Starting phenix.real_space_refine on Sat Jul 26 15:16:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bv1_30209/07_2025/7bv1_30209.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bv1_30209/07_2025/7bv1_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_30209/07_2025/7bv1_30209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bv1_30209/07_2025/7bv1_30209.map" model { file = "/net/cci-nas-00/data/ceres_data/7bv1_30209/07_2025/7bv1_30209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bv1_30209/07_2025/7bv1_30209.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ARG:plan': 1, 'ASP:plan': 3} 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: {'ARG:plan': 1, 'ASP: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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP: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: 4.83, per 1000 atoms: 0.55 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: 1.98 Conformation dependent library (CDL) restraints added in 961.6 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: 1.05 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: 2.86 Time building geometry restraints manager: 2.37 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.190 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 TRP 0.028 0.002 TRP A 162 HIS 0.004 0.001 HIS A 892 PHE 0.023 0.002 PHE A 471 TYR 0.021 0.002 TYR D 138 ARG 0.004 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.16942 ( 403) hydrogen bonds : angle 7.08470 ( 1191) metal coordination : bond 0.16178 ( 8) metal coordination : angle 5.60148 ( 6) covalent geometry : bond 0.00498 ( 8992) covalent geometry : angle 0.81572 (12222) *********************** 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 : 0.897 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: 1.0008 time to fit residues: 267.8487 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 : 0.959 ------------------------------------------------------------------------------- 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 92 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN 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 100 ASN B 176 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.189516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154828 restraints weight = 10170.499| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.11 r_work: 0.3645 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9000 Z= 0.151 Angle : 0.598 6.543 12228 Z= 0.319 Chirality : 0.045 0.170 1393 Planarity : 0.005 0.072 1555 Dihedral : 4.408 20.649 1206 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.73 % Allowed : 15.98 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1095 helix: -0.30 (0.23), residues: 518 sheet: -1.02 (0.45), residues: 111 loop : -1.11 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 162 HIS 0.007 0.001 HIS A 309 PHE 0.020 0.002 PHE A 652 TYR 0.016 0.002 TYR A 653 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 403) hydrogen bonds : angle 4.88930 ( 1191) metal coordination : bond 0.02424 ( 8) metal coordination : angle 2.97927 ( 6) covalent geometry : bond 0.00335 ( 8992) covalent geometry : angle 0.59461 (12222) *********************** 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 209 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7385 (m-80) cc_final: 0.6838 (m-80) REVERT: A 361 LEU cc_start: 0.7079 (mt) cc_final: 0.6617 (tt) REVERT: A 415 PHE cc_start: 0.7258 (t80) cc_final: 0.6837 (t80) REVERT: A 508 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7874 (mmtp) REVERT: A 553 ARG cc_start: 0.6056 (mmm-85) cc_final: 0.5332 (mtp85) REVERT: A 662 VAL cc_start: 0.7943 (m) cc_final: 0.7720 (t) REVERT: A 750 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7727 (mmp-170) REVERT: A 760 ASP cc_start: 0.6553 (p0) cc_final: 0.6286 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: A 815 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: B 155 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: B 176 ASN cc_start: 0.8209 (t0) cc_final: 0.7954 (t0) REVERT: C 3 MET cc_start: 0.6406 (ttp) cc_final: 0.5647 (tpt) REVERT: C 43 LYS cc_start: 0.5934 (ptpp) cc_final: 0.5694 (mtmm) REVERT: C 56 LEU cc_start: 0.7395 (tp) cc_final: 0.7180 (tp) outliers start: 36 outliers final: 14 residues processed: 189 average time/residue: 0.9528 time to fit residues: 195.2194 Evaluate side-chains 160 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 929 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 104 optimal weight: 0.0770 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 599 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 = 0.4206 r_free = 0.4206 target = 0.189700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156369 restraints weight = 10365.299| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.94 r_work: 0.3572 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9000 Z= 0.130 Angle : 0.532 7.868 12228 Z= 0.285 Chirality : 0.043 0.142 1393 Planarity : 0.004 0.052 1555 Dihedral : 4.186 20.686 1204 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.53 % Allowed : 17.74 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1095 helix: -0.06 (0.23), residues: 526 sheet: -0.94 (0.43), residues: 121 loop : -1.20 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.002 PHE A 652 TYR 0.023 0.002 TYR A 867 ARG 0.004 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 403) hydrogen bonds : angle 4.56250 ( 1191) metal coordination : bond 0.01636 ( 8) metal coordination : angle 2.41452 ( 6) covalent geometry : bond 0.00289 ( 8992) covalent geometry : angle 0.52958 (12222) *********************** 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 185 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7913 (mmm) cc_final: 0.7701 (mmt) REVERT: A 334 PHE cc_start: 0.7554 (m-80) cc_final: 0.7009 (m-80) REVERT: A 361 LEU cc_start: 0.7262 (mt) cc_final: 0.6742 (tt) REVERT: A 415 PHE cc_start: 0.7338 (t80) cc_final: 0.7054 (t80) REVERT: A 508 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7930 (mmtp) REVERT: A 553 ARG cc_start: 0.6403 (mmm-85) cc_final: 0.5632 (mtp85) REVERT: A 750 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7653 (mmp-170) REVERT: A 760 ASP cc_start: 0.6710 (p0) cc_final: 0.6470 (p0) REVERT: A 811 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: A 815 GLN cc_start: 0.8035 (mm110) cc_final: 0.7682 (mt0) REVERT: A 826 TYR cc_start: 0.7628 (m-80) cc_final: 0.7376 (m-10) REVERT: A 926 THR cc_start: 0.8187 (t) cc_final: 0.7986 (m) REVERT: B 137 THR cc_start: 0.8460 (m) cc_final: 0.8101 (p) REVERT: B 155 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: B 176 ASN cc_start: 0.8380 (t0) cc_final: 0.8012 (t160) REVERT: C 8 CYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7362 (m) outliers start: 34 outliers final: 18 residues processed: 174 average time/residue: 0.9890 time to fit residues: 186.5881 Evaluate side-chains 164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 372 LEU Chi-restraints excluded: chain A residue 402 THR 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 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 153 LEU 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 108 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 573 GLN A 815 GLN ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.184633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150887 restraints weight = 10243.660| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.88 r_work: 0.3546 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9000 Z= 0.184 Angle : 0.596 9.676 12228 Z= 0.314 Chirality : 0.045 0.146 1393 Planarity : 0.004 0.039 1555 Dihedral : 4.449 21.811 1204 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.46 % Allowed : 18.88 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1095 helix: -0.09 (0.23), residues: 517 sheet: -0.92 (0.42), residues: 121 loop : -1.29 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.009 0.002 HIS A 309 PHE 0.016 0.002 PHE A 652 TYR 0.018 0.002 TYR A 877 ARG 0.004 0.001 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 403) hydrogen bonds : angle 4.61398 ( 1191) metal coordination : bond 0.01940 ( 8) metal coordination : angle 2.89442 ( 6) covalent geometry : bond 0.00431 ( 8992) covalent geometry : angle 0.59294 (12222) *********************** 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 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8054 (mm) cc_final: 0.7506 (tt) REVERT: A 124 MET cc_start: 0.8043 (mmm) cc_final: 0.7837 (mmt) REVERT: A 161 ASP cc_start: 0.7470 (t0) cc_final: 0.7257 (t0) REVERT: A 334 PHE cc_start: 0.7804 (m-80) cc_final: 0.7287 (m-80) REVERT: A 361 LEU cc_start: 0.7236 (mt) cc_final: 0.6680 (tt) REVERT: A 508 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8188 (mmtp) REVERT: A 553 ARG cc_start: 0.6630 (mmm-85) cc_final: 0.5909 (mtp85) REVERT: A 750 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7842 (mmm160) REVERT: A 760 ASP cc_start: 0.7027 (p0) cc_final: 0.6776 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: A 815 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: A 826 TYR cc_start: 0.7564 (m-80) cc_final: 0.7292 (m-10) REVERT: B 137 THR cc_start: 0.8468 (m) cc_final: 0.8179 (p) REVERT: B 145 THR cc_start: 0.8189 (m) cc_final: 0.7783 (p) REVERT: B 155 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: B 176 ASN cc_start: 0.8476 (t0) cc_final: 0.7982 (t0) REVERT: C 8 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7515 (m) REVERT: C 35 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7379 (mp) outliers start: 43 outliers final: 18 residues processed: 166 average time/residue: 1.0309 time to fit residues: 184.6201 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 481 ASP Chi-restraints excluded: chain A residue 482 CYS 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 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 790 ASN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 543 ASN A 613 HIS A 815 GLN A 872 HIS B 100 ASN B 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.182919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148806 restraints weight = 10319.316| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.80 r_work: 0.3574 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9000 Z= 0.151 Angle : 0.543 9.906 12228 Z= 0.287 Chirality : 0.043 0.133 1393 Planarity : 0.004 0.033 1555 Dihedral : 4.344 20.934 1204 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.25 % Allowed : 20.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1095 helix: 0.05 (0.23), residues: 516 sheet: -0.87 (0.43), residues: 121 loop : -1.29 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.013 0.002 PHE A 753 TYR 0.028 0.002 TYR A 867 ARG 0.002 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 403) hydrogen bonds : angle 4.51951 ( 1191) metal coordination : bond 0.01268 ( 8) metal coordination : angle 2.14913 ( 6) covalent geometry : bond 0.00352 ( 8992) covalent geometry : angle 0.54081 (12222) *********************** 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 177 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.984 Fit side-chains REVERT: A 37 ILE cc_start: 0.8164 (mm) cc_final: 0.7605 (tt) REVERT: A 124 MET cc_start: 0.7962 (mmm) cc_final: 0.7760 (mmt) REVERT: A 334 PHE cc_start: 0.7874 (m-80) cc_final: 0.7356 (m-80) REVERT: A 361 LEU cc_start: 0.7368 (mt) cc_final: 0.6785 (tt) REVERT: A 508 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8155 (mmtp) REVERT: A 553 ARG cc_start: 0.6572 (mmm-85) cc_final: 0.5967 (mtp85) REVERT: A 750 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7773 (mmm160) REVERT: A 760 ASP cc_start: 0.7083 (p0) cc_final: 0.6773 (OUTLIER) REVERT: A 826 TYR cc_start: 0.7475 (m-80) cc_final: 0.7229 (m-10) REVERT: B 137 THR cc_start: 0.8476 (m) cc_final: 0.8208 (m) REVERT: B 145 THR cc_start: 0.8094 (m) cc_final: 0.7725 (p) REVERT: B 155 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 176 ASN cc_start: 0.8510 (t0) cc_final: 0.8017 (t0) REVERT: C 3 MET cc_start: 0.7220 (ttp) cc_final: 0.6469 (tpt) REVERT: C 8 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7167 (m) outliers start: 41 outliers final: 19 residues processed: 161 average time/residue: 1.0069 time to fit residues: 175.3463 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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 924 MET Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 155 GLU 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 88 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 790 ASN A 872 HIS B 118 ASN D 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150916 restraints weight = 10292.786| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.90 r_work: 0.3557 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9000 Z= 0.124 Angle : 0.523 9.262 12228 Z= 0.278 Chirality : 0.042 0.130 1393 Planarity : 0.003 0.032 1555 Dihedral : 4.242 20.912 1204 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.36 % Allowed : 20.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1095 helix: 0.21 (0.23), residues: 514 sheet: -0.70 (0.43), residues: 121 loop : -1.23 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 415 TYR 0.021 0.001 TYR A 867 ARG 0.002 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 403) hydrogen bonds : angle 4.39041 ( 1191) metal coordination : bond 0.00897 ( 8) metal coordination : angle 1.99319 ( 6) covalent geometry : bond 0.00279 ( 8992) covalent geometry : angle 0.52152 (12222) *********************** 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 176 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.852 Fit side-chains REVERT: A 37 ILE cc_start: 0.8133 (mm) cc_final: 0.7707 (tt) REVERT: A 198 ASN cc_start: 0.8206 (m-40) cc_final: 0.7980 (m110) REVERT: A 217 TYR cc_start: 0.6864 (p90) cc_final: 0.6642 (p90) REVERT: A 334 PHE cc_start: 0.7813 (m-80) cc_final: 0.7234 (m-80) REVERT: A 361 LEU cc_start: 0.7389 (mt) cc_final: 0.6783 (tt) REVERT: A 411 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7835 (ptmm) REVERT: A 508 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8262 (mmtp) REVERT: A 522 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: A 624 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8029 (mpt-90) REVERT: A 750 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7777 (mmm160) REVERT: A 760 ASP cc_start: 0.6833 (p0) cc_final: 0.6581 (OUTLIER) REVERT: A 826 TYR cc_start: 0.7436 (m-80) cc_final: 0.7212 (m-10) REVERT: B 90 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6819 (tmt) REVERT: B 137 THR cc_start: 0.8519 (m) cc_final: 0.8238 (p) REVERT: B 145 THR cc_start: 0.8107 (m) cc_final: 0.7749 (p) REVERT: B 176 ASN cc_start: 0.8500 (t0) cc_final: 0.8177 (t0) REVERT: B 179 ASN cc_start: 0.7570 (t0) cc_final: 0.7115 (t0) REVERT: C 35 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7209 (mt) outliers start: 42 outliers final: 22 residues processed: 158 average time/residue: 1.0122 time to fit residues: 172.6127 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 624 ARG 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 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 129 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 872 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.183140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149373 restraints weight = 10359.946| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.82 r_work: 0.3554 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9000 Z= 0.141 Angle : 0.530 10.139 12228 Z= 0.280 Chirality : 0.043 0.129 1393 Planarity : 0.003 0.032 1555 Dihedral : 4.257 20.032 1204 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.25 % Allowed : 20.44 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1095 helix: 0.20 (0.23), residues: 515 sheet: -0.66 (0.44), residues: 121 loop : -1.22 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.013 0.002 PHE A 753 TYR 0.019 0.002 TYR A 867 ARG 0.002 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 403) hydrogen bonds : angle 4.38737 ( 1191) metal coordination : bond 0.00870 ( 8) metal coordination : angle 1.99586 ( 6) covalent geometry : bond 0.00325 ( 8992) covalent geometry : angle 0.52833 (12222) *********************** 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 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.971 Fit side-chains REVERT: A 37 ILE cc_start: 0.8137 (mm) cc_final: 0.7706 (tt) REVERT: A 198 ASN cc_start: 0.8179 (m-40) cc_final: 0.7965 (m110) REVERT: A 334 PHE cc_start: 0.7806 (m-80) cc_final: 0.7257 (m-80) REVERT: A 361 LEU cc_start: 0.7294 (mt) cc_final: 0.6661 (tt) REVERT: A 411 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7805 (ptmm) REVERT: A 508 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8253 (mmtp) REVERT: A 624 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8006 (mpt-90) REVERT: A 750 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7764 (mmm160) REVERT: A 760 ASP cc_start: 0.6902 (p0) cc_final: 0.6600 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: B 90 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6824 (tmt) REVERT: B 118 ASN cc_start: 0.8751 (m-40) cc_final: 0.8503 (m-40) REVERT: B 137 THR cc_start: 0.8512 (m) cc_final: 0.8266 (m) REVERT: B 145 THR cc_start: 0.8072 (m) cc_final: 0.7742 (p) REVERT: B 179 ASN cc_start: 0.7647 (t0) cc_final: 0.7295 (t0) REVERT: B 180 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6708 (mm) REVERT: C 3 MET cc_start: 0.7242 (ttp) cc_final: 0.6523 (tpt) REVERT: C 31 GLN cc_start: 0.6924 (tt0) cc_final: 0.6601 (tp-100) outliers start: 41 outliers final: 26 residues processed: 158 average time/residue: 1.0219 time to fit residues: 175.1169 Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 591 THR Chi-restraints excluded: chain A residue 624 ARG 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 818 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR 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 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 16 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 108 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 600 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 = 0.4141 r_free = 0.4141 target = 0.183664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150177 restraints weight = 10337.365| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.95 r_work: 0.3548 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9000 Z= 0.163 Angle : 0.558 10.763 12228 Z= 0.296 Chirality : 0.044 0.132 1393 Planarity : 0.004 0.032 1555 Dihedral : 4.413 22.343 1204 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.25 % Allowed : 20.64 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1095 helix: 0.06 (0.23), residues: 521 sheet: -0.68 (0.44), residues: 121 loop : -1.40 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.008 0.001 HIS A 309 PHE 0.016 0.002 PHE A 415 TYR 0.022 0.002 TYR A 867 ARG 0.002 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 403) hydrogen bonds : angle 4.45500 ( 1191) metal coordination : bond 0.00957 ( 8) metal coordination : angle 2.23733 ( 6) covalent geometry : bond 0.00379 ( 8992) covalent geometry : angle 0.55593 (12222) *********************** 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 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.962 Fit side-chains REVERT: A 37 ILE cc_start: 0.8242 (mm) cc_final: 0.7815 (tt) REVERT: A 198 ASN cc_start: 0.8218 (m-40) cc_final: 0.8000 (m110) REVERT: A 260 ASP cc_start: 0.7086 (t0) cc_final: 0.6657 (m-30) REVERT: A 334 PHE cc_start: 0.7909 (m-80) cc_final: 0.7436 (m-80) REVERT: A 508 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8321 (mmtp) REVERT: A 519 MET cc_start: 0.7690 (mtm) cc_final: 0.7479 (ttm) REVERT: A 624 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8034 (mpt-90) REVERT: A 750 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7745 (mmm160) REVERT: A 760 ASP cc_start: 0.7176 (p0) cc_final: 0.6894 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: A 887 TYR cc_start: 0.7989 (t80) cc_final: 0.7706 (t80) REVERT: B 90 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6867 (tmt) REVERT: B 137 THR cc_start: 0.8503 (m) cc_final: 0.8265 (m) REVERT: B 145 THR cc_start: 0.7983 (m) cc_final: 0.7656 (p) REVERT: B 179 ASN cc_start: 0.7688 (t0) cc_final: 0.7388 (t0) REVERT: B 180 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6881 (mt) REVERT: C 3 MET cc_start: 0.7267 (ttp) cc_final: 0.6493 (tpt) REVERT: C 31 GLN cc_start: 0.7171 (tt0) cc_final: 0.6747 (tp-100) outliers start: 41 outliers final: 26 residues processed: 163 average time/residue: 1.0478 time to fit residues: 184.0085 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 624 ARG 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 818 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 ILE 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 46 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 40.0000 chunk 8 optimal weight: 0.0010 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 0.0570 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 191 GLN A 543 ASN A 872 HIS C 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.186698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153511 restraints weight = 10406.476| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.81 r_work: 0.3590 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9000 Z= 0.097 Angle : 0.505 10.714 12228 Z= 0.267 Chirality : 0.041 0.137 1393 Planarity : 0.003 0.034 1555 Dihedral : 4.036 17.811 1204 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.39 % Allowed : 22.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1095 helix: 0.46 (0.24), residues: 516 sheet: -0.55 (0.48), residues: 100 loop : -1.15 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 PHE 0.015 0.001 PHE A 415 TYR 0.014 0.001 TYR A 867 ARG 0.002 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 403) hydrogen bonds : angle 4.22139 ( 1191) metal coordination : bond 0.00440 ( 8) metal coordination : angle 1.63695 ( 6) covalent geometry : bond 0.00205 ( 8992) covalent geometry : angle 0.50407 (12222) *********************** 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: 23 poor density : 139 time to evaluate : 1.031 Fit side-chains REVERT: A 37 ILE cc_start: 0.8154 (mm) cc_final: 0.7814 (tt) REVERT: A 196 MET cc_start: 0.7625 (mtp) cc_final: 0.7345 (mtm) REVERT: A 260 ASP cc_start: 0.6849 (t0) cc_final: 0.6376 (m-30) REVERT: A 334 PHE cc_start: 0.7647 (m-80) cc_final: 0.7183 (m-80) REVERT: A 494 ILE cc_start: 0.8478 (mm) cc_final: 0.8193 (mp) REVERT: A 508 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8247 (mmtp) REVERT: A 624 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7947 (mpt-90) REVERT: A 750 ARG cc_start: 0.7866 (mmp-170) cc_final: 0.7653 (mmm160) REVERT: A 760 ASP cc_start: 0.6628 (p0) cc_final: 0.6414 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: A 887 TYR cc_start: 0.7862 (t80) cc_final: 0.7556 (t80) REVERT: B 90 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6709 (tmt) REVERT: B 137 THR cc_start: 0.8472 (m) cc_final: 0.8201 (p) REVERT: B 145 THR cc_start: 0.8129 (m) cc_final: 0.7802 (p) REVERT: B 179 ASN cc_start: 0.7662 (t0) cc_final: 0.7326 (t0) REVERT: B 180 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6743 (mt) REVERT: C 3 MET cc_start: 0.7247 (ttp) cc_final: 0.6400 (tpt) REVERT: C 31 GLN cc_start: 0.6884 (tt0) cc_final: 0.6431 (tp-100) outliers start: 23 outliers final: 10 residues processed: 153 average time/residue: 1.0015 time to fit residues: 166.0581 Evaluate side-chains 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 872 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.187481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154686 restraints weight = 10249.887| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.83 r_work: 0.3604 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9000 Z= 0.107 Angle : 0.514 10.680 12228 Z= 0.272 Chirality : 0.041 0.123 1393 Planarity : 0.004 0.060 1555 Dihedral : 4.011 20.033 1204 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.97 % Allowed : 23.24 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1095 helix: 0.46 (0.24), residues: 517 sheet: -0.57 (0.47), residues: 105 loop : -1.11 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.013 0.001 PHE A 415 TYR 0.027 0.001 TYR A 867 ARG 0.002 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 403) hydrogen bonds : angle 4.17708 ( 1191) metal coordination : bond 0.00618 ( 8) metal coordination : angle 1.82585 ( 6) covalent geometry : bond 0.00234 ( 8992) covalent geometry : angle 0.51214 (12222) ********************** 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 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.037 Fit side-chains REVERT: A 37 ILE cc_start: 0.8234 (mm) cc_final: 0.7953 (tt) REVERT: A 196 MET cc_start: 0.7765 (mtp) cc_final: 0.7442 (mtm) REVERT: A 260 ASP cc_start: 0.6928 (t0) cc_final: 0.6496 (m-30) REVERT: A 334 PHE cc_start: 0.7722 (m-80) cc_final: 0.7231 (m-80) REVERT: A 508 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8242 (mmtp) REVERT: A 624 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7982 (mpt-90) REVERT: A 750 ARG cc_start: 0.7869 (mmp-170) cc_final: 0.7656 (mmm160) REVERT: A 760 ASP cc_start: 0.6622 (p0) cc_final: 0.6413 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: A 887 TYR cc_start: 0.7935 (t80) cc_final: 0.7700 (t80) REVERT: B 90 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6793 (tmt) REVERT: B 137 THR cc_start: 0.8491 (m) cc_final: 0.8264 (m) REVERT: B 145 THR cc_start: 0.8127 (m) cc_final: 0.7812 (p) REVERT: B 179 ASN cc_start: 0.7693 (t0) cc_final: 0.7388 (t0) REVERT: B 180 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6860 (mt) REVERT: C 3 MET cc_start: 0.7325 (ttp) cc_final: 0.6554 (tpt) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 0.9937 time to fit residues: 156.4479 Evaluate side-chains 141 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 386 ASN A 543 ASN A 791 ASN A 872 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151631 restraints weight = 10204.078| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.89 r_work: 0.3563 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5452 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= 0.145 Angle : 0.547 10.755 12228 Z= 0.290 Chirality : 0.043 0.177 1393 Planarity : 0.004 0.058 1555 Dihedral : 4.210 20.780 1204 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.07 % Allowed : 23.03 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1095 helix: 0.25 (0.23), residues: 521 sheet: -0.53 (0.46), residues: 123 loop : -1.23 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 290 HIS 0.006 0.001 HIS A 309 PHE 0.016 0.002 PHE A 415 TYR 0.028 0.002 TYR A 867 ARG 0.002 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 403) hydrogen bonds : angle 4.29096 ( 1191) metal coordination : bond 0.00842 ( 8) metal coordination : angle 1.86710 ( 6) covalent geometry : bond 0.00338 ( 8992) covalent geometry : angle 0.54596 (12222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7087.11 seconds wall clock time: 121 minutes 25.76 seconds (7285.76 seconds total)