Starting phenix.real_space_refine on Thu Aug 6 04:07:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw9_41663/08_2026/8tw9_41663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw9_41663/08_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_41663/08_2026/8tw9_41663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_2026/8tw9_41663.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_2026/8tw9_41663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_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-2.2rc3-6140/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: 2.25, 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: 0.88 Conformation dependent library (CDL) restraints added in 494.5 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: 1.43 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: 2.95 Time building geometry restraints manager: 1.12 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: 1.210 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.670 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- 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= 0.797 Angle : 1.744 38.408 18977 Z= 1.101 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 1.66874 / 1.10 (18965) hydrogen bonds : bond 0.16596 / 15.12 ( 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 : 0.492 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: 0.1044 time to fit residues: 30.7181 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 : 0.441 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.073422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062649 restraints weight = 61558.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063993 restraints weight = 31635.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064860 restraints weight = 20197.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065382 restraints weight = 15023.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065761 restraints weight = 12517.227| |-----------------------------------------------------------------------------| 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) = 0.066 | | 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) = 0.066 | | 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: 0.7931 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13936 Z= 0.170 Angle : 0.801 36.316 18977 Z= 0.370 Chirality : 0.046 0.181 2098 Planarity : 0.005 0.046 2365 Dihedral : 12.533 123.404 2038 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 1.56 % Allowed : 8.75 % Favored : 89.69 % 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: 0.11 (0.20), residues: 1640 helix: 0.84 (0.20), residues: 630 sheet: -0.05 (0.31), residues: 276 loop : -0.45 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 69 TYR 0.021 0.002 TYR B 269 PHE 0.031 0.002 PHE E 830 TRP 0.018 0.002 TRP E 683 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (13932) covalent geometry : angle 0.69888 / 0.37 (18965) hydrogen bonds : bond 0.05495 / 5.36 ( 631) hydrogen bonds : angle 5.47946 / 5.42 ( 1771) metal coordination : bond 0.02159 / 1.04 ( 4) metal coordination : angle 15.55627 / 8.58 ( 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 147 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8852 (mmm) cc_final: 0.8471 (mmm) REVERT: E 741 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7726 (mt-10) REVERT: E 973 ASN cc_start: 0.7626 (m-40) cc_final: 0.7022 (t0) REVERT: E 1077 LEU cc_start: 0.8123 (tp) cc_final: 0.7729 (pp) REVERT: D 38 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7701 (tm-30) REVERT: D 96 LYS cc_start: 0.9156 (tttp) cc_final: 0.8642 (ttmm) REVERT: B 63 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7115 (ttm-80) REVERT: B 180 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8200 (mm) REVERT: B 363 MET cc_start: 0.8619 (mmt) cc_final: 0.8078 (mmt) outliers start: 22 outliers final: 9 residues processed: 138 average time/residue: 0.1027 time to fit residues: 21.5292 Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 HIS E 828 ASN E 859 GLN E 999 GLN E1033 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 = 0.3301 r_free = 0.3301 target = 0.067118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056369 restraints weight = 63637.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.057558 restraints weight = 34104.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058327 restraints weight = 22447.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058800 restraints weight = 17104.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059031 restraints weight = 14404.859| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13936 Z= 0.280 Angle : 0.833 33.266 18977 Z= 0.389 Chirality : 0.048 0.277 2098 Planarity : 0.005 0.046 2365 Dihedral : 12.242 114.368 2035 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 2.49 % Allowed : 9.60 % Favored : 87.91 % 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: 0.09 (0.20), residues: 1640 helix: 0.83 (0.20), residues: 640 sheet: 0.04 (0.31), residues: 282 loop : -0.55 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 69 TYR 0.029 0.003 TYR E 488 PHE 0.041 0.003 PHE E 830 TRP 0.015 0.002 TRP E 683 HIS 0.007 0.002 HIS E 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 (13932) covalent geometry : angle 0.74484 / 0.39 (18965) hydrogen bonds : bond 0.05524 / 5.17 ( 631) hydrogen bonds : angle 5.43444 / 5.43 ( 1771) metal coordination : bond 0.01698 / 0.80 ( 4) metal coordination : angle 14.85359 / 8.15 ( 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 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.474 Fit side-chains REVERT: E 50 MET cc_start: 0.8983 (mmm) cc_final: 0.8606 (mmm) REVERT: E 391 SER cc_start: 0.7563 (m) cc_final: 0.7237 (p) REVERT: E 973 ASN cc_start: 0.8053 (m-40) cc_final: 0.7404 (t0) REVERT: E 1077 LEU cc_start: 0.8300 (tp) cc_final: 0.8095 (pp) REVERT: D 38 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 96 LYS cc_start: 0.9182 (tttp) cc_final: 0.8701 (ttmm) REVERT: B 180 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8403 (mm) REVERT: B 282 ILE cc_start: 0.8757 (mm) cc_final: 0.8475 (mm) REVERT: B 363 MET cc_start: 0.8387 (mmt) cc_final: 0.7800 (mmt) outliers start: 35 outliers final: 21 residues processed: 118 average time/residue: 0.0862 time to fit residues: 16.3236 Evaluate side-chains 106 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 771 VAL 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 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 82 THR 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 192 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055453 restraints weight = 63189.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056656 restraints weight = 33083.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057421 restraints weight = 21558.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057931 restraints weight = 16343.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.058256 restraints weight = 13643.836| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13936 Z= 0.243 Angle : 0.738 27.234 18977 Z= 0.346 Chirality : 0.046 0.311 2098 Planarity : 0.004 0.040 2365 Dihedral : 12.076 110.665 2035 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 1.99 % Allowed : 11.02 % Favored : 86.98 % 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: 0.19 (0.21), residues: 1640 helix: 1.04 (0.20), residues: 641 sheet: 0.03 (0.32), residues: 270 loop : -0.59 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 325 TYR 0.028 0.002 TYR E1059 PHE 0.025 0.002 PHE E 830 TRP 0.011 0.002 TRP E 683 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (13932) covalent geometry : angle 0.66226 / 0.34 (18965) hydrogen bonds : bond 0.04956 / 4.71 ( 631) hydrogen bonds : angle 5.22637 / 5.20 ( 1771) metal coordination : bond 0.01299 / 0.61 ( 4) metal coordination : angle 12.92417 / 7.16 ( 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 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.464 Fit side-chains REVERT: E 50 MET cc_start: 0.8957 (mmm) cc_final: 0.8574 (mmm) REVERT: E 973 ASN cc_start: 0.8199 (m-40) cc_final: 0.7502 (t0) REVERT: E 1052 MET cc_start: 0.4268 (ttm) cc_final: 0.3787 (ttp) REVERT: D 96 LYS cc_start: 0.9176 (tttp) cc_final: 0.8746 (ttmm) REVERT: B 86 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8911 (p) REVERT: B 275 MET cc_start: 0.8589 (tpp) cc_final: 0.7594 (ttt) REVERT: B 282 ILE cc_start: 0.8805 (mm) cc_final: 0.8526 (mm) REVERT: B 363 MET cc_start: 0.8416 (mmt) cc_final: 0.7836 (mmt) outliers start: 28 outliers final: 22 residues processed: 107 average time/residue: 0.0832 time to fit residues: 14.7084 Evaluate side-chains 106 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 310 MET Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 338 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 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 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 320 THR 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: 1.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3313 r_free = 0.3313 target = 0.067496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056638 restraints weight = 62475.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057864 restraints weight = 32874.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058655 restraints weight = 21441.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059179 restraints weight = 16188.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059508 restraints weight = 13512.036| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13936 Z= 0.135 Angle : 0.632 23.137 18977 Z= 0.298 Chirality : 0.042 0.154 2098 Planarity : 0.004 0.042 2365 Dihedral : 11.850 109.470 2035 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.56 % Allowed : 10.74 % Favored : 86.70 % 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: 1.47 (0.21), residues: 636 sheet: -0.02 (0.32), residues: 265 loop : -0.44 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 267 TYR 0.019 0.001 TYR E1059 PHE 0.027 0.001 PHE E 830 TRP 0.011 0.001 TRP E1026 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (13932) covalent geometry : angle 0.57291 / 0.30 (18965) hydrogen bonds : bond 0.04333 / 4.13 ( 631) hydrogen bonds : angle 4.93235 / 4.91 ( 1771) metal coordination : bond 0.00803 / 0.35 ( 4) metal coordination : angle 10.59942 / 6.02 ( 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 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8895 (mmm) cc_final: 0.8442 (mmm) REVERT: E 694 MET cc_start: 0.7510 (tpt) cc_final: 0.6981 (tpt) REVERT: E 843 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7744 (t) REVERT: E 973 ASN cc_start: 0.8229 (m-40) cc_final: 0.7524 (t0) REVERT: D 96 LYS cc_start: 0.9154 (tttp) cc_final: 0.8807 (ttmm) REVERT: B 86 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8924 (p) REVERT: B 180 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (mm) REVERT: B 275 MET cc_start: 0.8606 (tpp) cc_final: 0.7608 (ttt) REVERT: B 282 ILE cc_start: 0.8797 (mm) cc_final: 0.8519 (mm) REVERT: B 363 MET cc_start: 0.8351 (mmt) cc_final: 0.7795 (mmt) outliers start: 36 outliers final: 21 residues processed: 120 average time/residue: 0.0867 time to fit residues: 16.9898 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 310 MET Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 459 MET 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 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 18 ILE 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 180 LEU 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: 10.0000 chunk 1 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3281 r_free = 0.3281 target = 0.066131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055441 restraints weight = 63998.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056604 restraints weight = 34279.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.057375 restraints weight = 22624.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.057883 restraints weight = 17188.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.058191 restraints weight = 14350.871| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13936 Z= 0.212 Angle : 0.677 22.074 18977 Z= 0.321 Chirality : 0.043 0.146 2098 Planarity : 0.004 0.042 2365 Dihedral : 11.822 107.487 2035 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.78 % Favored : 96.10 % Rotamer: Outliers : 2.70 % Allowed : 10.60 % Favored : 86.70 % 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: 0.40 (0.21), residues: 1640 helix: 1.39 (0.20), residues: 642 sheet: -0.10 (0.32), residues: 263 loop : -0.55 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.018 0.002 TYR E1059 PHE 0.030 0.002 PHE E 830 TRP 0.009 0.002 TRP E1026 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (13932) covalent geometry : angle 0.62234 / 0.32 (18965) hydrogen bonds : bond 0.04562 / 4.31 ( 631) hydrogen bonds : angle 5.00076 / 4.98 ( 1771) metal coordination : bond 0.01149 / 0.54 ( 4) metal coordination : angle 10.61614 / 5.98 ( 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 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8889 (mmm) cc_final: 0.8450 (mmm) REVERT: E 694 MET cc_start: 0.7586 (tpt) cc_final: 0.7062 (tpt) REVERT: E 843 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7818 (t) REVERT: E 858 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8698 (tp) REVERT: E 973 ASN cc_start: 0.8304 (m-40) cc_final: 0.7629 (t0) REVERT: B 86 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8933 (p) REVERT: B 180 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8529 (mm) REVERT: B 282 ILE cc_start: 0.8803 (mm) cc_final: 0.8517 (mm) REVERT: B 363 MET cc_start: 0.8341 (mmt) cc_final: 0.7785 (mmt) outliers start: 38 outliers final: 25 residues processed: 108 average time/residue: 0.0899 time to fit residues: 15.6765 Evaluate side-chains 109 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 310 MET Chi-restraints excluded: chain E residue 311 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3282 r_free = 0.3282 target = 0.066173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055484 restraints weight = 63913.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056656 restraints weight = 34335.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057430 restraints weight = 22686.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057920 restraints weight = 17246.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.058249 restraints weight = 14474.921| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13936 Z= 0.185 Angle : 0.646 21.256 18977 Z= 0.309 Chirality : 0.043 0.237 2098 Planarity : 0.004 0.042 2365 Dihedral : 11.778 106.353 2035 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 2.63 % Allowed : 10.95 % Favored : 86.42 % 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: 0.41 (0.21), residues: 1640 helix: 1.42 (0.20), residues: 644 sheet: -0.10 (0.32), residues: 264 loop : -0.56 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.017 0.002 TYR E1059 PHE 0.026 0.002 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 0.00412 / 0.19 (13932) covalent geometry : angle 0.59440 / 0.31 (18965) hydrogen bonds : bond 0.04417 / 4.18 ( 631) hydrogen bonds : angle 4.94708 / 4.96 ( 1771) metal coordination : bond 0.01023 / 0.48 ( 4) metal coordination : angle 10.11095 / 5.71 ( 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 121 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8891 (mmm) cc_final: 0.8468 (mmm) REVERT: E 843 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7799 (t) REVERT: E 858 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8627 (tp) REVERT: B 86 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.8977 (p) REVERT: B 275 MET cc_start: 0.8581 (tpp) cc_final: 0.7532 (ttt) REVERT: B 282 ILE cc_start: 0.8819 (mm) cc_final: 0.8536 (mm) REVERT: B 363 MET cc_start: 0.8294 (mmt) cc_final: 0.7826 (mmt) outliers start: 37 outliers final: 28 residues processed: 112 average time/residue: 0.0896 time to fit residues: 16.2809 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 310 MET Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 338 THR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 140 optimal weight: 0.0000 chunk 21 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3334 r_free = 0.3334 target = 0.068021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057393 restraints weight = 63555.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058597 restraints weight = 33797.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059380 restraints weight = 22148.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059887 restraints weight = 16781.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060226 restraints weight = 14052.516| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13936 Z= 0.108 Angle : 0.594 18.861 18977 Z= 0.285 Chirality : 0.042 0.160 2098 Planarity : 0.004 0.043 2365 Dihedral : 11.639 105.722 2035 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 1.85 % Allowed : 11.38 % Favored : 86.77 % 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: 1.69 (0.21), residues: 646 sheet: 0.02 (0.33), residues: 257 loop : -0.45 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.012 0.001 TYR B 226 PHE 0.019 0.001 PHE E 830 TRP 0.011 0.001 TRP E 78 HIS 0.002 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (13932) covalent geometry : angle 0.54755 / 0.28 (18965) hydrogen bonds : bond 0.03776 / 3.62 ( 631) hydrogen bonds : angle 4.70138 / 4.68 ( 1771) metal coordination : bond 0.00570 / 0.24 ( 4) metal coordination : angle 9.16382 / 5.27 ( 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 127 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8793 (mmm) cc_final: 0.8568 (mmm) REVERT: E 843 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7592 (t) REVERT: E 858 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8607 (tp) REVERT: E 909 MET cc_start: 0.8274 (ptt) cc_final: 0.8013 (ptt) REVERT: E 973 ASN cc_start: 0.7627 (m-40) cc_final: 0.7076 (t0) REVERT: D 96 LYS cc_start: 0.9107 (tttp) cc_final: 0.8791 (ttmm) REVERT: B 86 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8882 (p) REVERT: B 275 MET cc_start: 0.8592 (tpp) cc_final: 0.7895 (ttt) REVERT: B 282 ILE cc_start: 0.8833 (mm) cc_final: 0.8553 (mm) REVERT: B 363 MET cc_start: 0.8217 (mmt) cc_final: 0.7710 (mmt) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 0.0952 time to fit residues: 18.2081 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR 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 971 VAL Chi-restraints excluded: chain E residue 1023 CYS 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 172 VAL Chi-restraints excluded: chain B residue 195 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 131 optimal weight: 0.0870 chunk 15 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 444 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 = 0.3332 r_free = 0.3332 target = 0.067899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057237 restraints weight = 64014.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058440 restraints weight = 34101.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059207 restraints weight = 22348.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059735 restraints weight = 17019.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060040 restraints weight = 14199.685| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13936 Z= 0.112 Angle : 0.592 19.169 18977 Z= 0.281 Chirality : 0.041 0.140 2098 Planarity : 0.004 0.097 2365 Dihedral : 11.590 104.988 2035 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 1.64 % Allowed : 11.81 % Favored : 86.56 % 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: 0.76 (0.21), residues: 1640 helix: 1.73 (0.21), residues: 645 sheet: 0.03 (0.32), residues: 266 loop : -0.37 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.011 0.001 TYR E1059 PHE 0.027 0.001 PHE E 830 TRP 0.040 0.002 TRP B 284 HIS 0.003 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13932) covalent geometry : angle 0.54497 / 0.28 (18965) hydrogen bonds : bond 0.03731 / 3.54 ( 631) hydrogen bonds : angle 4.67408 / 4.65 ( 1771) metal coordination : bond 0.00552 / 0.25 ( 4) metal coordination : angle 9.24838 / 5.32 ( 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 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: E 843 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7521 (t) REVERT: E 909 MET cc_start: 0.8280 (ptt) cc_final: 0.8061 (ptt) REVERT: E 973 ASN cc_start: 0.7724 (m-40) cc_final: 0.7126 (t0) REVERT: B 86 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8934 (p) REVERT: B 275 MET cc_start: 0.8588 (tpp) cc_final: 0.7891 (ttt) REVERT: B 363 MET cc_start: 0.8198 (mmt) cc_final: 0.7690 (mmt) outliers start: 23 outliers final: 19 residues processed: 107 average time/residue: 0.0901 time to fit residues: 15.6540 Evaluate side-chains 110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR 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 971 VAL Chi-restraints excluded: chain E residue 1023 CYS 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 823 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 = 0.3278 r_free = 0.3278 target = 0.065575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054964 restraints weight = 64823.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056121 restraints weight = 34633.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056878 restraints weight = 22841.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057363 restraints weight = 17331.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057661 restraints weight = 14562.902| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13936 Z= 0.232 Angle : 0.687 21.420 18977 Z= 0.327 Chirality : 0.043 0.163 2098 Planarity : 0.005 0.085 2365 Dihedral : 11.648 103.614 2035 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 1.78 % Allowed : 11.88 % 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: 0.58 (0.21), residues: 1640 helix: 1.52 (0.20), residues: 646 sheet: -0.13 (0.32), residues: 265 loop : -0.39 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 370 TYR 0.021 0.002 TYR E1059 PHE 0.028 0.002 PHE E 830 TRP 0.035 0.002 TRP B 284 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (13932) covalent geometry : angle 0.63897 / 0.33 (18965) hydrogen bonds : bond 0.04394 / 4.14 ( 631) hydrogen bonds : angle 4.88544 / 4.89 ( 1771) metal coordination : bond 0.01295 / 0.62 ( 4) metal coordination : angle 10.08819 / 5.68 ( 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 109 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.531 Fit side-chains REVERT: E 843 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7792 (t) REVERT: E 858 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8700 (tp) REVERT: E 973 ASN cc_start: 0.7838 (m-40) cc_final: 0.7224 (t0) REVERT: B 86 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8934 (p) REVERT: B 363 MET cc_start: 0.8288 (mmt) cc_final: 0.7809 (mmt) outliers start: 25 outliers final: 22 residues processed: 105 average time/residue: 0.0953 time to fit residues: 16.2466 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 THR 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 372 THR Chi-restraints excluded: chain E residue 565 VAL 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 971 VAL Chi-restraints excluded: chain E residue 1023 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 0.0070 chunk 70 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3310 r_free = 0.3310 target = 0.066929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056303 restraints weight = 64337.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057477 restraints weight = 34355.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058245 restraints weight = 22621.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058752 restraints weight = 17162.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058988 restraints weight = 14370.140| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- 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 = 0.87 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 = 0.90 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: 0.8165 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13936 Z= 0.131 Angle : 0.619 19.929 18977 Z= 0.295 Chirality : 0.042 0.142 2098 Planarity : 0.004 0.080 2365 Dihedral : 11.577 103.604 2035 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 1.56 % Allowed : 12.09 % 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: 0.70 (0.21), residues: 1640 helix: 1.70 (0.20), residues: 644 sheet: -0.02 (0.32), residues: 261 loop : -0.41 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 18 TYR 0.020 0.001 TYR E1059 PHE 0.025 0.001 PHE E 830 TRP 0.035 0.002 TRP B 284 HIS 0.003 0.001 HIS E 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (13932) covalent geometry : angle 0.57428 / 0.29 (18965) hydrogen bonds : bond 0.03965 / 3.76 ( 631) hydrogen bonds : angle 4.74731 / 4.74 ( 1771) metal coordination : bond 0.00742 / 0.33 ( 4) metal coordination : angle 9.24797 / 5.26 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.70 seconds wall clock time: 35 minutes 28.69 seconds (2128.69 seconds total)