Starting phenix.real_space_refine on Sat Aug 23 16:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw9_41663/08_2025/8tw9_41663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw9_41663/08_2025/8tw9_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_2025/8tw9_41663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_2025/8tw9_41663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_2025/8tw9_41663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw9_41663/08_2025/8tw9_41663.map" } 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-2.0-5787/lib/python3.9/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: 3.05, per 1000 atoms: 0.22 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: 0.85 Conformation dependent library (CDL) restraints added in 630.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.63 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: 2.16 Time building geometry restraints manager: 1.25 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=" 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 bond pdb=" C GLY B 355 " pdb=" N MET B 356 " ideal model delta sigma weight residual 1.328 1.206 0.122 1.62e-02 3.81e+03 5.68e+01 bond pdb=" C1' DG P 2 " pdb=" N9 DG P 2 " ideal model delta sigma weight residual 1.460 1.344 0.116 2.00e-02 2.50e+03 3.37e+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: 1409 0.082 - 0.165: 568 0.165 - 0.247: 93 0.247 - 0.329: 23 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: 1.310 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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= 0.754 Angle : 1.743 38.408 18977 Z= 1.087 Chirality : 0.088 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 aren 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 covalent geometry : bond 0.01260 (13932) covalent geometry : angle 1.66743 (18965) hydrogen bonds : bond 0.16596 ( 631) hydrogen bonds : angle 7.19588 ( 1771) metal coordination : bond 0.32325 ( 4) metal coordination : angle 20.25073 ( 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 : 0.610 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: 0.8501 (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: 0.1148 time to fit residues: 33.4228 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 : 0.563 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.072666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.061970 restraints weight = 62169.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.063266 restraints weight = 32748.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064109 restraints weight = 21200.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064651 restraints weight = 15920.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064976 restraints weight = 13225.699| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13936 Z= 0.156 Angle : 0.747 36.104 18977 Z= 0.342 Chirality : 0.044 0.152 2098 Planarity : 0.004 0.043 2365 Dihedral : 12.270 118.930 2038 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 1.35 % Allowed : 9.17 % Favored : 89.47 % 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 aren not related in a simple way. whole: 0.16 (0.20), residues: 1640 helix: 0.90 (0.20), residues: 636 sheet: 0.06 (0.30), residues: 282 loop : -0.50 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 325 TYR 0.019 0.002 TYR B 269 PHE 0.033 0.002 PHE E 830 TRP 0.015 0.002 TRP E1143 HIS 0.005 0.001 HIS E 388 Details of bonding type rmsd covalent geometry : bond 0.00335 (13932) covalent geometry : angle 0.65185 (18965) hydrogen bonds : bond 0.05057 ( 631) hydrogen bonds : angle 5.36911 ( 1771) metal coordination : bond 0.01228 ( 4) metal coordination : angle 14.56103 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8879 (mmm) cc_final: 0.8442 (mmm) REVERT: E 973 ASN cc_start: 0.7677 (m-40) cc_final: 0.7082 (t0) REVERT: E 981 LEU cc_start: 0.8893 (mt) cc_final: 0.8692 (mt) REVERT: E 1077 LEU cc_start: 0.8111 (tp) cc_final: 0.7778 (pp) REVERT: D 38 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7638 (tm-30) REVERT: D 96 LYS cc_start: 0.9136 (tttp) cc_final: 0.8640 (ttmm) REVERT: B 180 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8251 (mm) REVERT: B 363 MET cc_start: 0.8531 (mmt) cc_final: 0.7953 (mmt) outliers start: 19 outliers final: 6 residues processed: 139 average time/residue: 0.0999 time to fit residues: 21.0185 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1023 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 HIS E 999 GLN E1033 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056965 restraints weight = 63073.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058216 restraints weight = 32909.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059026 restraints weight = 21288.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059553 restraints weight = 15973.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059857 restraints weight = 13260.476| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13936 Z= 0.200 Angle : 0.722 28.359 18977 Z= 0.336 Chirality : 0.044 0.141 2098 Planarity : 0.005 0.038 2365 Dihedral : 11.852 108.889 2035 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 2.49 % Allowed : 9.03 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1640 helix: 1.17 (0.20), residues: 634 sheet: 0.06 (0.31), residues: 281 loop : -0.38 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 862 TYR 0.023 0.002 TYR E 488 PHE 0.026 0.002 PHE E 830 TRP 0.013 0.002 TRP E 683 HIS 0.007 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00446 (13932) covalent geometry : angle 0.65095 (18965) hydrogen bonds : bond 0.04812 ( 631) hydrogen bonds : angle 5.07288 ( 1771) metal coordination : bond 0.01104 ( 4) metal coordination : angle 12.46385 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.541 Fit side-chains REVERT: E 50 MET cc_start: 0.8941 (mmm) cc_final: 0.8638 (mmm) REVERT: E 287 MET cc_start: 0.8758 (ttp) cc_final: 0.8532 (ttm) REVERT: E 391 SER cc_start: 0.7526 (m) cc_final: 0.7165 (p) REVERT: E 694 MET cc_start: 0.7382 (tpt) cc_final: 0.6777 (tpt) REVERT: E 973 ASN cc_start: 0.8154 (m-40) cc_final: 0.7444 (t0) REVERT: E 1077 LEU cc_start: 0.8309 (tp) cc_final: 0.8039 (pp) REVERT: D 32 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8304 (ptp) REVERT: D 96 LYS cc_start: 0.9184 (tttp) cc_final: 0.8793 (ttmm) REVERT: B 282 ILE cc_start: 0.8776 (mm) cc_final: 0.8512 (mm) REVERT: B 363 MET cc_start: 0.8347 (mmt) cc_final: 0.7782 (mmt) outliers start: 35 outliers final: 22 residues processed: 126 average time/residue: 0.0929 time to fit residues: 18.3015 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 402 ILE 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 812 MET 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 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 859 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055258 restraints weight = 62917.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056423 restraints weight = 33893.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.057182 restraints weight = 22394.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.057678 restraints weight = 17058.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057992 restraints weight = 14290.660| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- 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 = 0.74 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 = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13936 Z= 0.236 Angle : 0.708 23.372 18977 Z= 0.335 Chirality : 0.044 0.150 2098 Planarity : 0.005 0.042 2365 Dihedral : 11.737 106.354 2035 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 2.70 % Allowed : 9.89 % Favored : 87.41 % 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 aren not related in a simple way. whole: 0.27 (0.20), residues: 1640 helix: 1.17 (0.20), residues: 643 sheet: -0.07 (0.32), residues: 258 loop : -0.55 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 18 TYR 0.022 0.002 TYR E1059 PHE 0.033 0.002 PHE E 830 TRP 0.010 0.002 TRP E1143 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00530 (13932) covalent geometry : angle 0.64599 (18965) hydrogen bonds : bond 0.04633 ( 631) hydrogen bonds : angle 5.08803 ( 1771) metal coordination : bond 0.01318 ( 4) metal coordination : angle 11.55582 ( 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 127 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.343 Fit side-chains REVERT: E 50 MET cc_start: 0.8930 (mmm) cc_final: 0.8363 (mmm) REVERT: E 287 MET cc_start: 0.8744 (ttp) cc_final: 0.8489 (ttp) REVERT: E 694 MET cc_start: 0.7439 (tpt) cc_final: 0.6869 (tpt) REVERT: E 858 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8734 (tp) REVERT: D 32 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8287 (ptp) REVERT: D 96 LYS cc_start: 0.9160 (tttp) cc_final: 0.8801 (ttmm) REVERT: B 86 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8976 (p) REVERT: B 180 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8488 (mm) REVERT: B 282 ILE cc_start: 0.8820 (mm) cc_final: 0.8545 (mm) REVERT: B 363 MET cc_start: 0.8398 (mmt) cc_final: 0.7801 (mmt) outliers start: 38 outliers final: 24 residues processed: 115 average time/residue: 0.0896 time to fit residues: 16.4826 Evaluate side-chains 108 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 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 812 MET 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 904 SER 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 32 MET 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 82 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 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 = 0.3285 r_free = 0.3285 target = 0.066272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055663 restraints weight = 63865.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056839 restraints weight = 34224.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057612 restraints weight = 22445.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058114 restraints weight = 17015.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058434 restraints weight = 14222.080| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.179 Angle : 0.637 21.143 18977 Z= 0.301 Chirality : 0.042 0.134 2098 Planarity : 0.004 0.045 2365 Dihedral : 11.508 107.441 2035 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 2.70 % Allowed : 10.46 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1640 helix: 1.41 (0.20), residues: 644 sheet: -0.08 (0.32), residues: 263 loop : -0.49 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1105 TYR 0.016 0.002 TYR E1059 PHE 0.021 0.002 PHE E 830 TRP 0.009 0.001 TRP E 683 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00399 (13932) covalent geometry : angle 0.58207 (18965) hydrogen bonds : bond 0.04293 ( 631) hydrogen bonds : angle 4.91289 ( 1771) metal coordination : bond 0.00931 ( 4) metal coordination : angle 10.27901 ( 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 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8878 (mmm) cc_final: 0.8478 (mmm) REVERT: E 287 MET cc_start: 0.8618 (ttp) cc_final: 0.8371 (ttp) REVERT: E 858 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8734 (tp) REVERT: E 973 ASN cc_start: 0.7803 (m-40) cc_final: 0.7201 (t0) REVERT: D 32 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8560 (ptp) REVERT: D 96 LYS cc_start: 0.9134 (tttp) cc_final: 0.8790 (ttmm) REVERT: B 86 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9033 (p) REVERT: B 282 ILE cc_start: 0.8851 (mm) cc_final: 0.8572 (mm) REVERT: B 363 MET cc_start: 0.8268 (mmt) cc_final: 0.7800 (mmt) outliers start: 38 outliers final: 26 residues processed: 112 average time/residue: 0.0877 time to fit residues: 15.8135 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 812 MET 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 904 SER 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 32 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054405 restraints weight = 64310.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055557 restraints weight = 34439.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056313 restraints weight = 22671.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056804 restraints weight = 17228.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.057120 restraints weight = 14438.292| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13936 Z= 0.236 Angle : 0.687 21.396 18977 Z= 0.326 Chirality : 0.044 0.205 2098 Planarity : 0.004 0.045 2365 Dihedral : 11.504 106.609 2035 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 3.27 % Allowed : 10.38 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1640 helix: 1.29 (0.20), residues: 643 sheet: -0.32 (0.31), residues: 270 loop : -0.53 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1105 TYR 0.016 0.002 TYR E 313 PHE 0.021 0.002 PHE E 830 TRP 0.009 0.002 TRP E 683 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00530 (13932) covalent geometry : angle 0.63337 (18965) hydrogen bonds : bond 0.04616 ( 631) hydrogen bonds : angle 5.04645 ( 1771) metal coordination : bond 0.01313 ( 4) metal coordination : angle 10.58019 ( 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 133 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8908 (mmm) cc_final: 0.8464 (mmm) REVERT: E 287 MET cc_start: 0.8669 (ttp) cc_final: 0.8415 (ttp) REVERT: E 843 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7769 (t) REVERT: E 858 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8544 (tp) REVERT: E 973 ASN cc_start: 0.8015 (m-40) cc_final: 0.7304 (t0) REVERT: D 32 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8391 (ptp) REVERT: D 96 LYS cc_start: 0.9132 (tttp) cc_final: 0.8792 (ttmm) REVERT: B 86 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9030 (p) REVERT: B 282 ILE cc_start: 0.8816 (mm) cc_final: 0.8517 (mm) REVERT: B 363 MET cc_start: 0.8267 (mmt) cc_final: 0.7787 (mmt) outliers start: 46 outliers final: 34 residues processed: 122 average time/residue: 0.0942 time to fit residues: 18.3633 Evaluate side-chains 122 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 391 SER 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 771 VAL Chi-restraints excluded: chain E residue 812 MET 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 904 SER Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 914 VAL 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 32 MET 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 82 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 999 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 = 0.3298 r_free = 0.3298 target = 0.066682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056068 restraints weight = 63547.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057237 restraints weight = 33995.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058013 restraints weight = 22387.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058514 restraints weight = 16946.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058813 restraints weight = 14178.045| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13936 Z= 0.133 Angle : 0.603 18.759 18977 Z= 0.284 Chirality : 0.041 0.141 2098 Planarity : 0.004 0.049 2365 Dihedral : 11.321 108.742 2035 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.28 % Allowed : 11.38 % 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 aren not related in a simple way. whole: 0.56 (0.21), residues: 1640 helix: 1.59 (0.21), residues: 646 sheet: -0.17 (0.32), residues: 261 loop : -0.46 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1105 TYR 0.016 0.001 TYR E1059 PHE 0.019 0.001 PHE E 830 TRP 0.010 0.001 TRP E 683 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00291 (13932) covalent geometry : angle 0.55563 (18965) hydrogen bonds : bond 0.03947 ( 631) hydrogen bonds : angle 4.78643 ( 1771) metal coordination : bond 0.00704 ( 4) metal coordination : angle 9.29865 ( 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 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8841 (mmm) cc_final: 0.8580 (mmm) REVERT: E 287 MET cc_start: 0.8450 (ttp) cc_final: 0.8242 (ttp) REVERT: E 843 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7563 (t) REVERT: E 858 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8687 (tp) REVERT: E 973 ASN cc_start: 0.7991 (m-40) cc_final: 0.7314 (t0) REVERT: D 32 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8397 (ptp) REVERT: B 86 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9023 (p) REVERT: B 180 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8426 (mm) REVERT: B 282 ILE cc_start: 0.8830 (mm) cc_final: 0.8546 (mm) REVERT: B 363 MET cc_start: 0.8225 (mmt) cc_final: 0.7715 (mmt) outliers start: 32 outliers final: 24 residues processed: 117 average time/residue: 0.0953 time to fit residues: 17.6162 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 904 SER 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 1141 ILE Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 32 MET 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 70 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 LEU 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: 1.9990 chunk 111 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 937 HIS E 999 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.065979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055367 restraints weight = 63527.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056534 restraints weight = 34017.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057302 restraints weight = 22376.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057791 restraints weight = 16972.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058077 restraints weight = 14229.512| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.175 Angle : 0.632 19.657 18977 Z= 0.299 Chirality : 0.042 0.155 2098 Planarity : 0.004 0.046 2365 Dihedral : 11.306 108.554 2035 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.72 % Favored : 96.16 % Rotamer: Outliers : 2.84 % Allowed : 11.24 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.21), residues: 1640 helix: 1.55 (0.20), residues: 645 sheet: -0.25 (0.32), residues: 265 loop : -0.42 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1105 TYR 0.024 0.002 TYR E1059 PHE 0.018 0.002 PHE E 830 TRP 0.031 0.001 TRP B 284 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00393 (13932) covalent geometry : angle 0.58466 (18965) hydrogen bonds : bond 0.04128 ( 631) hydrogen bonds : angle 4.84914 ( 1771) metal coordination : bond 0.00985 ( 4) metal coordination : angle 9.57306 ( 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: 40 poor density : 87 time to evaluate : 0.545 Fit side-chains REVERT: E 50 MET cc_start: 0.8863 (mmm) cc_final: 0.8573 (mmm) REVERT: E 120 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: E 287 MET cc_start: 0.8457 (ttp) cc_final: 0.8251 (ttp) REVERT: E 843 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7640 (t) REVERT: E 909 MET cc_start: 0.8344 (ptt) cc_final: 0.8121 (ptt) REVERT: E 973 ASN cc_start: 0.8130 (m-40) cc_final: 0.7396 (t0) REVERT: D 32 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8529 (ptp) REVERT: B 86 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9043 (p) REVERT: B 282 ILE cc_start: 0.8840 (mm) cc_final: 0.8561 (mm) REVERT: B 363 MET cc_start: 0.8283 (mmt) cc_final: 0.7730 (mmt) outliers start: 40 outliers final: 30 residues processed: 117 average time/residue: 0.0853 time to fit residues: 16.1307 Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 134 VAL 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 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 904 SER 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 1005 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 32 MET 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 70 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 20.0000 chunk 57 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 828 ASN E 859 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056862 restraints weight = 63890.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058054 restraints weight = 33968.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058829 restraints weight = 22276.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059321 restraints weight = 16894.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059653 restraints weight = 14180.163| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13936 Z= 0.112 Angle : 0.587 18.259 18977 Z= 0.276 Chirality : 0.041 0.150 2098 Planarity : 0.004 0.050 2365 Dihedral : 11.168 109.577 2035 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.28 % Allowed : 11.52 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.21), residues: 1640 helix: 1.78 (0.21), residues: 645 sheet: -0.15 (0.32), residues: 267 loop : -0.34 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1105 TYR 0.010 0.001 TYR E 313 PHE 0.017 0.001 PHE E 830 TRP 0.028 0.001 TRP B 284 HIS 0.003 0.000 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00245 (13932) covalent geometry : angle 0.54130 (18965) hydrogen bonds : bond 0.03630 ( 631) hydrogen bonds : angle 4.65940 ( 1771) metal coordination : bond 0.00557 ( 4) metal coordination : angle 9.08616 ( 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 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: C 739 LEU cc_start: 0.8557 (mp) cc_final: 0.8353 (mt) REVERT: E 50 MET cc_start: 0.8750 (mmm) cc_final: 0.8349 (mmm) REVERT: E 120 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: E 843 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7461 (t) REVERT: E 909 MET cc_start: 0.8281 (ptt) cc_final: 0.8000 (ptt) REVERT: E 973 ASN cc_start: 0.8130 (m-40) cc_final: 0.7394 (t0) REVERT: D 32 MET cc_start: 0.8869 (ptm) cc_final: 0.8461 (ptp) REVERT: D 38 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 86 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9029 (p) REVERT: B 282 ILE cc_start: 0.8821 (mm) cc_final: 0.8532 (mm) REVERT: B 296 ILE cc_start: 0.8701 (tp) cc_final: 0.8475 (tp) REVERT: B 363 MET cc_start: 0.8167 (mmt) cc_final: 0.7622 (mmt) outliers start: 32 outliers final: 28 residues processed: 119 average time/residue: 0.0931 time to fit residues: 17.5404 Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS 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 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 1005 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 D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 101 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 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 = 0.3352 r_free = 0.3352 target = 0.068627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058071 restraints weight = 63479.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059299 restraints weight = 33617.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060099 restraints weight = 21912.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060606 restraints weight = 16566.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060938 restraints weight = 13827.269| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13936 Z= 0.100 Angle : 0.580 18.535 18977 Z= 0.270 Chirality : 0.040 0.154 2098 Planarity : 0.004 0.044 2365 Dihedral : 11.029 109.860 2035 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.13 % Allowed : 11.95 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.21), residues: 1640 helix: 1.90 (0.21), residues: 651 sheet: 0.03 (0.33), residues: 260 loop : -0.34 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1105 TYR 0.010 0.001 TYR B 95 PHE 0.025 0.001 PHE E 830 TRP 0.023 0.001 TRP B 284 HIS 0.004 0.000 HIS E 557 Details of bonding type rmsd covalent geometry : bond 0.00217 (13932) covalent geometry : angle 0.53310 (18965) hydrogen bonds : bond 0.03338 ( 631) hydrogen bonds : angle 4.50257 ( 1771) metal coordination : bond 0.00447 ( 4) metal coordination : angle 9.10718 ( 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 128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8593 (mmm) cc_final: 0.8393 (mmm) REVERT: E 120 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: E 437 GLN cc_start: 0.8315 (mt0) cc_final: 0.7607 (mp10) REVERT: E 447 LEU cc_start: 0.8185 (tp) cc_final: 0.7961 (tp) REVERT: E 843 SER cc_start: 0.7527 (OUTLIER) cc_final: 0.7276 (t) REVERT: E 909 MET cc_start: 0.8218 (ptt) cc_final: 0.7811 (ptt) REVERT: D 32 MET cc_start: 0.8834 (ptm) cc_final: 0.8503 (ptp) REVERT: D 38 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7239 (tm-30) REVERT: B 86 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9066 (p) REVERT: B 270 VAL cc_start: 0.9047 (t) cc_final: 0.8798 (t) REVERT: B 296 ILE cc_start: 0.8606 (tp) cc_final: 0.8398 (tp) REVERT: B 363 MET cc_start: 0.8075 (mmt) cc_final: 0.7542 (mmt) outliers start: 30 outliers final: 24 residues processed: 122 average time/residue: 0.0814 time to fit residues: 16.0587 Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS 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 879 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 1005 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 70 LEU 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: 5.9990 chunk 70 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 823 HIS E 859 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.054713 restraints weight = 65116.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055836 restraints weight = 35508.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056570 restraints weight = 23639.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057041 restraints weight = 18150.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057296 restraints weight = 15308.959| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13936 Z= 0.235 Angle : 0.697 22.331 18977 Z= 0.330 Chirality : 0.043 0.154 2098 Planarity : 0.005 0.049 2365 Dihedral : 11.165 107.236 2035 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 2.35 % Allowed : 11.81 % Favored : 85.85 % 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 aren not related in a simple way. whole: 0.56 (0.21), residues: 1640 helix: 1.59 (0.20), residues: 643 sheet: -0.34 (0.31), residues: 267 loop : -0.40 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1105 TYR 0.021 0.002 TYR E1059 PHE 0.026 0.002 PHE E 830 TRP 0.021 0.002 TRP B 284 HIS 0.004 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00530 (13932) covalent geometry : angle 0.64562 (18965) hydrogen bonds : bond 0.04412 ( 631) hydrogen bonds : angle 4.88809 ( 1771) metal coordination : bond 0.01412 ( 4) metal coordination : angle 10.43097 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.89 seconds wall clock time: 35 minutes 9.34 seconds (2109.34 seconds total)