Starting phenix.real_space_refine on Thu Mar 13 06:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bv1_30209/03_2025/7bv1_30209.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bv1_30209/03_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_30209/03_2025/7bv1_30209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_2025/7bv1_30209.map" model { file = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_2025/7bv1_30209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bv1_30209/03_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.09, per 1000 atoms: 0.69 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.43 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: 3.45 Time building geometry restraints manager: 2.81 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.210 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.820 ------------------------------------------------------------------------------- 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 : 0.005 0.052 8992 Z= 0.327 Angle : 0.816 8.000 12222 Z= 0.527 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 *********************** 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 : 0.937 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: 1.2362 time to fit residues: 330.6164 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 : 1.003 ------------------------------------------------------------------------------- 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 0.034 8992 Z= 0.214 Angle : 0.595 6.543 12222 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 *********************** 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 : 0.874 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: 0.9688 time to fit residues: 198.3511 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 : 0.984 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.3740 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.187811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.153644 restraints weight = 10395.064| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.82 r_work: 0.3592 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8992 Z= 0.187 Angle : 0.529 7.851 12222 Z= 0.285 Chirality : 0.042 0.142 1393 Planarity : 0.004 0.052 1555 Dihedral : 4.179 20.651 1204 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.52 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: -0.99 (0.25), residues: 1095 helix: -0.05 (0.23), residues: 526 sheet: -0.94 (0.43), residues: 121 loop : -1.19 (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 0.021 0.002 TYR A 867 ARG 0.004 0.000 ARG A 392 *********************** 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 : 0.938 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7871 (mmm) cc_final: 0.7631 (mmt) REVERT: A 334 PHE cc_start: 0.7511 (m-80) cc_final: 0.6963 (m-80) REVERT: A 361 LEU cc_start: 0.7222 (mt) cc_final: 0.6690 (tt) REVERT: A 415 PHE cc_start: 0.7359 (t80) cc_final: 0.7020 (t80) REVERT: A 508 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7917 (mmtp) REVERT: A 553 ARG cc_start: 0.6338 (mmm-85) cc_final: 0.5529 (mtp85) REVERT: A 750 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7626 (mmp-170) REVERT: A 760 ASP cc_start: 0.6622 (p0) cc_final: 0.6388 (p0) REVERT: A 811 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: A 815 GLN cc_start: 0.7936 (mm110) cc_final: 0.7710 (mt0) REVERT: A 826 TYR cc_start: 0.7649 (m-80) cc_final: 0.7377 (m-10) REVERT: A 926 THR cc_start: 0.8135 (t) cc_final: 0.7923 (m) REVERT: B 137 THR cc_start: 0.8430 (m) cc_final: 0.8056 (p) REVERT: B 155 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: B 176 ASN cc_start: 0.8399 (t0) cc_final: 0.8013 (t160) REVERT: C 8 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7338 (m) outliers start: 34 outliers final: 18 residues processed: 174 average time/residue: 0.9468 time to fit residues: 178.5577 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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: 0.0170 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 B 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.185118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151023 restraints weight = 10249.288| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.99 r_work: 0.3508 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8992 Z= 0.274 Angle : 0.581 9.586 12222 Z= 0.309 Chirality : 0.045 0.139 1393 Planarity : 0.004 0.040 1555 Dihedral : 4.403 21.831 1204 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.46 % Allowed : 18.57 % Favored : 76.97 % 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: -1.05 (0.24), residues: 1095 helix: -0.07 (0.23), residues: 517 sheet: -0.91 (0.42), residues: 121 loop : -1.26 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.010 0.002 HIS A 309 PHE 0.016 0.002 PHE A 652 TYR 0.015 0.002 TYR A 546 ARG 0.003 0.001 ARG A 392 *********************** 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 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.7998 (mm) cc_final: 0.7406 (tt) REVERT: A 124 MET cc_start: 0.8012 (mmm) cc_final: 0.7799 (mmt) REVERT: A 161 ASP cc_start: 0.7450 (t0) cc_final: 0.7163 (t0) REVERT: A 334 PHE cc_start: 0.7719 (m-80) cc_final: 0.7186 (m-80) REVERT: A 361 LEU cc_start: 0.7177 (mt) cc_final: 0.6611 (tt) REVERT: A 415 PHE cc_start: 0.7573 (t80) cc_final: 0.7200 (t80) REVERT: A 508 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8137 (mmtp) REVERT: A 553 ARG cc_start: 0.6489 (mmm-85) cc_final: 0.5713 (mtp85) REVERT: A 750 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7867 (mmm160) REVERT: A 760 ASP cc_start: 0.6996 (p0) cc_final: 0.6736 (OUTLIER) REVERT: A 815 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: A 826 TYR cc_start: 0.7589 (m-80) cc_final: 0.7286 (m-10) REVERT: B 137 THR cc_start: 0.8430 (m) cc_final: 0.8117 (p) REVERT: B 145 THR cc_start: 0.8146 (m) cc_final: 0.7762 (p) REVERT: B 155 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: B 176 ASN cc_start: 0.8426 (t0) cc_final: 0.7924 (t0) REVERT: C 8 CYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7457 (m) REVERT: C 35 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7241 (mp) REVERT: C 62 MET cc_start: 0.6209 (pmm) cc_final: 0.5909 (pmm) outliers start: 43 outliers final: 18 residues processed: 169 average time/residue: 1.0258 time to fit residues: 187.2717 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 815 GLN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 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: 10.0000 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 752 HIS A 872 HIS B 100 ASN B 118 ASN B 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.182038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148586 restraints weight = 10242.876| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.87 r_work: 0.3509 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8992 Z= 0.356 Angle : 0.620 10.027 12222 Z= 0.329 Chirality : 0.047 0.145 1393 Planarity : 0.004 0.039 1555 Dihedral : 4.689 22.675 1204 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.08 % Allowed : 19.19 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.24), residues: 1095 helix: -0.19 (0.23), residues: 515 sheet: -0.98 (0.42), residues: 121 loop : -1.38 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.008 0.002 HIS A 309 PHE 0.016 0.002 PHE A 652 TYR 0.025 0.002 TYR A 867 ARG 0.004 0.001 ARG A 651 *********************** 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 188 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 333 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8109 (pt) REVERT: A 334 PHE cc_start: 0.7972 (m-80) cc_final: 0.7404 (m-80) REVERT: A 361 LEU cc_start: 0.7203 (mt) cc_final: 0.6581 (tt) REVERT: A 508 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8268 (mmtp) REVERT: A 553 ARG cc_start: 0.6713 (mmm-85) cc_final: 0.6486 (mmm-85) REVERT: A 750 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7763 (mmm160) REVERT: A 760 ASP cc_start: 0.7377 (p0) cc_final: 0.7034 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: A 826 TYR cc_start: 0.7527 (m-80) cc_final: 0.7247 (m-10) REVERT: A 887 TYR cc_start: 0.7974 (t80) cc_final: 0.7624 (t80) REVERT: B 90 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6787 (tmt) REVERT: B 137 THR cc_start: 0.8537 (m) cc_final: 0.8265 (m) REVERT: B 145 THR cc_start: 0.8182 (m) cc_final: 0.7797 (p) REVERT: B 176 ASN cc_start: 0.8570 (t0) cc_final: 0.8244 (t0) REVERT: B 179 ASN cc_start: 0.7685 (t0) cc_final: 0.7227 (t0) REVERT: C 35 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7480 (mp) REVERT: C 43 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6441 (mtmp) outliers start: 49 outliers final: 26 residues processed: 170 average time/residue: 1.0279 time to fit residues: 188.5638 Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 333 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 343 SER 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 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain 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 C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain 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: 3.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 B 158 GLN D 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.183311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150119 restraints weight = 10168.093| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.92 r_work: 0.3541 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8992 Z= 0.245 Angle : 0.560 9.995 12222 Z= 0.298 Chirality : 0.043 0.134 1393 Planarity : 0.004 0.032 1555 Dihedral : 4.510 21.458 1204 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.05 % Allowed : 21.27 % Favored : 74.69 % 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: -1.07 (0.24), residues: 1095 helix: -0.01 (0.23), residues: 514 sheet: -0.82 (0.43), residues: 121 loop : -1.40 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.015 0.002 PHE A 415 TYR 0.016 0.002 TYR A 867 ARG 0.003 0.000 ARG A 726 *********************** 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 175 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8178 (mm) cc_final: 0.7633 (tt) REVERT: A 334 PHE cc_start: 0.7896 (m-80) cc_final: 0.7336 (m-80) REVERT: A 508 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8245 (mmtp) REVERT: A 519 MET cc_start: 0.7827 (mtm) cc_final: 0.7613 (ttm) REVERT: A 553 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.6086 (mtp85) REVERT: A 718 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8464 (ttpt) REVERT: A 750 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7761 (mmm160) REVERT: A 760 ASP cc_start: 0.7346 (p0) cc_final: 0.7001 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: A 826 TYR cc_start: 0.7428 (m-80) cc_final: 0.7218 (m-10) REVERT: A 887 TYR cc_start: 0.7971 (t80) cc_final: 0.7626 (t80) REVERT: B 90 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7105 (tmm) REVERT: B 118 ASN cc_start: 0.8693 (m-40) cc_final: 0.8459 (m-40) REVERT: B 137 THR cc_start: 0.8534 (m) cc_final: 0.8268 (m) REVERT: B 145 THR cc_start: 0.8156 (m) cc_final: 0.7809 (p) REVERT: B 179 ASN cc_start: 0.7733 (t0) cc_final: 0.7434 (t0) REVERT: C 3 MET cc_start: 0.7373 (ttp) cc_final: 0.6599 (tpt) REVERT: C 35 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7456 (mp) outliers start: 39 outliers final: 22 residues processed: 159 average time/residue: 1.2039 time to fit residues: 206.0295 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 718 LYS Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 924 MET 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: 6.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 752 HIS A 872 HIS B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.183551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149946 restraints weight = 10290.581| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.80 r_work: 0.3586 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8992 Z= 0.163 Angle : 0.521 10.726 12222 Z= 0.276 Chirality : 0.042 0.125 1393 Planarity : 0.003 0.033 1555 Dihedral : 4.263 21.299 1204 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.73 % Allowed : 20.64 % Favored : 75.62 % 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: -0.80 (0.25), residues: 1095 helix: 0.24 (0.24), residues: 514 sheet: -0.68 (0.44), residues: 121 loop : -1.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.013 0.001 PHE A 920 TYR 0.018 0.001 TYR A 453 ARG 0.002 0.000 ARG A 726 *********************** 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 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8142 (mm) cc_final: 0.7727 (tt) REVERT: A 196 MET cc_start: 0.7693 (mtp) cc_final: 0.7404 (mtm) REVERT: A 198 ASN cc_start: 0.8157 (m-40) cc_final: 0.7920 (m110) REVERT: A 334 PHE cc_start: 0.7796 (m-80) cc_final: 0.7275 (m-80) REVERT: A 361 LEU cc_start: 0.7117 (mp) cc_final: 0.6634 (tp) REVERT: A 508 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8268 (mmtp) REVERT: A 624 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8010 (mpt-90) REVERT: A 750 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7749 (mmm160) REVERT: A 760 ASP cc_start: 0.7131 (p0) cc_final: 0.6823 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: A 887 TYR cc_start: 0.7923 (t80) cc_final: 0.7608 (t80) REVERT: B 137 THR cc_start: 0.8515 (m) cc_final: 0.8274 (m) REVERT: B 145 THR cc_start: 0.8071 (m) cc_final: 0.7740 (p) REVERT: B 179 ASN cc_start: 0.7702 (t0) cc_final: 0.7401 (t0) REVERT: B 180 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6502 (mm) REVERT: C 3 MET cc_start: 0.7338 (ttp) cc_final: 0.6644 (tpt) REVERT: C 31 GLN cc_start: 0.6879 (tt0) cc_final: 0.6561 (tp-100) REVERT: C 35 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7338 (mp) REVERT: C 43 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6456 (mtmp) outliers start: 36 outliers final: 22 residues processed: 153 average time/residue: 1.1120 time to fit residues: 184.6059 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 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 761 ASP Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain 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: 9.9990 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 C 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149739 restraints weight = 10314.003| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.88 r_work: 0.3532 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8992 Z= 0.277 Angle : 0.575 10.349 12222 Z= 0.304 Chirality : 0.044 0.130 1393 Planarity : 0.004 0.033 1555 Dihedral : 4.478 20.745 1204 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.36 % Allowed : 20.33 % 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: -1.06 (0.24), residues: 1095 helix: 0.03 (0.23), residues: 520 sheet: -0.71 (0.44), residues: 121 loop : -1.48 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 916 HIS 0.009 0.001 HIS A 309 PHE 0.014 0.002 PHE A 753 TYR 0.016 0.002 TYR A 606 ARG 0.003 0.000 ARG A 651 *********************** 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 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8197 (mm) cc_final: 0.7741 (tt) REVERT: A 196 MET cc_start: 0.7831 (mtp) cc_final: 0.7501 (mtm) REVERT: A 198 ASN cc_start: 0.8155 (m-40) cc_final: 0.7914 (m110) REVERT: A 260 ASP cc_start: 0.7100 (t0) cc_final: 0.6706 (m-30) REVERT: A 334 PHE cc_start: 0.7836 (m-80) cc_final: 0.7331 (m-80) REVERT: A 508 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8296 (mmtp) REVERT: A 624 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8118 (mpt-90) REVERT: A 718 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8502 (ttpt) REVERT: A 750 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7757 (mmm160) REVERT: A 760 ASP cc_start: 0.7362 (p0) cc_final: 0.7036 (OUTLIER) REVERT: A 811 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: A 887 TYR cc_start: 0.7992 (t80) cc_final: 0.7739 (t80) REVERT: B 87 MET cc_start: 0.7910 (mtm) cc_final: 0.7650 (OUTLIER) REVERT: B 90 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6843 (tmt) REVERT: B 137 THR cc_start: 0.8537 (m) cc_final: 0.8290 (m) REVERT: B 145 THR cc_start: 0.8060 (m) cc_final: 0.7725 (p) REVERT: B 179 ASN cc_start: 0.7751 (t0) cc_final: 0.7465 (t0) REVERT: C 3 MET cc_start: 0.7380 (ttp) cc_final: 0.6632 (tpt) REVERT: C 31 GLN cc_start: 0.7143 (tt0) cc_final: 0.6826 (tp40) REVERT: C 43 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6474 (mtmp) outliers start: 42 outliers final: 25 residues processed: 157 average time/residue: 1.0371 time to fit residues: 175.5808 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 415 PHE 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 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 718 LYS Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU 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 C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 43 LYS 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: 4.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 872 HIS B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148824 restraints weight = 10281.854| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.87 r_work: 0.3492 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8992 Z= 0.308 Angle : 0.595 10.484 12222 Z= 0.316 Chirality : 0.046 0.133 1393 Planarity : 0.004 0.034 1555 Dihedral : 4.644 23.128 1204 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -1.17 (0.24), residues: 1095 helix: -0.04 (0.23), residues: 520 sheet: -0.77 (0.45), residues: 121 loop : -1.56 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.009 0.001 HIS A 309 PHE 0.014 0.002 PHE A 652 TYR 0.018 0.002 TYR A 606 ARG 0.003 0.001 ARG A 651 *********************** 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 179 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8206 (mm) cc_final: 0.7689 (tt) REVERT: A 196 MET cc_start: 0.7866 (mtp) cc_final: 0.7542 (mtm) REVERT: A 260 ASP cc_start: 0.7135 (t0) cc_final: 0.6727 (m-30) REVERT: A 334 PHE cc_start: 0.7887 (m-80) cc_final: 0.7418 (m-80) REVERT: A 361 LEU cc_start: 0.6907 (mp) cc_final: 0.6706 (mp) REVERT: A 508 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8230 (mmtp) REVERT: A 718 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8473 (ttpt) REVERT: A 750 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7738 (mmm160) REVERT: A 887 TYR cc_start: 0.8039 (t80) cc_final: 0.7816 (t80) REVERT: B 87 MET cc_start: 0.7848 (mtm) cc_final: 0.7579 (OUTLIER) REVERT: B 90 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6988 (tmt) REVERT: B 118 ASN cc_start: 0.8773 (m-40) cc_final: 0.8508 (m-40) REVERT: B 145 THR cc_start: 0.8149 (m) cc_final: 0.7803 (p) REVERT: B 179 ASN cc_start: 0.7759 (t0) cc_final: 0.7489 (t0) REVERT: C 3 MET cc_start: 0.7425 (ttp) cc_final: 0.6788 (tpt) REVERT: C 27 LYS cc_start: 0.6992 (tttp) cc_final: 0.6751 (mtpp) REVERT: C 31 GLN cc_start: 0.7210 (tt0) cc_final: 0.6839 (tp-100) REVERT: C 43 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6449 (mtmp) outliers start: 42 outliers final: 25 residues processed: 164 average time/residue: 1.0571 time to fit residues: 187.1979 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 343 SER 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 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 876 GLU 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 C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 872 HIS A 874 ASN B 158 GLN C 34 GLN C 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152143 restraints weight = 10230.412| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.90 r_work: 0.3562 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8992 Z= 0.156 Angle : 0.529 10.975 12222 Z= 0.282 Chirality : 0.042 0.127 1393 Planarity : 0.003 0.035 1555 Dihedral : 4.304 19.863 1204 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.80 % Allowed : 22.41 % 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: -0.88 (0.25), residues: 1095 helix: 0.20 (0.23), residues: 522 sheet: -0.73 (0.48), residues: 105 loop : -1.38 (0.26), residues: 468 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 0.013 0.001 PHE A 920 TYR 0.014 0.001 TYR A 606 ARG 0.002 0.000 ARG A 197 ********************** 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 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8208 (mm) cc_final: 0.7826 (tt) REVERT: A 196 MET cc_start: 0.7794 (mtp) cc_final: 0.7493 (mtm) REVERT: A 260 ASP cc_start: 0.7010 (t0) cc_final: 0.6542 (m-30) REVERT: A 334 PHE cc_start: 0.7791 (m-80) cc_final: 0.7330 (m-80) REVERT: A 494 ILE cc_start: 0.8554 (mm) cc_final: 0.8245 (mp) REVERT: A 508 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8227 (mmtp) REVERT: A 522 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7134 (pp20) REVERT: A 887 TYR cc_start: 0.7963 (t80) cc_final: 0.7721 (t80) REVERT: B 145 THR cc_start: 0.8185 (m) cc_final: 0.7842 (p) REVERT: B 179 ASN cc_start: 0.7767 (t0) cc_final: 0.7530 (t0) REVERT: C 3 MET cc_start: 0.7471 (ttp) cc_final: 0.6786 (tpt) REVERT: C 31 GLN cc_start: 0.7093 (tt0) cc_final: 0.6718 (tp40) REVERT: C 43 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6437 (mtmp) outliers start: 27 outliers final: 18 residues processed: 157 average time/residue: 1.1013 time to fit residues: 186.7987 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 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 522 GLU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 492 GLN A 543 ASN A 752 HIS A 872 HIS A 874 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144485 restraints weight = 10197.741| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.91 r_work: 0.3528 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8992 Z= 0.339 Angle : 0.622 10.862 12222 Z= 0.329 Chirality : 0.046 0.143 1393 Planarity : 0.004 0.033 1555 Dihedral : 4.665 22.687 1204 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.42 % Allowed : 22.10 % Favored : 74.48 % 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: -1.14 (0.24), residues: 1095 helix: -0.07 (0.23), residues: 521 sheet: -0.76 (0.45), residues: 121 loop : -1.50 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.009 0.001 HIS A 309 PHE 0.015 0.002 PHE A 652 TYR 0.020 0.002 TYR A 606 ARG 0.004 0.001 ARG A 750 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7055.08 seconds wall clock time: 123 minutes 7.47 seconds (7387.47 seconds total)