Starting phenix.real_space_refine on Thu Jul 31 11:22:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw9_41663/07_2025/8tw9_41663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw9_41663/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2025/8tw9_41663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2025/8tw9_41663.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2025/8tw9_41663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw9_41663/07_2025/8tw9_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.76, per 1000 atoms: 0.57 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 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: 4.50 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: 4.81 Time building geometry restraints manager: 3.70 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- 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 : 9.65 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 Details of bonding type rmsd hydrogen bonds : bond 0.16596 ( 631) hydrogen bonds : angle 7.19588 ( 1771) metal coordination : bond 0.32325 ( 4) metal coordination : angle 20.25073 ( 12) covalent geometry : bond 0.01260 (13932) covalent geometry : angle 1.66743 (18965) *********************** 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 : 1.472 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: 0.2733 time to fit residues: 79.1255 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 : 1.717 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.073472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062845 restraints weight = 61643.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064149 restraints weight = 32395.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064993 restraints weight = 20960.677| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- 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 = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13936 Z= 0.148 Angle : 0.734 35.456 18977 Z= 0.337 Chirality : 0.044 0.161 2098 Planarity : 0.004 0.043 2365 Dihedral : 12.258 118.900 2038 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.11 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 0.018 0.002 TYR B 269 ARG 0.005 0.001 ARG E 325 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 631) hydrogen bonds : angle 5.32868 ( 1771) metal coordination : bond 0.01247 ( 4) metal coordination : angle 14.10635 ( 12) covalent geometry : bond 0.00312 (13932) covalent geometry : angle 0.64286 (18965) *********************** 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 151 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 MET cc_start: 0.8841 (mmm) cc_final: 0.8427 (mmm) REVERT: E 188 LEU cc_start: 0.8801 (mt) cc_final: 0.8534 (mp) REVERT: E 973 ASN cc_start: 0.7664 (m-40) cc_final: 0.7070 (t0) REVERT: E 981 LEU cc_start: 0.8873 (mt) cc_final: 0.8652 (mt) REVERT: E 1077 LEU cc_start: 0.8122 (tp) cc_final: 0.7763 (pp) REVERT: D 38 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7725 (tm-30) REVERT: D 96 LYS cc_start: 0.9120 (tttp) cc_final: 0.8630 (ttmm) REVERT: B 136 MET cc_start: 0.8171 (mtm) cc_final: 0.7919 (mtm) REVERT: B 180 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 363 MET cc_start: 0.8548 (mmt) cc_final: 0.7965 (mmt) outliers start: 19 outliers final: 6 residues processed: 145 average time/residue: 0.2902 time to fit residues: 63.4284 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 : 1.832 ------------------------------------------------------------------------------- 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 128 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055421 restraints weight = 63335.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056636 restraints weight = 33228.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.057420 restraints weight = 21605.222| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13936 Z= 0.280 Angle : 0.824 30.752 18977 Z= 0.383 Chirality : 0.047 0.172 2098 Planarity : 0.005 0.047 2365 Dihedral : 12.000 108.757 2035 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 2.42 % Allowed : 9.46 % Favored : 88.12 % 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: 0.07 (0.20), residues: 1640 helix: 0.85 (0.20), residues: 633 sheet: 0.07 (0.32), residues: 264 loop : -0.59 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 683 HIS 0.008 0.002 HIS B 166 PHE 0.026 0.003 PHE E 830 TYR 0.031 0.003 TYR E 488 ARG 0.005 0.001 ARG E 862 Details of bonding type rmsd hydrogen bonds : bond 0.05460 ( 631) hydrogen bonds : angle 5.35190 ( 1771) metal coordination : bond 0.01643 ( 4) metal coordination : angle 14.30561 ( 12) covalent geometry : bond 0.00624 (13932) covalent geometry : angle 0.74155 (18965) *********************** 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 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 4.011 Fit side-chains REVERT: E 50 MET cc_start: 0.8957 (mmm) cc_final: 0.8287 (mmm) REVERT: E 188 LEU cc_start: 0.8982 (mt) cc_final: 0.8629 (mp) REVERT: E 391 SER cc_start: 0.7687 (m) cc_final: 0.7264 (p) REVERT: E 926 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8648 (tt) REVERT: E 973 ASN cc_start: 0.8205 (m-40) cc_final: 0.7480 (t0) REVERT: E 1077 LEU cc_start: 0.8337 (tp) cc_final: 0.8121 (pp) REVERT: D 32 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8497 (ptp) REVERT: D 96 LYS cc_start: 0.9209 (tttp) cc_final: 0.8795 (ttmm) REVERT: B 180 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8487 (mm) REVERT: B 282 ILE cc_start: 0.8784 (mm) cc_final: 0.8512 (mm) REVERT: B 363 MET cc_start: 0.8419 (mmt) cc_final: 0.7882 (mmt) outliers start: 34 outliers final: 22 residues processed: 116 average time/residue: 0.3300 time to fit residues: 61.9186 Evaluate side-chains 107 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 771 VAL Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 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 4 VAL Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057198 restraints weight = 62355.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058447 restraints weight = 32499.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059250 restraints weight = 21030.605| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13936 Z= 0.136 Angle : 0.632 24.684 18977 Z= 0.294 Chirality : 0.042 0.162 2098 Planarity : 0.004 0.045 2365 Dihedral : 11.719 108.930 2035 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 2.13 % Allowed : 10.24 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.21), residues: 636 sheet: 0.13 (0.32), residues: 278 loop : -0.35 (0.23), residues: 726 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 0.022 0.001 PHE E 830 TYR 0.018 0.001 TYR E1059 ARG 0.003 0.000 ARG B 267 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 631) hydrogen bonds : angle 4.94427 ( 1771) metal coordination : bond 0.00725 ( 4) metal coordination : angle 11.12096 ( 12) covalent geometry : bond 0.00300 (13932) covalent geometry : angle 0.56673 (18965) *********************** 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 130 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 1.902 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8910 (mmm) cc_final: 0.8492 (mmm) REVERT: E 188 LEU cc_start: 0.8869 (mt) cc_final: 0.8593 (mp) REVERT: E 391 SER cc_start: 0.7706 (m) cc_final: 0.7302 (p) REVERT: E 694 MET cc_start: 0.7405 (tpt) cc_final: 0.6855 (tpt) REVERT: E 926 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8684 (tt) REVERT: E 973 ASN cc_start: 0.8239 (m-40) cc_final: 0.7473 (t0) REVERT: E 1030 LEU cc_start: 0.9260 (mp) cc_final: 0.9057 (mp) REVERT: E 1077 LEU cc_start: 0.8337 (tp) cc_final: 0.8042 (pp) REVERT: D 32 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8369 (ptp) REVERT: D 96 LYS cc_start: 0.9163 (tttp) cc_final: 0.8792 (ttmm) REVERT: B 86 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8943 (p) REVERT: B 282 ILE cc_start: 0.8809 (mm) cc_final: 0.8539 (mm) REVERT: B 363 MET cc_start: 0.8371 (mmt) cc_final: 0.7842 (mmt) outliers start: 30 outliers final: 15 residues processed: 121 average time/residue: 0.3165 time to fit residues: 60.2058 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 727 SER Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 904 SER Chi-restraints excluded: chain E residue 907 CYS Chi-restraints excluded: chain E residue 926 LEU Chi-restraints excluded: chain E residue 971 VAL Chi-restraints excluded: chain E residue 1023 CYS Chi-restraints excluded: chain 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 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3270 r_free = 0.3270 target = 0.065648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055082 restraints weight = 63910.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056260 restraints weight = 34142.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.057016 restraints weight = 22412.327| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13936 Z= 0.231 Angle : 0.690 23.101 18977 Z= 0.327 Chirality : 0.044 0.210 2098 Planarity : 0.005 0.047 2365 Dihedral : 11.601 106.711 2035 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 2.42 % Allowed : 10.38 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.21), residues: 1640 helix: 1.17 (0.20), residues: 643 sheet: -0.11 (0.32), residues: 269 loop : -0.49 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 880 HIS 0.005 0.001 HIS E 535 PHE 0.025 0.002 PHE E 830 TYR 0.018 0.002 TYR E1059 ARG 0.003 0.001 ARG E 862 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 631) hydrogen bonds : angle 5.05394 ( 1771) metal coordination : bond 0.01337 ( 4) metal coordination : angle 11.11731 ( 12) covalent geometry : bond 0.00520 (13932) covalent geometry : angle 0.63086 (18965) *********************** 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 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 1.480 Fit side-chains REVERT: E 50 MET cc_start: 0.8927 (mmm) cc_final: 0.8433 (mmm) REVERT: E 694 MET cc_start: 0.7539 (tpt) cc_final: 0.6995 (tpt) REVERT: E 973 ASN cc_start: 0.8372 (m-40) cc_final: 0.7662 (t0) REVERT: E 1030 LEU cc_start: 0.9260 (mp) cc_final: 0.9054 (mp) REVERT: E 1077 LEU cc_start: 0.8324 (tp) cc_final: 0.8119 (pp) REVERT: D 32 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8252 (ptp) REVERT: D 96 LYS cc_start: 0.9154 (tttp) cc_final: 0.8788 (ttmm) REVERT: B 86 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9029 (p) REVERT: B 282 ILE cc_start: 0.8812 (mm) cc_final: 0.8536 (mm) REVERT: B 363 MET cc_start: 0.8374 (mmt) cc_final: 0.7788 (mmt) outliers start: 34 outliers final: 25 residues processed: 110 average time/residue: 0.2110 time to fit residues: 37.0801 Evaluate side-chains 109 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 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 32 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.056608 restraints weight = 63705.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057813 restraints weight = 34070.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058592 restraints weight = 22354.315| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 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 = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13936 Z= 0.125 Angle : 0.600 20.352 18977 Z= 0.283 Chirality : 0.041 0.155 2098 Planarity : 0.004 0.044 2365 Dihedral : 11.416 107.822 2035 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 1.99 % Allowed : 11.10 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.21), residues: 645 sheet: -0.11 (0.32), residues: 274 loop : -0.40 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 683 HIS 0.003 0.001 HIS B 166 PHE 0.022 0.001 PHE E 830 TYR 0.015 0.001 TYR E1059 ARG 0.004 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 631) hydrogen bonds : angle 4.79758 ( 1771) metal coordination : bond 0.00647 ( 4) metal coordination : angle 9.65685 ( 12) covalent geometry : bond 0.00273 (13932) covalent geometry : angle 0.54865 (18965) *********************** 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 126 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 2.831 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8854 (mmm) cc_final: 0.8555 (mmm) REVERT: E 188 LEU cc_start: 0.8836 (mt) cc_final: 0.8603 (mp) REVERT: E 287 MET cc_start: 0.8675 (ttp) cc_final: 0.8396 (ttm) REVERT: E 843 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7566 (t) REVERT: E 1030 LEU cc_start: 0.9231 (mp) cc_final: 0.9014 (mp) REVERT: E 1077 LEU cc_start: 0.8304 (tp) cc_final: 0.8034 (pp) REVERT: D 32 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8506 (ptp) REVERT: D 96 LYS cc_start: 0.9105 (tttp) cc_final: 0.8717 (ttmm) REVERT: B 86 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8968 (p) REVERT: B 282 ILE cc_start: 0.8867 (mm) cc_final: 0.8591 (mm) REVERT: B 363 MET cc_start: 0.8257 (mmt) cc_final: 0.7749 (mmt) outliers start: 28 outliers final: 19 residues processed: 117 average time/residue: 0.2664 time to fit residues: 49.4547 Evaluate side-chains 111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 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 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 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 29 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 156 optimal weight: 0.0020 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.5594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056246 restraints weight = 63824.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057436 restraints weight = 34084.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058207 restraints weight = 22352.158| |-----------------------------------------------------------------------------| 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 = 0.89 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 = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13936 Z= 0.143 Angle : 0.606 20.278 18977 Z= 0.285 Chirality : 0.041 0.155 2098 Planarity : 0.004 0.047 2365 Dihedral : 11.327 107.611 2035 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer: Outliers : 2.49 % Allowed : 10.81 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.21), residues: 1640 helix: 1.61 (0.21), residues: 644 sheet: -0.14 (0.32), residues: 272 loop : -0.37 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 284 HIS 0.004 0.001 HIS B 166 PHE 0.020 0.001 PHE E 830 TYR 0.014 0.001 TYR E1059 ARG 0.003 0.000 ARG E1105 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 631) hydrogen bonds : angle 4.76130 ( 1771) metal coordination : bond 0.00796 ( 4) metal coordination : angle 9.57277 ( 12) covalent geometry : bond 0.00319 (13932) covalent geometry : angle 0.55663 (18965) *********************** 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 125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8841 (mmm) cc_final: 0.8593 (mmm) REVERT: E 188 LEU cc_start: 0.8836 (mt) cc_final: 0.8609 (mp) REVERT: E 287 MET cc_start: 0.8715 (ttp) cc_final: 0.8513 (ttm) REVERT: E 843 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7591 (t) REVERT: E 973 ASN cc_start: 0.7807 (m-40) cc_final: 0.7136 (t0) REVERT: E 1030 LEU cc_start: 0.9231 (mp) cc_final: 0.9029 (mp) REVERT: E 1077 LEU cc_start: 0.8308 (tp) cc_final: 0.8025 (pp) REVERT: D 32 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8376 (ptp) REVERT: D 96 LYS cc_start: 0.9102 (tttp) cc_final: 0.8774 (ttmm) REVERT: B 86 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9040 (p) REVERT: B 180 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 282 ILE cc_start: 0.8825 (mm) cc_final: 0.8537 (mm) REVERT: B 363 MET cc_start: 0.8255 (mmt) cc_final: 0.7747 (mmt) outliers start: 35 outliers final: 25 residues processed: 112 average time/residue: 0.2186 time to fit residues: 38.9607 Evaluate side-chains 117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 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 32 MET 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 18 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU 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 300 MET 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 160 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** E 823 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054047 restraints weight = 64403.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055204 restraints weight = 34473.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.055955 restraints weight = 22733.683| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13936 Z= 0.269 Angle : 0.720 22.386 18977 Z= 0.342 Chirality : 0.044 0.178 2098 Planarity : 0.005 0.049 2365 Dihedral : 11.480 105.791 2035 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.56 % Allowed : 10.95 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.21), residues: 1640 helix: 1.28 (0.20), residues: 644 sheet: -0.40 (0.31), residues: 270 loop : -0.52 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 284 HIS 0.005 0.001 HIS B 166 PHE 0.021 0.002 PHE E 494 TYR 0.028 0.002 TYR E1059 ARG 0.004 0.001 ARG E1050 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 631) hydrogen bonds : angle 5.12270 ( 1771) metal coordination : bond 0.01497 ( 4) metal coordination : angle 11.00819 ( 12) covalent geometry : bond 0.00604 (13932) covalent geometry : angle 0.66480 (18965) *********************** 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 120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8885 (mmm) cc_final: 0.8454 (mmm) REVERT: E 287 MET cc_start: 0.8842 (ttp) cc_final: 0.8598 (ttm) REVERT: E 973 ASN cc_start: 0.8017 (m-40) cc_final: 0.7268 (t0) REVERT: E 1077 LEU cc_start: 0.8360 (tp) cc_final: 0.8104 (pp) REVERT: D 32 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8508 (ptp) REVERT: D 96 LYS cc_start: 0.9149 (tttp) cc_final: 0.8787 (ttmm) REVERT: B 86 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9016 (p) REVERT: B 194 MET cc_start: 0.8347 (mtp) cc_final: 0.8130 (mtp) REVERT: B 363 MET cc_start: 0.8258 (mmt) cc_final: 0.7816 (mmt) outliers start: 36 outliers final: 30 residues processed: 112 average time/residue: 0.2231 time to fit residues: 39.7511 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 771 VAL 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 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 D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 95 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056174 restraints weight = 63794.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.057362 restraints weight = 33926.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058134 restraints weight = 22267.026| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4376 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= 0.123 Angle : 0.596 18.822 18977 Z= 0.283 Chirality : 0.041 0.142 2098 Planarity : 0.004 0.049 2365 Dihedral : 11.270 108.416 2035 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 1.99 % Allowed : 11.45 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.21), residues: 1640 helix: 1.63 (0.21), residues: 645 sheet: -0.27 (0.32), residues: 267 loop : -0.45 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 284 HIS 0.003 0.001 HIS B 166 PHE 0.018 0.001 PHE E 830 TYR 0.020 0.001 TYR E1059 ARG 0.004 0.000 ARG E1105 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 631) hydrogen bonds : angle 4.77087 ( 1771) metal coordination : bond 0.00627 ( 4) metal coordination : angle 9.19128 ( 12) covalent geometry : bond 0.00269 (13932) covalent geometry : angle 0.54940 (18965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: E 50 MET cc_start: 0.8833 (mmm) cc_final: 0.8607 (mmm) REVERT: E 188 LEU cc_start: 0.8821 (mt) cc_final: 0.8616 (mp) REVERT: E 843 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.7604 (t) REVERT: E 973 ASN cc_start: 0.7969 (m-40) cc_final: 0.7278 (t0) REVERT: E 1077 LEU cc_start: 0.8316 (tp) cc_final: 0.8010 (pp) REVERT: D 32 MET cc_start: 0.8871 (ptm) cc_final: 0.8427 (ptp) REVERT: D 96 LYS cc_start: 0.9095 (tttp) cc_final: 0.8766 (ttmm) REVERT: B 86 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 363 MET cc_start: 0.8228 (mmt) cc_final: 0.7704 (mmt) outliers start: 28 outliers final: 25 residues processed: 113 average time/residue: 0.2217 time to fit residues: 40.0267 Evaluate side-chains 114 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 D residue 4 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 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 88 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** E 937 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055997 restraints weight = 64126.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057184 restraints weight = 34146.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057952 restraints weight = 22379.987| |-----------------------------------------------------------------------------| 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 = 0.93 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 = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13936 Z= 0.143 Angle : 0.605 19.392 18977 Z= 0.285 Chirality : 0.041 0.154 2098 Planarity : 0.004 0.046 2365 Dihedral : 11.201 108.824 2035 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 11.52 % 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 (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: 0.64 (0.21), residues: 1640 helix: 1.70 (0.20), residues: 644 sheet: -0.27 (0.32), residues: 267 loop : -0.41 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 284 HIS 0.003 0.001 HIS B 166 PHE 0.019 0.001 PHE E1076 TYR 0.021 0.001 TYR E1059 ARG 0.003 0.000 ARG E1105 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 631) hydrogen bonds : angle 4.77155 ( 1771) metal coordination : bond 0.00806 ( 4) metal coordination : angle 9.28399 ( 12) covalent geometry : bond 0.00321 (13932) covalent geometry : angle 0.55809 (18965) ********************** 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: 30 poor density : 90 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: E 188 LEU cc_start: 0.8840 (mt) cc_final: 0.8626 (mp) REVERT: E 843 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7550 (t) REVERT: E 909 MET cc_start: 0.8154 (ptt) cc_final: 0.7882 (ptt) REVERT: E 973 ASN cc_start: 0.8048 (m-40) cc_final: 0.7279 (t0) REVERT: E 1077 LEU cc_start: 0.8334 (tp) cc_final: 0.7957 (pp) REVERT: D 32 MET cc_start: 0.8877 (ptm) cc_final: 0.8457 (ptp) REVERT: D 96 LYS cc_start: 0.9106 (tttp) cc_final: 0.8769 (ttmm) REVERT: B 86 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9032 (p) REVERT: B 363 MET cc_start: 0.8254 (mmt) cc_final: 0.7704 (mmt) outliers start: 30 outliers final: 26 residues processed: 114 average time/residue: 0.2160 time to fit residues: 39.3129 Evaluate side-chains 115 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 18 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 356 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056352 restraints weight = 64494.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057547 restraints weight = 34135.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058317 restraints weight = 22322.919| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13936 Z= 0.129 Angle : 0.602 19.098 18977 Z= 0.282 Chirality : 0.041 0.168 2098 Planarity : 0.004 0.046 2365 Dihedral : 11.139 108.957 2035 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 2.06 % Allowed : 11.66 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.21), residues: 1640 helix: 1.75 (0.20), residues: 645 sheet: -0.25 (0.32), residues: 273 loop : -0.33 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 284 HIS 0.003 0.001 HIS B 166 PHE 0.018 0.001 PHE E 830 TYR 0.021 0.001 TYR E1059 ARG 0.003 0.000 ARG E1105 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 631) hydrogen bonds : angle 4.71137 ( 1771) metal coordination : bond 0.00693 ( 4) metal coordination : angle 9.13135 ( 12) covalent geometry : bond 0.00287 (13932) covalent geometry : angle 0.55650 (18965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4585.68 seconds wall clock time: 84 minutes 38.20 seconds (5078.20 seconds total)