle : 0.676 28.426 18977 Z= 0.316 Chirality : 0.043 0.223 2098 Planarity : 0.004 0.040 2365 Dihedral : 11.987 112.820 2035 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 2.28 % Allowed : 9.89 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.54 (0.21), residues: 1640 helix: 1.34 (0.21), residues: 640 sheet: 0.12 (0.32), residues: 276 loop : -0.35 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 988 TYR 0.024 0.002 TYR E1059 PHE 0.035 0.002 PHE E 830 TRP 0.012 0.002 TRP E 78 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (13932) covalent geometry : angle 0.60515 / 0.31 (18965) hydrogen bonds : bond 0.04585 / 4.36 ( 631) hydrogen bonds : angle 5.07195 / 5.05 ( 1771) metal coordination : bond 0.00975 / 0.45 ( 4) metal coordination : angle 11.97768 / 6.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8902 (mmm) cc_final: 0.8576 (mmm) REVERT: E 391 SER cc_start: 0.7536 (m) cc_final: 0.7189 (p) REVERT: E 694 MET cc_start: 0.7361 (tpt) cc_final: 0.6730 (tpt) REVERT: E 858 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8672 (tp) REVERT: E 973 ASN cc_start: 0.8073 (m-40) cc_final: 0.7394 (t0) REVERT: E 1077 LEU cc_start: 0.8305 (tp) cc_final: 0.7952 (tt) REVERT: D 38 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 96 LYS cc_start: 0.9178 (tttp) cc_final: 0.8783 (ttmm) REVERT: B 86 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8880 (p) REVERT: B 363 MET cc_start: 0.8353 (mmt) cc_final: 0.7774 (mmt) outliers start: 32 outliers final: 20 residues processed: 118 average time/residue: 0.0858 time to fit residues: 16.0913 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 94 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 859 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058095 restraints weight = 62325.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059347 restraints weight = 32627.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060164 restraints weight = 21168.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060694 restraints weight = 15910.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061038 restraints weight = 13228.570| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13936 Z= 0.146 Angle : 0.625 24.101 18977 Z= 0.295 Chirality : 0.043 0.298 2098 Planarity : 0.004 0.040 2365 Dihedral : 11.813 109.516 2035 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.05 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 10.60 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.73 (0.21), residues: 1640 helix: 1.59 (0.21), residues: 635 sheet: 0.25 (0.33), residues: 255 loop : -0.34 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 267 TYR 0.018 0.001 TYR E1059 PHE 0.027 0.002 PHE E 830 TRP 0.009 0.001 TRP E1143 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (13932) covalent geometry : angle 0.56559 / 0.29 (18965) hydrogen bonds : bond 0.04257 / 4.04 ( 631) hydrogen bonds : angle 4.89795 / 4.89 ( 1771) metal coordination : bond 0.00826 / 0.37 ( 4) metal coordination : angle 10.58407 / 6.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8854 (mmm) cc_final: 0.8616 (mmm) REVERT: E 391 SER cc_start: 0.7599 (m) cc_final: 0.7214 (p) REVERT: E 694 MET cc_start: 0.7483 (tpt) cc_final: 0.6955 (tpt) REVERT: E 843 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7532 (t) REVERT: E 973 ASN cc_start: 0.8155 (m-40) cc_final: 0.7474 (t0) REVERT: E 1077 LEU cc_start: 0.8343 (tp) cc_final: 0.7989 (tt) REVERT: D 38 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 86 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8972 (p) REVERT: B 282 ILE cc_start: 0.8778 (mm) cc_final: 0.8506 (mm) REVERT: B 363 MET cc_start: 0.8312 (mmt) cc_final: 0.7744 (mmt) outliers start: 32 outliers final: 22 residues processed: 121 average time/residue: 0.0789 time to fit residues: 15.3196 Evaluate side-chains 118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056057 restraints weight = 63258.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057233 restraints weight = 34217.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058003 restraints weight = 22584.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058498 restraints weight = 17187.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058830 restraints weight = 14396.724| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13936 Z= 0.219 Angle : 0.678 22.341 18977 Z= 0.323 Chirality : 0.043 0.162 2098 Planarity : 0.004 0.042 2365 Dihedral : 11.795 106.289 2035 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 2.84 % Allowed : 10.88 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.52 (0.21), residues: 1640 helix: 1.45 (0.21), residues: 636 sheet: 0.00 (0.32), residues: 270 loop : -0.45 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 267 TYR 0.021 0.002 TYR E1059 PHE 0.022 0.002 PHE E 830 TRP 0.021 0.002 TRP B 284 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (13932) covalent geometry : angle 0.62317 / 0.32 (18965) hydrogen bonds : bond 0.04560 / 4.29 ( 631) hydrogen bonds : angle 5.02849 / 4.97 ( 1771) metal coordination : bond 0.01194 / 0.57 ( 4) metal coordination : angle 10.64727 / 6.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8898 (mmm) cc_final: 0.8673 (mmm) REVERT: E 391 SER cc_start: 0.7605 (m) cc_final: 0.7210 (p) REVERT: E 694 MET cc_start: 0.7525 (tpt) cc_final: 0.6981 (tpt) REVERT: E 843 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7756 (t) REVERT: E 858 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8673 (tp) REVERT: E 1077 LEU cc_start: 0.8342 (tp) cc_final: 0.8124 (pp) REVERT: B 86 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8952 (p) REVERT: B 363 MET cc_start: 0.8369 (mmt) cc_final: 0.7816 (mmt) outliers start: 40 outliers final: 23 residues processed: 114 average time/residue: 0.0757 time to fit residues: 14.2190 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056411 restraints weight = 62836.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057628 restraints weight = 33240.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058425 restraints weight = 21610.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058952 restraints weight = 16291.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059300 restraints weight = 13530.663| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13936 Z= 0.161 Angle : 0.620 21.035 18977 Z= 0.296 Chirality : 0.042 0.159 2098 Planarity : 0.004 0.041 2365 Dihedral : 11.724 105.254 2035 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 2.49 % Allowed : 11.02 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.64 (0.21), residues: 1640 helix: 1.63 (0.21), residues: 637 sheet: -0.07 (0.32), residues: 267 loop : -0.40 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.017 0.001 TYR E1059 PHE 0.019 0.002 PHE E 830 TRP 0.009 0.001 TRP E1026 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (13932) covalent geometry : angle 0.56790 / 0.30 (18965) hydrogen bonds : bond 0.04195 / 3.96 ( 631) hydrogen bonds : angle 4.89431 / 4.86 ( 1771) metal coordination : bond 0.00879 / 0.40 ( 4) metal coordination : angle 9.93733 / 5.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8877 (mmm) cc_final: 0.8480 (mmm) REVERT: E 287 MET cc_start: 0.8579 (ttp) cc_final: 0.8228 (ttp) REVERT: E 391 SER cc_start: 0.7741 (m) cc_final: 0.7503 (t) REVERT: E 694 MET cc_start: 0.7626 (tpt) cc_final: 0.7112 (tpt) REVERT: E 843 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7635 (t) REVERT: E 858 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8646 (tp) REVERT: E 973 ASN cc_start: 0.7842 (m-40) cc_final: 0.7208 (t0) REVERT: E 1077 LEU cc_start: 0.8321 (tp) cc_final: 0.8090 (pp) REVERT: B 86 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.8990 (p) REVERT: B 363 MET cc_start: 0.8309 (mmt) cc_final: 0.7866 (mmt) outliers start: 35 outliers final: 22 residues processed: 111 average time/residue: 0.0741 time to fit residues: 13.6471 Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055701 restraints weight = 63554.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056868 restraints weight = 34220.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057638 restraints weight = 22583.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058101 restraints weight = 17168.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058428 restraints weight = 14493.831| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13936 Z= 0.199 Angle : 0.650 20.819 18977 Z= 0.312 Chirality : 0.043 0.161 2098 Planarity : 0.004 0.044 2365 Dihedral : 11.696 103.832 2035 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 2.20 % Allowed : 11.45 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.50 (0.21), residues: 1640 helix: 1.55 (0.20), residues: 641 sheet: -0.23 (0.32), residues: 266 loop : -0.49 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.027 0.002 TYR E1059 PHE 0.017 0.002 PHE E 830 TRP 0.013 0.002 TRP B 284 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (13932) covalent geometry : angle 0.59887 / 0.31 (18965) hydrogen bonds : bond 0.04360 / 4.10 ( 631) hydrogen bonds : angle 4.93232 / 4.89 ( 1771) metal coordination : bond 0.01112 / 0.53 ( 4) metal coordination : angle 10.02673 / 5.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8887 (mmm) cc_final: 0.8495 (mmm) REVERT: E 287 MET cc_start: 0.8558 (ttp) cc_final: 0.8210 (ttp) REVERT: E 843 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7697 (t) REVERT: E 858 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8579 (tp) REVERT: E 973 ASN cc_start: 0.7820 (m-40) cc_final: 0.7190 (t0) REVERT: E 1077 LEU cc_start: 0.8330 (tp) cc_final: 0.8098 (pp) REVERT: D 32 MET cc_start: 0.8873 (ptm) cc_final: 0.8622 (ptp) REVERT: B 86 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8948 (p) REVERT: B 363 MET cc_start: 0.8303 (mmt) cc_final: 0.7815 (mmt) outliers start: 31 outliers final: 24 residues processed: 105 average time/residue: 0.0778 time to fit residues: 13.4485 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 131 optimal weight: 0.0170 chunk 15 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.056268 restraints weight = 64146.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057447 restraints weight = 34268.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058208 restraints weight = 22516.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058706 restraints weight = 17094.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058998 restraints weight = 14314.448| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13936 Z= 0.150 Angle : 0.608 19.780 18977 Z= 0.291 Chirality : 0.042 0.143 2098 Planarity : 0.004 0.043 2365 Dihedral : 11.621 103.670 2035 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.20 % Allowed : 11.59 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.64 (0.21), residues: 1640 helix: 1.68 (0.20), residues: 644 sheet: -0.16 (0.32), residues: 266 loop : -0.43 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.017 0.001 TYR E1059 PHE 0.018 0.001 PHE E 830 TRP 0.010 0.001 TRP E1026 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (13932) covalent geometry : angle 0.55971 / 0.29 (18965) hydrogen bonds : bond 0.04049 / 3.84 ( 631) hydrogen bonds : angle 4.84000 / 4.80 ( 1771) metal coordination : bond 0.00825 / 0.38 ( 4) metal coordination : angle 9.46100 / 5.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8827 (mmm) cc_final: 0.8517 (mmm) REVERT: E 287 MET cc_start: 0.8462 (ttp) cc_final: 0.8130 (ttp) REVERT: E 843 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7595 (t) REVERT: E 858 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8657 (tp) REVERT: E 909 MET cc_start: 0.8304 (ptt) cc_final: 0.8030 (ptt) REVERT: E 973 ASN cc_start: 0.7897 (m-40) cc_final: 0.7288 (t0) REVERT: E 1077 LEU cc_start: 0.8314 (tp) cc_final: 0.8054 (pp) REVERT: D 32 MET cc_start: 0.8871 (ptm) cc_final: 0.8665 (ptp) REVERT: B 86 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.8994 (p) REVERT: B 363 MET cc_start: 0.8256 (mmt) cc_final: 0.7771 (mmt) outliers start: 31 outliers final: 26 residues processed: 113 average time/residue: 0.0747 time to fit residues: 13.8814 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 937 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056001 restraints weight = 64154.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057172 restraints weight = 34363.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057925 restraints weight = 22609.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058423 restraints weight = 17205.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058726 restraints weight = 14417.768| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13936 Z= 0.159 Angle : 0.615 19.660 18977 Z= 0.293 Chirality : 0.042 0.143 2098 Planarity : 0.004 0.047 2365 Dihedral : 11.557 103.152 2035 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 2.20 % Allowed : 11.66 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.69 (0.21), residues: 1640 helix: 1.72 (0.20), residues: 644 sheet: -0.14 (0.32), residues: 266 loop : -0.40 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 267 TYR 0.025 0.002 TYR E1059 PHE 0.018 0.002 PHE E 830 TRP 0.011 0.001 TRP B 284 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (13932) covalent geometry : angle 0.56715 / 0.29 (18965) hydrogen bonds : bond 0.04060 / 3.84 ( 631) hydrogen bonds : angle 4.83765 / 4.81 ( 1771) metal coordination : bond 0.00867 / 0.41 ( 4) metal coordination : angle 9.46380 / 5.38 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8818 (mmm) cc_final: 0.8555 (mmm) REVERT: E 287 MET cc_start: 0.8419 (ttp) cc_final: 0.8099 (ttp) REVERT: E 843 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7616 (t) REVERT: E 909 MET cc_start: 0.8278 (ptt) cc_final: 0.8039 (ptt) REVERT: E 973 ASN cc_start: 0.7928 (m-40) cc_final: 0.7287 (t0) REVERT: E 1077 LEU cc_start: 0.8337 (tp) cc_final: 0.8043 (pp) REVERT: B 86 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8943 (p) REVERT: B 363 MET cc_start: 0.8252 (mmt) cc_final: 0.7744 (mmt) outliers start: 31 outliers final: 28 residues processed: 113 average time/residue: 0.0811 time to fit residues: 14.8813 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056513 restraints weight = 63995.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057695 restraints weight = 34131.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058458 restraints weight = 22390.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058954 restraints weight = 16994.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059263 restraints weight = 14247.860| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13936 Z= 0.135 Angle : 0.597 19.163 18977 Z= 0.284 Chirality : 0.041 0.139 2098 Planarity : 0.004 0.046 2365 Dihedral : 11.495 102.963 2035 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 2.13 % Allowed : 11.95 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 are not related in a simple way. whole: 0.78 (0.21), residues: 1640 helix: 1.83 (0.21), residues: 642 sheet: -0.08 (0.32), residues: 266 loop : -0.38 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.016 0.001 TYR E1059 PHE 0.017 0.001 PHE E 830 TRP 0.010 0.001 TRP E 425 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13932) covalent geometry : angle 0.54997 / 0.28 (18965) hydrogen bonds : bond 0.03877 / 3.68 ( 631) hydrogen bonds : angle 4.78015 / 4.74 ( 1771) metal coordination : bond 0.00754 / 0.35 ( 4) metal coordination : angle 9.22163 / 5.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.05 seconds wall clock time: 31 minutes 48.53 seconds (1908.53 seconds total)