Starting phenix.real_space_refine on Tue Mar 3 20:52:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bv1_30209/03_2026/7bv1_30209.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bv1_30209/03_2026/7bv1_30209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_2026/7bv1_30209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_2026/7bv1_30209.map" model { file = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_2026/7bv1_30209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_2026/7bv1_30209.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 64 5.16 5 C 5626 2.51 5 N 1460 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8799 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6724 Classifications: {'peptide': 836} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 807} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 865 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 727 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1825 SG CYS A 301 40.360 63.172 37.957 1.00 10.69 S ATOM 1866 SG CYS A 306 40.337 62.023 34.421 1.00 7.82 S ATOM 1898 SG CYS A 310 43.496 61.958 36.510 1.00 18.90 S ATOM 3300 SG CYS A 487 23.293 58.642 47.127 1.00 13.60 S ATOM 4553 SG CYS A 645 21.979 58.294 43.851 1.00 17.07 S ATOM 4559 SG CYS A 646 25.396 60.467 44.225 1.00 15.31 S Time building chain proxies: 2.12, per 1000 atoms: 0.24 Number of scatterers: 8799 At special positions: 0 Unit cell: (90.246, 93.288, 127.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 64 16.00 O 1647 8.00 N 1460 7.00 C 5626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 338.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 50.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.964A pdb=" N TYR A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.620A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.630A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.351A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 248' Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.671A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.611A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.820A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.702A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.651A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.528A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.796A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.954A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.343A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.635A pdb=" N ALA A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.765A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.820A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 852 through 867 removed outlier: 3.683A pdb=" N ILE A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.588A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.626A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.920A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.740A pdb=" N CYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.662A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.579A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.816A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.805A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.922A pdb=" N THR D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 4.344A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.637A pdb=" N GLY A 203 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 354 removed outlier: 3.595A pdb=" N VAL A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354 removed outlier: 3.595A pdb=" N VAL A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 7.007A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 7.007A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.768A pdb=" N ASN A 414 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AB2, first strand: chain 'D' and resid 146 through 149 removed outlier: 3.986A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2798 1.34 - 1.46: 2134 1.46 - 1.59: 3963 1.59 - 1.71: 0 1.71 - 1.84: 97 Bond restraints: 8992 Sorted by residual: bond pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta sigma weight residual 1.457 1.499 -0.043 1.07e-02 8.73e+03 1.60e+01 bond pdb=" N LYS A 263 " pdb=" CA LYS A 263 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.27e+01 bond pdb=" N ILE D 166 " pdb=" CA ILE D 166 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" N ILE A 847 " pdb=" CA ILE A 847 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N VAL A 844 " pdb=" CA VAL A 844 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.18e-02 7.18e+03 8.85e+00 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 11449 1.60 - 3.20: 666 3.20 - 4.80: 86 4.80 - 6.40: 16 6.40 - 8.00: 5 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C PRO D 121 " pdb=" CA PRO D 121 " pdb=" CB PRO D 121 " ideal model delta sigma weight residual 111.40 107.43 3.97 9.10e-01 1.21e+00 1.90e+01 angle pdb=" CA ALA A 660 " pdb=" C ALA A 660 " pdb=" O ALA A 660 " ideal model delta sigma weight residual 120.82 116.78 4.04 1.05e+00 9.07e-01 1.48e+01 angle pdb=" CA ALA D 125 " pdb=" C ALA D 125 " pdb=" O ALA D 125 " ideal model delta sigma weight residual 122.27 118.08 4.19 1.16e+00 7.43e-01 1.31e+01 angle pdb=" N GLN A 661 " pdb=" CA GLN A 661 " pdb=" C GLN A 661 " ideal model delta sigma weight residual 111.36 115.27 -3.91 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N LEU A 401 " pdb=" CA LEU A 401 " pdb=" C LEU A 401 " ideal model delta sigma weight residual 112.54 116.87 -4.33 1.22e+00 6.72e-01 1.26e+01 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 4739 18.13 - 36.25: 496 36.25 - 54.38: 87 54.38 - 72.51: 14 72.51 - 90.63: 7 Dihedral angle restraints: 5343 sinusoidal: 2045 harmonic: 3298 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual -180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C ASP A 208 " pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" CB ASP A 208 " ideal model delta harmonic sigma weight residual -122.60 -131.33 8.73 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 5340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1156 0.070 - 0.140: 193 0.140 - 0.210: 32 0.210 - 0.280: 8 0.280 - 0.350: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ASN A 150 " pdb=" N ASN A 150 " pdb=" C ASN A 150 " pdb=" CB ASN A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ILE D 120 " pdb=" N ILE D 120 " pdb=" C ILE D 120 " pdb=" CB ILE D 120 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 888 " pdb=" CA ILE A 888 " pdb=" CG1 ILE A 888 " pdb=" CG2 ILE A 888 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 1390 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 232 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 667 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C VAL A 667 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 667 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 668 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 161 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C ASP A 161 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A 161 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 162 " 0.012 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2132 2.79 - 3.32: 8266 3.32 - 3.85: 13878 3.85 - 4.37: 17030 4.37 - 4.90: 28844 Nonbonded interactions: 70150 Sorted by model distance: nonbonded pdb=" OD1 ASP A 194 " pdb=" OH TYR A 289 " model vdw 2.266 3.040 nonbonded pdb=" O ASP A 684 " pdb=" OG1 THR A 687 " model vdw 2.269 3.040 nonbonded pdb=" N GLU A 136 " pdb=" OE1 GLU A 136 " model vdw 2.380 3.120 nonbonded pdb=" O PRO A 322 " pdb=" OG SER A 325 " model vdw 2.387 3.040 nonbonded pdb=" OG1 THR A 409 " pdb=" OE2 GLU C 23 " model vdw 2.392 3.040 ... (remaining 70145 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 85 through 95 or (resid 96 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 121 or (resid 122 and ( \ name N or name CA or name C or name O or name CB )) or resid 123 through 126 or \ (resid 127 and (name N or name CA or name C or name O or name CB )) or resid 128 \ through 133 or (resid 134 and (name N or name CA or name C or name O or name CB \ )) or resid 135 or (resid 136 and (name N or name CA or name C or name O or nam \ e CB )) or resid 137 through 138 or (resid 139 and (name N or name CA or name C \ or name O or name CB )) or resid 140 through 169 or resid 176 through 181 or (re \ sid 182 and (name N or name CA or name C or name O or name CB )) or resid 183 th \ rough 189)) selection = (chain 'D' and (resid 85 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 189)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.570 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.007 0.366 9000 Z= 0.373 Angle : 0.825 8.000 12228 Z= 0.528 Chirality : 0.058 0.350 1393 Planarity : 0.005 0.056 1555 Dihedral : 15.134 90.631 3209 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.24), residues: 1095 helix: -0.92 (0.23), residues: 491 sheet: -1.23 (0.43), residues: 125 loop : -1.51 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 197 TYR 0.021 0.002 TYR D 138 PHE 0.023 0.002 PHE A 471 TRP 0.028 0.002 TRP A 162 HIS 0.004 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8992) covalent geometry : angle 0.81572 (12222) hydrogen bonds : bond 0.16942 ( 403) hydrogen bonds : angle 7.08470 ( 1191) metal coordination : bond 0.16178 ( 8) metal coordination : angle 5.60148 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6846 (m-80) cc_final: 0.6589 (m-80) REVERT: A 760 ASP cc_start: 0.5906 (p0) cc_final: 0.5679 (p0) outliers start: 0 outliers final: 1 residues processed: 248 average time/residue: 0.4535 time to fit residues: 120.8579 Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 543 ASN A 703 ASN A 773 GLN A 781 ASN A 790 ASN A 815 GLN A 872 HIS A 886 GLN A 928 HIS B 176 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.187945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153829 restraints weight = 10263.925| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.97 r_work: 0.3646 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9000 Z= 0.184 Angle : 0.605 6.827 12228 Z= 0.324 Chirality : 0.045 0.186 1393 Planarity : 0.005 0.079 1555 Dihedral : 4.436 21.405 1206 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.73 % Allowed : 16.39 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.24), residues: 1095 helix: -0.34 (0.23), residues: 518 sheet: -1.06 (0.45), residues: 111 loop : -1.19 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 80 TYR 0.018 0.002 TYR A 887 PHE 0.019 0.002 PHE A 652 TRP 0.019 0.002 TRP A 162 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8992) covalent geometry : angle 0.60010 (12222) hydrogen bonds : bond 0.04407 ( 403) hydrogen bonds : angle 4.97213 ( 1191) metal coordination : bond 0.02583 ( 8) metal coordination : angle 3.48329 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.6377 (p0) cc_final: 0.6156 (p0) REVERT: A 334 PHE cc_start: 0.7552 (m-80) cc_final: 0.6999 (m-80) REVERT: A 361 LEU cc_start: 0.7151 (mt) cc_final: 0.6698 (tt) REVERT: A 415 PHE cc_start: 0.7215 (t80) cc_final: 0.6885 (t80) REVERT: A 508 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7927 (mmtp) REVERT: A 553 ARG cc_start: 0.6137 (mmm-85) cc_final: 0.5472 (mtp85) REVERT: A 662 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7734 (t) REVERT: A 750 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7701 (mmp-170) REVERT: A 760 ASP cc_start: 0.6613 (p0) cc_final: 0.6366 (p0) REVERT: A 811 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: A 815 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: A 859 PHE cc_start: 0.8210 (m-80) cc_final: 0.7944 (m-80) REVERT: B 155 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: B 176 ASN cc_start: 0.8270 (t0) cc_final: 0.7939 (t0) REVERT: C 56 LEU cc_start: 0.7461 (tp) cc_final: 0.7250 (tp) REVERT: D 93 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6934 (p) outliers start: 36 outliers final: 14 residues processed: 189 average time/residue: 0.4289 time to fit residues: 87.4692 Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 404 ASN A 543 ASN A 573 GLN A 599 HIS A 698 GLN ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.183220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148789 restraints weight = 10312.741| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.83 r_work: 0.3538 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9000 Z= 0.239 Angle : 0.645 7.817 12228 Z= 0.343 Chirality : 0.047 0.161 1393 Planarity : 0.005 0.053 1555 Dihedral : 4.749 23.768 1204 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.46 % Allowed : 17.12 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.24), residues: 1095 helix: -0.38 (0.22), residues: 520 sheet: -1.03 (0.43), residues: 121 loop : -1.38 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 392 TYR 0.021 0.003 TYR A 867 PHE 0.020 0.002 PHE A 652 TRP 0.015 0.002 TRP A 162 HIS 0.008 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 8992) covalent geometry : angle 0.64011 (12222) hydrogen bonds : bond 0.05213 ( 403) hydrogen bonds : angle 4.85361 ( 1191) metal coordination : bond 0.02527 ( 8) metal coordination : angle 3.45342 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.220 Fit side-chains REVERT: A 158 ASN cc_start: 0.8074 (m-40) cc_final: 0.7854 (m-40) REVERT: A 167 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: A 334 PHE cc_start: 0.7824 (m-80) cc_final: 0.7343 (m-80) REVERT: A 361 LEU cc_start: 0.7209 (mt) cc_final: 0.6660 (tt) REVERT: A 370 GLU cc_start: 0.7798 (mp0) cc_final: 0.7578 (mp0) REVERT: A 508 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8215 (mmtp) REVERT: A 522 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: A 760 ASP cc_start: 0.7232 (p0) cc_final: 0.6923 (p0) REVERT: A 811 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: A 815 GLN cc_start: 0.8004 (mt0) cc_final: 0.7726 (mt0) REVERT: A 826 TYR cc_start: 0.7577 (m-80) cc_final: 0.7340 (m-10) REVERT: A 859 PHE cc_start: 0.8392 (m-80) cc_final: 0.7992 (m-80) REVERT: A 876 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6372 (pt0) REVERT: B 155 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: B 176 ASN cc_start: 0.8532 (t0) cc_final: 0.7942 (t0) REVERT: C 3 MET cc_start: 0.7154 (ttp) cc_final: 0.6379 (tpt) REVERT: C 35 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7429 (mp) outliers start: 43 outliers final: 18 residues processed: 173 average time/residue: 0.4805 time to fit residues: 88.9921 Evaluate side-chains 159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 408 GLN A 543 ASN A 613 HIS A 790 ASN A 815 GLN A 872 HIS B 118 ASN B 158 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153137 restraints weight = 10477.196| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.89 r_work: 0.3585 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9000 Z= 0.118 Angle : 0.530 8.208 12228 Z= 0.281 Chirality : 0.042 0.160 1393 Planarity : 0.004 0.040 1555 Dihedral : 4.343 21.598 1204 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.32 % Allowed : 20.64 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1095 helix: 0.06 (0.23), residues: 515 sheet: -0.93 (0.42), residues: 121 loop : -1.29 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.017 0.001 TYR A 289 PHE 0.014 0.002 PHE A 920 TRP 0.007 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8992) covalent geometry : angle 0.52882 (12222) hydrogen bonds : bond 0.03669 ( 403) hydrogen bonds : angle 4.50261 ( 1191) metal coordination : bond 0.00963 ( 8) metal coordination : angle 1.89058 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.291 Fit side-chains REVERT: A 37 ILE cc_start: 0.8074 (mm) cc_final: 0.7539 (tt) REVERT: A 198 ASN cc_start: 0.8202 (m-40) cc_final: 0.7999 (m110) REVERT: A 334 PHE cc_start: 0.7797 (m-80) cc_final: 0.7274 (m-80) REVERT: A 361 LEU cc_start: 0.7245 (mt) cc_final: 0.6697 (tt) REVERT: A 370 GLU cc_start: 0.7715 (mp0) cc_final: 0.7410 (mp0) REVERT: A 508 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8188 (mmtp) REVERT: A 522 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: A 750 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (mmm160) REVERT: A 760 ASP cc_start: 0.7100 (p0) cc_final: 0.6814 (OUTLIER) REVERT: A 815 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7733 (mt0) REVERT: A 826 TYR cc_start: 0.7549 (m-80) cc_final: 0.7289 (m-10) REVERT: A 859 PHE cc_start: 0.8391 (m-80) cc_final: 0.7909 (m-80) REVERT: A 876 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6423 (pt0) REVERT: B 82 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7394 (pttp) REVERT: B 176 ASN cc_start: 0.8495 (t0) cc_final: 0.8014 (t0) REVERT: C 3 MET cc_start: 0.7286 (ttp) cc_final: 0.6479 (tpt) REVERT: C 35 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7408 (mp) outliers start: 32 outliers final: 14 residues processed: 154 average time/residue: 0.4695 time to fit residues: 77.8093 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.0870 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 543 ASN A 790 ASN A 815 GLN A 872 HIS B 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.182932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148909 restraints weight = 10344.851| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.81 r_work: 0.3543 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9000 Z= 0.145 Angle : 0.532 9.588 12228 Z= 0.282 Chirality : 0.043 0.135 1393 Planarity : 0.004 0.034 1555 Dihedral : 4.316 21.130 1204 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.36 % Allowed : 19.29 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1095 helix: 0.12 (0.23), residues: 517 sheet: -0.88 (0.42), residues: 121 loop : -1.28 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.028 0.002 TYR A 867 PHE 0.015 0.002 PHE A 753 TRP 0.007 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8992) covalent geometry : angle 0.53070 (12222) hydrogen bonds : bond 0.03928 ( 403) hydrogen bonds : angle 4.46068 ( 1191) metal coordination : bond 0.01104 ( 8) metal coordination : angle 1.91108 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.280 Fit side-chains REVERT: A 37 ILE cc_start: 0.8116 (mm) cc_final: 0.7662 (tt) REVERT: A 198 ASN cc_start: 0.8201 (m-40) cc_final: 0.7991 (m110) REVERT: A 334 PHE cc_start: 0.7802 (m-80) cc_final: 0.7273 (m-80) REVERT: A 361 LEU cc_start: 0.7355 (mt) cc_final: 0.6760 (tt) REVERT: A 508 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8227 (mmtp) REVERT: A 522 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: A 750 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7793 (mmm160) REVERT: A 760 ASP cc_start: 0.7146 (p0) cc_final: 0.6856 (OUTLIER) REVERT: A 815 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: A 826 TYR cc_start: 0.7475 (m-80) cc_final: 0.7243 (m-10) REVERT: A 859 PHE cc_start: 0.8368 (m-80) cc_final: 0.7981 (m-80) REVERT: A 876 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6615 (pt0) REVERT: B 90 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6773 (tmt) REVERT: B 118 ASN cc_start: 0.8728 (m-40) cc_final: 0.8476 (m-40) REVERT: B 176 ASN cc_start: 0.8500 (t0) cc_final: 0.8109 (t0) REVERT: B 179 ASN cc_start: 0.7659 (t0) cc_final: 0.7209 (t0) REVERT: C 3 MET cc_start: 0.7247 (ttp) cc_final: 0.6546 (tpt) REVERT: D 87 MET cc_start: 0.5431 (tpp) cc_final: 0.4594 (mtm) outliers start: 42 outliers final: 20 residues processed: 156 average time/residue: 0.4496 time to fit residues: 75.5035 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 224 GLN A 543 ASN A 791 ASN A 815 GLN A 872 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.182958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149203 restraints weight = 10268.901| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.79 r_work: 0.3526 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9000 Z= 0.135 Angle : 0.521 9.860 12228 Z= 0.275 Chirality : 0.043 0.133 1393 Planarity : 0.004 0.033 1555 Dihedral : 4.270 20.134 1204 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.15 % Allowed : 19.50 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1095 helix: 0.24 (0.23), residues: 515 sheet: -0.78 (0.43), residues: 121 loop : -1.22 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.022 0.002 TYR A 867 PHE 0.015 0.002 PHE A 753 TRP 0.007 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8992) covalent geometry : angle 0.51956 (12222) hydrogen bonds : bond 0.03787 ( 403) hydrogen bonds : angle 4.41309 ( 1191) metal coordination : bond 0.00940 ( 8) metal coordination : angle 1.92478 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.333 Fit side-chains REVERT: A 37 ILE cc_start: 0.8074 (mm) cc_final: 0.7611 (tt) REVERT: A 161 ASP cc_start: 0.6727 (t0) cc_final: 0.6256 (t0) REVERT: A 198 ASN cc_start: 0.8129 (m-40) cc_final: 0.7901 (m110) REVERT: A 334 PHE cc_start: 0.7725 (m-80) cc_final: 0.7131 (m-80) REVERT: A 361 LEU cc_start: 0.7367 (mt) cc_final: 0.6697 (tt) REVERT: A 508 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8260 (mmtp) REVERT: A 522 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7396 (pp20) REVERT: A 553 ARG cc_start: 0.6438 (mmm-85) cc_final: 0.6007 (mtp85) REVERT: A 750 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7812 (mmm160) REVERT: A 760 ASP cc_start: 0.7050 (p0) cc_final: 0.6763 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: A 815 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: A 826 TYR cc_start: 0.7464 (m-80) cc_final: 0.7207 (m-10) REVERT: A 859 PHE cc_start: 0.8366 (m-80) cc_final: 0.7902 (m-80) REVERT: A 876 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6679 (pt0) REVERT: B 90 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6594 (tmt) REVERT: B 176 ASN cc_start: 0.8507 (t0) cc_final: 0.7946 (t0) REVERT: B 179 ASN cc_start: 0.7680 (t0) cc_final: 0.7202 (t0) REVERT: B 180 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6497 (mm) REVERT: C 3 MET cc_start: 0.7207 (ttp) cc_final: 0.6405 (tpt) REVERT: C 35 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7117 (mt) REVERT: C 43 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6398 (mttp) REVERT: D 87 MET cc_start: 0.5497 (tpp) cc_final: 0.5259 (ttp) outliers start: 40 outliers final: 20 residues processed: 153 average time/residue: 0.4543 time to fit residues: 74.9908 Evaluate side-chains 150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 209 ASN A 543 ASN A 600 ASN A 752 HIS A 815 GLN A 872 HIS D 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.180703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147424 restraints weight = 10323.958| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.94 r_work: 0.3500 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9000 Z= 0.258 Angle : 0.637 10.150 12228 Z= 0.336 Chirality : 0.048 0.152 1393 Planarity : 0.004 0.042 1555 Dihedral : 4.811 22.904 1204 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.98 % Allowed : 18.57 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1095 helix: -0.18 (0.23), residues: 527 sheet: -1.02 (0.41), residues: 134 loop : -1.51 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 190 TYR 0.026 0.002 TYR A 867 PHE 0.016 0.003 PHE A 652 TRP 0.009 0.002 TRP A 162 HIS 0.009 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 8992) covalent geometry : angle 0.63400 (12222) hydrogen bonds : bond 0.05160 ( 403) hydrogen bonds : angle 4.73550 ( 1191) metal coordination : bond 0.01593 ( 8) metal coordination : angle 3.02840 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.329 Fit side-chains REVERT: A 37 ILE cc_start: 0.8136 (mm) cc_final: 0.7576 (tt) REVERT: A 161 ASP cc_start: 0.7337 (t0) cc_final: 0.6936 (t0) REVERT: A 260 ASP cc_start: 0.7513 (t0) cc_final: 0.7110 (m-30) REVERT: A 334 PHE cc_start: 0.7943 (m-80) cc_final: 0.7465 (m-80) REVERT: A 508 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8284 (mmtp) REVERT: A 522 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: A 553 ARG cc_start: 0.6711 (mmm-85) cc_final: 0.6258 (mtp85) REVERT: A 718 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8537 (ttpt) REVERT: A 750 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7710 (mmm160) REVERT: A 811 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: A 826 TYR cc_start: 0.7458 (m-80) cc_final: 0.7238 (m-10) REVERT: A 859 PHE cc_start: 0.8452 (m-80) cc_final: 0.7997 (m-80) REVERT: A 887 TYR cc_start: 0.7947 (t80) cc_final: 0.7708 (t80) REVERT: B 90 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6959 (tmt) REVERT: B 137 THR cc_start: 0.8528 (m) cc_final: 0.8278 (m) REVERT: B 165 LYS cc_start: 0.7207 (mtmm) cc_final: 0.6662 (mptm) REVERT: B 179 ASN cc_start: 0.7775 (t0) cc_final: 0.7461 (t0) REVERT: B 180 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6515 (mm) REVERT: C 3 MET cc_start: 0.7417 (ttp) cc_final: 0.6708 (tpt) REVERT: C 31 GLN cc_start: 0.7144 (tt0) cc_final: 0.6831 (tp-100) outliers start: 48 outliers final: 25 residues processed: 162 average time/residue: 0.4946 time to fit residues: 86.0799 Evaluate side-chains 151 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 752 HIS A 872 HIS B 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.184880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152499 restraints weight = 10149.089| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.86 r_work: 0.3581 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9000 Z= 0.109 Angle : 0.513 10.411 12228 Z= 0.272 Chirality : 0.042 0.126 1393 Planarity : 0.003 0.036 1555 Dihedral : 4.345 21.751 1204 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.11 % Allowed : 21.16 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.25), residues: 1095 helix: 0.27 (0.24), residues: 516 sheet: -0.77 (0.46), residues: 105 loop : -1.24 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.017 0.001 TYR A 867 PHE 0.018 0.001 PHE A 415 TRP 0.007 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8992) covalent geometry : angle 0.51231 (12222) hydrogen bonds : bond 0.03443 ( 403) hydrogen bonds : angle 4.36482 ( 1191) metal coordination : bond 0.00617 ( 8) metal coordination : angle 1.51634 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.304 Fit side-chains REVERT: A 37 ILE cc_start: 0.8150 (mm) cc_final: 0.7681 (tt) REVERT: A 161 ASP cc_start: 0.7184 (t0) cc_final: 0.6810 (t0) REVERT: A 196 MET cc_start: 0.7691 (mtp) cc_final: 0.7421 (mtm) REVERT: A 198 ASN cc_start: 0.8214 (m-40) cc_final: 0.7976 (m110) REVERT: A 334 PHE cc_start: 0.7841 (m-80) cc_final: 0.7389 (m-80) REVERT: A 411 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7815 (ptmm) REVERT: A 494 ILE cc_start: 0.8538 (mm) cc_final: 0.8240 (mp) REVERT: A 508 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8299 (mmtp) REVERT: A 522 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: A 553 ARG cc_start: 0.6742 (mmm-85) cc_final: 0.6330 (mtp85) REVERT: A 750 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7716 (mmm160) REVERT: A 760 ASP cc_start: 0.7226 (p0) cc_final: 0.6901 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: A 859 PHE cc_start: 0.8399 (m-80) cc_final: 0.8041 (m-80) REVERT: A 887 TYR cc_start: 0.7915 (t80) cc_final: 0.7674 (t80) REVERT: B 90 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7148 (tmm) REVERT: B 137 THR cc_start: 0.8501 (m) cc_final: 0.8266 (m) REVERT: B 179 ASN cc_start: 0.7733 (t0) cc_final: 0.7469 (t0) REVERT: B 180 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6900 (mt) REVERT: C 3 MET cc_start: 0.7378 (ttp) cc_final: 0.6631 (tpt) REVERT: C 31 GLN cc_start: 0.6811 (tt0) cc_final: 0.6505 (tp-100) outliers start: 30 outliers final: 13 residues processed: 160 average time/residue: 0.4532 time to fit residues: 78.4331 Evaluate side-chains 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 872 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151925 restraints weight = 10170.627| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.89 r_work: 0.3577 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9000 Z= 0.115 Angle : 0.513 9.483 12228 Z= 0.271 Chirality : 0.042 0.124 1393 Planarity : 0.003 0.036 1555 Dihedral : 4.224 19.506 1204 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.11 % Allowed : 21.06 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1095 helix: 0.40 (0.24), residues: 514 sheet: -0.71 (0.48), residues: 100 loop : -1.23 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.024 0.001 TYR A 453 PHE 0.013 0.001 PHE A 415 TRP 0.006 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8992) covalent geometry : angle 0.51130 (12222) hydrogen bonds : bond 0.03502 ( 403) hydrogen bonds : angle 4.30210 ( 1191) metal coordination : bond 0.00693 ( 8) metal coordination : angle 1.71153 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.315 Fit side-chains REVERT: A 37 ILE cc_start: 0.8203 (mm) cc_final: 0.7850 (tt) REVERT: A 161 ASP cc_start: 0.7189 (t0) cc_final: 0.6814 (t0) REVERT: A 196 MET cc_start: 0.7781 (mtp) cc_final: 0.7465 (mtm) REVERT: A 198 ASN cc_start: 0.8211 (m-40) cc_final: 0.8000 (m110) REVERT: A 260 ASP cc_start: 0.7009 (t0) cc_final: 0.6527 (m-30) REVERT: A 334 PHE cc_start: 0.7810 (m-80) cc_final: 0.7303 (m-80) REVERT: A 494 ILE cc_start: 0.8537 (mm) cc_final: 0.8241 (mp) REVERT: A 508 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8245 (mmtp) REVERT: A 522 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7398 (pp20) REVERT: A 553 ARG cc_start: 0.6731 (mmm-85) cc_final: 0.6369 (mtp85) REVERT: A 624 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8046 (mpt-90) REVERT: A 750 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7709 (mmm160) REVERT: A 760 ASP cc_start: 0.7084 (p0) cc_final: 0.6803 (p0) REVERT: A 811 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: A 859 PHE cc_start: 0.8365 (m-80) cc_final: 0.8023 (m-80) REVERT: A 887 TYR cc_start: 0.7889 (t80) cc_final: 0.7653 (t80) REVERT: B 90 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6942 (tmt) REVERT: B 137 THR cc_start: 0.8498 (m) cc_final: 0.8262 (m) REVERT: B 179 ASN cc_start: 0.7709 (t0) cc_final: 0.7453 (t0) REVERT: B 180 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6907 (mt) REVERT: C 3 MET cc_start: 0.7369 (ttp) cc_final: 0.6641 (tpt) REVERT: C 31 GLN cc_start: 0.6981 (tt0) cc_final: 0.6626 (tp-100) outliers start: 30 outliers final: 17 residues processed: 151 average time/residue: 0.4767 time to fit residues: 77.4653 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 0.0060 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 552 ASN A 872 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.184472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151688 restraints weight = 10213.101| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.90 r_work: 0.3546 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9000 Z= 0.122 Angle : 0.519 8.522 12228 Z= 0.275 Chirality : 0.042 0.126 1393 Planarity : 0.003 0.035 1555 Dihedral : 4.231 20.738 1204 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.90 % Allowed : 21.58 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1095 helix: 0.38 (0.24), residues: 514 sheet: -0.51 (0.46), residues: 110 loop : -1.25 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 726 TYR 0.021 0.001 TYR A 453 PHE 0.018 0.002 PHE A 415 TRP 0.006 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8992) covalent geometry : angle 0.51795 (12222) hydrogen bonds : bond 0.03545 ( 403) hydrogen bonds : angle 4.28023 ( 1191) metal coordination : bond 0.00666 ( 8) metal coordination : angle 1.63545 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.312 Fit side-chains REVERT: A 37 ILE cc_start: 0.8189 (mm) cc_final: 0.7834 (tt) REVERT: A 161 ASP cc_start: 0.7258 (t0) cc_final: 0.6949 (t0) REVERT: A 196 MET cc_start: 0.7795 (mtp) cc_final: 0.7490 (mtm) REVERT: A 260 ASP cc_start: 0.7030 (t0) cc_final: 0.6567 (m-30) REVERT: A 334 PHE cc_start: 0.7796 (m-80) cc_final: 0.7306 (m-80) REVERT: A 508 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8281 (mmtp) REVERT: A 522 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: A 553 ARG cc_start: 0.6745 (mmm-85) cc_final: 0.6360 (mtp85) REVERT: A 624 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8020 (mpt-90) REVERT: A 750 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7747 (mmm160) REVERT: A 760 ASP cc_start: 0.7159 (p0) cc_final: 0.6873 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: A 859 PHE cc_start: 0.8366 (m-80) cc_final: 0.8026 (m-80) REVERT: B 90 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6992 (tmt) REVERT: B 137 THR cc_start: 0.8502 (m) cc_final: 0.8266 (m) REVERT: B 179 ASN cc_start: 0.7711 (t0) cc_final: 0.7467 (t0) REVERT: B 180 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6886 (mt) REVERT: C 3 MET cc_start: 0.7380 (ttp) cc_final: 0.6663 (tpt) REVERT: C 31 GLN cc_start: 0.7072 (tt0) cc_final: 0.6685 (tp-100) outliers start: 28 outliers final: 20 residues processed: 153 average time/residue: 0.4467 time to fit residues: 73.8848 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 198 ASN A 543 ASN A 552 ASN A 872 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.182607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149405 restraints weight = 10173.634| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.92 r_work: 0.3493 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9000 Z= 0.160 Angle : 0.552 8.407 12228 Z= 0.293 Chirality : 0.044 0.130 1393 Planarity : 0.004 0.035 1555 Dihedral : 4.413 22.073 1204 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.32 % Allowed : 21.47 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1095 helix: 0.20 (0.23), residues: 520 sheet: -0.75 (0.45), residues: 123 loop : -1.35 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.022 0.002 TYR A 887 PHE 0.013 0.002 PHE A 753 TRP 0.007 0.001 TRP A 290 HIS 0.008 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8992) covalent geometry : angle 0.55070 (12222) hydrogen bonds : bond 0.04077 ( 403) hydrogen bonds : angle 4.37559 ( 1191) metal coordination : bond 0.00980 ( 8) metal coordination : angle 1.94637 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.43 seconds wall clock time: 55 minutes 35.22 seconds (3335.22 seconds total)