Starting phenix.real_space_refine on Mon Dec 30 15:30:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw9_41663/12_2024/8tw9_41663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw9_41663/12_2024/8tw9_41663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw9_41663/12_2024/8tw9_41663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw9_41663/12_2024/8tw9_41663.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw9_41663/12_2024/8tw9_41663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw9_41663/12_2024/8tw9_41663.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ASP:plan': 5} 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: {'GLN:plan1': 2, 'GLU:plan': 1, '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: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4} 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: 8.34, per 1000 atoms: 0.61 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: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.28 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: 5.77 Time building geometry restraints manager: 3.88 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: 1.010 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 41.040 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- 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 : 0.013 0.225 13932 Z= 0.808 Angle : 1.667 19.676 18965 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 : 9.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (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 TRP 0.106 0.012 TRP E 384 HIS 0.021 0.004 HIS E 388 PHE 0.071 0.010 PHE E 347 TYR 0.119 0.016 TYR E 485 ARG 0.017 0.002 ARG E 781 *********************** 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 : 1.777 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: 0.7195 (m-80) REVERT: E 286 VAL cc_start: 0.8501 (t) cc_final: 0.8226 (p) REVERT: E 651 THR cc_start: 0.8696 (m) cc_final: 0.8425 (p) REVERT: E 1154 ILE cc_start: 0.8453 (mt) cc_final: 0.8244 (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: 0.2808 time to fit residues: 81.5827 Evaluate side-chains 106 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 139 optimal weight: 0.0470 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 728 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13932 Z= 0.199 Angle : 0.642 13.496 18965 Z= 0.336 Chirality : 0.044 0.162 2098 Planarity : 0.004 0.043 2365 Dihedral : 12.259 118.977 2038 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 1.35 % Allowed : 8.89 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1640 helix: 0.93 (0.20), residues: 636 sheet: 0.04 (0.30), residues: 282 loop : -0.48 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1143 HIS 0.004 0.001 HIS E 388 PHE 0.033 0.002 PHE E 830 TYR 0.017 0.002 TYR B 269 ARG 0.005 0.001 ARG E 325 *********************** 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 149 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8836 (mmm) cc_final: 0.8395 (mmm) REVERT: E 188 LEU cc_start: 0.8844 (mt) cc_final: 0.8541 (mp) REVERT: E 286 VAL cc_start: 0.8668 (t) cc_final: 0.8458 (p) REVERT: E 772 ASP cc_start: 0.8490 (t0) cc_final: 0.8272 (t0) REVERT: E 812 MET cc_start: 0.9128 (ttm) cc_final: 0.8906 (ttp) REVERT: E 973 ASN cc_start: 0.7510 (m-40) cc_final: 0.7063 (t0) REVERT: E 1077 LEU cc_start: 0.8241 (tp) cc_final: 0.7913 (pp) REVERT: D 30 MET cc_start: 0.7590 (mmt) cc_final: 0.7349 (mmp) REVERT: D 38 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7540 (tm-30) REVERT: D 96 LYS cc_start: 0.9260 (tttp) cc_final: 0.8600 (ttmm) REVERT: B 180 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8249 (mm) REVERT: B 363 MET cc_start: 0.8697 (mmt) cc_final: 0.8122 (mmt) outliers start: 19 outliers final: 6 residues processed: 143 average time/residue: 0.2524 time to fit residues: 54.7398 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 HIS E1033 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13932 Z= 0.243 Angle : 0.616 11.006 18965 Z= 0.316 Chirality : 0.043 0.145 2098 Planarity : 0.004 0.040 2365 Dihedral : 11.825 110.546 2035 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.26 % Rotamer: Outliers : 1.99 % Allowed : 9.46 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1640 helix: 1.33 (0.21), residues: 635 sheet: 0.09 (0.31), residues: 287 loop : -0.26 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 683 HIS 0.006 0.001 HIS B 166 PHE 0.030 0.002 PHE E 830 TYR 0.017 0.002 TYR E 488 ARG 0.003 0.000 ARG B 267 *********************** 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 141 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.832 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8874 (mmm) cc_final: 0.8550 (mmm) REVERT: E 391 SER cc_start: 0.7562 (m) cc_final: 0.7226 (p) REVERT: E 694 MET cc_start: 0.7903 (tpt) cc_final: 0.7294 (tpt) REVERT: E 926 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8466 (tp) REVERT: E 973 ASN cc_start: 0.7894 (m-40) cc_final: 0.7402 (t0) REVERT: E 1077 LEU cc_start: 0.8333 (tp) cc_final: 0.8103 (pp) REVERT: D 38 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7528 (tm-30) REVERT: D 96 LYS cc_start: 0.9306 (tttp) cc_final: 0.8753 (ttmm) REVERT: B 136 MET cc_start: 0.7898 (mtm) cc_final: 0.7572 (mtm) REVERT: B 282 ILE cc_start: 0.8731 (mm) cc_final: 0.8477 (mm) REVERT: B 363 MET cc_start: 0.8433 (mmt) cc_final: 0.7837 (mmt) outliers start: 28 outliers final: 17 residues processed: 130 average time/residue: 0.2362 time to fit residues: 48.2949 Evaluate side-chains 113 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 926 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 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 148 optimal weight: 10.0000 chunk 112 optimal weight: 0.0770 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 0.0770 chunk 71 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13932 Z= 0.211 Angle : 0.568 10.546 18965 Z= 0.291 Chirality : 0.042 0.161 2098 Planarity : 0.004 0.045 2365 Dihedral : 11.614 107.436 2035 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.68 % Favored : 97.20 % Rotamer: Outliers : 2.49 % Allowed : 9.67 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1640 helix: 1.62 (0.21), residues: 636 sheet: 0.24 (0.32), residues: 273 loop : -0.22 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1143 HIS 0.003 0.001 HIS B 166 PHE 0.027 0.002 PHE E 830 TYR 0.019 0.001 TYR E1059 ARG 0.004 0.000 ARG B 267 *********************** 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 136 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8821 (mmm) cc_final: 0.8604 (mmm) REVERT: E 391 SER cc_start: 0.7665 (m) cc_final: 0.7248 (p) REVERT: E 694 MET cc_start: 0.7993 (tpt) cc_final: 0.7469 (tpt) REVERT: E 973 ASN cc_start: 0.8039 (m-40) cc_final: 0.7474 (t0) REVERT: E 1077 LEU cc_start: 0.8392 (tp) cc_final: 0.8097 (pp) REVERT: D 38 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7463 (tm-30) REVERT: D 96 LYS cc_start: 0.9304 (tttp) cc_final: 0.8771 (ttmm) REVERT: B 86 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 282 ILE cc_start: 0.8788 (mm) cc_final: 0.8526 (mm) REVERT: B 363 MET cc_start: 0.8408 (mmt) cc_final: 0.7854 (mmt) outliers start: 35 outliers final: 20 residues processed: 124 average time/residue: 0.2376 time to fit residues: 46.4896 Evaluate side-chains 116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 459 MET 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 907 CYS Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13932 Z= 0.318 Angle : 0.629 9.124 18965 Z= 0.326 Chirality : 0.044 0.207 2098 Planarity : 0.004 0.050 2365 Dihedral : 11.501 104.101 2035 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 2.70 % Allowed : 9.96 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1640 helix: 1.34 (0.20), residues: 643 sheet: 0.13 (0.32), residues: 272 loop : -0.42 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 284 HIS 0.005 0.001 HIS B 166 PHE 0.028 0.002 PHE E 830 TYR 0.020 0.002 TYR E 488 ARG 0.003 0.001 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 1.654 Fit side-chains REVERT: E 50 MET cc_start: 0.8902 (mmm) cc_final: 0.8374 (mmm) REVERT: E 694 MET cc_start: 0.8043 (tpt) cc_final: 0.7485 (tpt) REVERT: D 32 MET cc_start: 0.8905 (ptm) cc_final: 0.8659 (ptp) REVERT: D 76 ASP cc_start: 0.8682 (m-30) cc_final: 0.8444 (m-30) REVERT: D 96 LYS cc_start: 0.9284 (tttp) cc_final: 0.8766 (ttmm) REVERT: B 86 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8601 (p) REVERT: B 282 ILE cc_start: 0.8813 (mm) cc_final: 0.8538 (mm) REVERT: B 363 MET cc_start: 0.8457 (mmt) cc_final: 0.7923 (mmt) outliers start: 38 outliers final: 25 residues processed: 117 average time/residue: 0.2280 time to fit residues: 43.2709 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 812 MET Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 858 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 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 53 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13932 Z= 0.244 Angle : 0.580 8.745 18965 Z= 0.298 Chirality : 0.042 0.163 2098 Planarity : 0.004 0.047 2365 Dihedral : 11.425 104.773 2035 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 10.31 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1640 helix: 1.52 (0.20), residues: 644 sheet: 0.01 (0.32), residues: 266 loop : -0.38 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.004 0.001 HIS B 166 PHE 0.023 0.002 PHE E 830 TYR 0.019 0.002 TYR E1059 ARG 0.006 0.000 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8870 (mmm) cc_final: 0.8448 (mmm) REVERT: E 843 SER cc_start: 0.7528 (OUTLIER) cc_final: 0.7177 (t) REVERT: D 96 LYS cc_start: 0.9266 (tttp) cc_final: 0.8761 (ttmm) REVERT: B 86 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8548 (p) REVERT: B 180 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8337 (mm) REVERT: B 282 ILE cc_start: 0.8855 (mm) cc_final: 0.8579 (mm) REVERT: B 363 MET cc_start: 0.8382 (mmt) cc_final: 0.7915 (mmt) outliers start: 36 outliers final: 28 residues processed: 115 average time/residue: 0.2247 time to fit residues: 41.5534 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 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 843 SER Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 926 LEU Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13932 Z= 0.313 Angle : 0.621 12.183 18965 Z= 0.316 Chirality : 0.043 0.168 2098 Planarity : 0.004 0.048 2365 Dihedral : 11.401 104.763 2035 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 2.63 % Allowed : 10.10 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1640 helix: 1.42 (0.20), residues: 644 sheet: -0.23 (0.31), residues: 270 loop : -0.43 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 284 HIS 0.005 0.001 HIS B 166 PHE 0.022 0.002 PHE E 830 TYR 0.021 0.002 TYR E1059 ARG 0.004 0.000 ARG B 267 *********************** 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 123 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8891 (mmm) cc_final: 0.8469 (mmm) REVERT: E 909 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8293 (ptt) REVERT: E 973 ASN cc_start: 0.7714 (m-40) cc_final: 0.7210 (t0) REVERT: D 96 LYS cc_start: 0.9269 (tttp) cc_final: 0.8732 (ttmm) REVERT: B 86 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8570 (p) REVERT: B 180 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8515 (mm) REVERT: B 282 ILE cc_start: 0.8817 (mm) cc_final: 0.8525 (mm) REVERT: B 363 MET cc_start: 0.8453 (mmt) cc_final: 0.7955 (mmt) outliers start: 37 outliers final: 29 residues processed: 114 average time/residue: 0.2342 time to fit residues: 42.7286 Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 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 904 SER Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 909 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1103 THR Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 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 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 63 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 937 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13932 Z= 0.236 Angle : 0.574 8.607 18965 Z= 0.294 Chirality : 0.042 0.147 2098 Planarity : 0.004 0.049 2365 Dihedral : 11.305 106.077 2035 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 10.46 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1640 helix: 1.57 (0.20), residues: 646 sheet: -0.15 (0.32), residues: 264 loop : -0.43 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 683 HIS 0.004 0.001 HIS B 166 PHE 0.020 0.002 PHE E 830 TYR 0.018 0.001 TYR E1059 ARG 0.003 0.000 ARG E1105 *********************** 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 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8846 (mmm) cc_final: 0.8496 (mmm) REVERT: E 843 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.7172 (t) REVERT: E 973 ASN cc_start: 0.7769 (m-40) cc_final: 0.7266 (t0) REVERT: D 96 LYS cc_start: 0.9253 (tttp) cc_final: 0.8758 (ttmm) REVERT: B 86 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8491 (p) REVERT: B 180 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 275 MET cc_start: 0.8696 (tmm) cc_final: 0.8482 (tmm) REVERT: B 282 ILE cc_start: 0.8811 (mm) cc_final: 0.8516 (mm) REVERT: B 363 MET cc_start: 0.8399 (mmt) cc_final: 0.7873 (mmt) outliers start: 35 outliers final: 28 residues processed: 119 average time/residue: 0.2328 time to fit residues: 44.0277 Evaluate side-chains 118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 843 SER Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 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 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 180 LEU 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 152 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 0.044 13932 Z= 0.282 Angle : 0.599 9.377 18965 Z= 0.306 Chirality : 0.043 0.144 2098 Planarity : 0.004 0.047 2365 Dihedral : 11.295 106.724 2035 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 2.49 % Allowed : 10.46 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1640 helix: 1.54 (0.20), residues: 646 sheet: -0.28 (0.32), residues: 265 loop : -0.39 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 683 HIS 0.004 0.001 HIS B 166 PHE 0.020 0.002 PHE E 830 TYR 0.019 0.002 TYR E1059 ARG 0.003 0.000 ARG E1105 *********************** 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 122 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8845 (mmm) cc_final: 0.8507 (mmm) REVERT: E 843 SER cc_start: 0.7568 (OUTLIER) cc_final: 0.7221 (t) REVERT: E 909 MET cc_start: 0.8338 (ptt) cc_final: 0.8050 (ptt) REVERT: E 973 ASN cc_start: 0.7797 (m-40) cc_final: 0.7278 (t0) REVERT: D 96 LYS cc_start: 0.9258 (tttp) cc_final: 0.8763 (ttmm) REVERT: B 86 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 180 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8578 (mm) REVERT: B 194 MET cc_start: 0.8226 (mtp) cc_final: 0.8025 (mtp) REVERT: B 282 ILE cc_start: 0.8828 (mm) cc_final: 0.8545 (mm) REVERT: B 363 MET cc_start: 0.8439 (mmt) cc_final: 0.7943 (mmt) outliers start: 35 outliers final: 31 residues processed: 116 average time/residue: 0.2391 time to fit residues: 45.1016 Evaluate side-chains 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 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 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 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 180 LEU 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 156 optimal weight: 0.0970 chunk 95 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 828 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13932 Z= 0.161 Angle : 0.544 9.345 18965 Z= 0.277 Chirality : 0.041 0.142 2098 Planarity : 0.004 0.049 2365 Dihedral : 11.137 108.417 2035 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 1.85 % Allowed : 11.17 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1640 helix: 1.73 (0.21), residues: 657 sheet: -0.12 (0.33), residues: 259 loop : -0.34 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 683 HIS 0.003 0.001 HIS B 166 PHE 0.019 0.001 PHE E 830 TYR 0.015 0.001 TYR E1059 ARG 0.003 0.000 ARG B 267 ********************** 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 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 2.482 Fit side-chains REVERT: E 843 SER cc_start: 0.7239 (OUTLIER) cc_final: 0.6966 (t) REVERT: E 909 MET cc_start: 0.8185 (ptt) cc_final: 0.7814 (ptt) REVERT: E 973 ASN cc_start: 0.7823 (m-40) cc_final: 0.7292 (t0) REVERT: D 96 LYS cc_start: 0.9233 (tttp) cc_final: 0.8748 (ttmm) REVERT: B 86 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8474 (p) REVERT: B 180 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 282 ILE cc_start: 0.8851 (mm) cc_final: 0.8559 (mm) REVERT: B 363 MET cc_start: 0.8313 (mmt) cc_final: 0.7807 (mmt) outliers start: 26 outliers final: 22 residues processed: 115 average time/residue: 0.2515 time to fit residues: 45.3461 Evaluate side-chains 112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 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 858 ILE Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain E residue 1141 ILE Chi-restraints excluded: chain E residue 1150 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 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 180 LEU 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 139 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 0.0570 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 131 optimal weight: 0.0970 chunk 54 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 overall best weight: 1.8316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 444 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056699 restraints weight = 64158.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057894 restraints weight = 34105.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058659 restraints weight = 22314.498| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13932 Z= 0.170 Angle : 0.560 13.056 18965 Z= 0.282 Chirality : 0.041 0.151 2098 Planarity : 0.004 0.048 2365 Dihedral : 11.089 108.506 2035 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 1.85 % Allowed : 11.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1640 helix: 1.75 (0.20), residues: 658 sheet: -0.10 (0.33), residues: 259 loop : -0.31 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 425 HIS 0.003 0.001 HIS B 166 PHE 0.023 0.001 PHE E 830 TYR 0.014 0.001 TYR E1059 ARG 0.005 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.93 seconds wall clock time: 43 minutes 49.17 seconds (2629.17 seconds total)