Starting phenix.real_space_refine on Sat Dec 28 14:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bv1_30209/12_2024/7bv1_30209.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bv1_30209/12_2024/7bv1_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_30209/12_2024/7bv1_30209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bv1_30209/12_2024/7bv1_30209.map" model { file = "/net/cci-nas-00/data/ceres_data/7bv1_30209/12_2024/7bv1_30209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bv1_30209/12_2024/7bv1_30209.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 64 5.16 5 C 5626 2.51 5 N 1460 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.30, per 1000 atoms: 0.60 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 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: 1.23 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: 3.25 Time building geometry restraints manager: 2.72 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.410 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 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 : 0.999 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: 1.0776 time to fit residues: 287.2372 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 : 1.036 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2662 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= 0.215 Angle : 0.595 6.543 12222 Z= 0.319 Chirality : 0.045 0.170 1393 Planarity : 0.005 0.073 1555 Dihedral : 4.409 20.646 1206 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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 0.004 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 : 1.010 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.6258 (p0) cc_final: 0.6026 (p0) REVERT: A 334 PHE cc_start: 0.7382 (m-80) cc_final: 0.6974 (m-80) REVERT: A 415 PHE cc_start: 0.6844 (t80) cc_final: 0.6619 (t80) REVERT: A 508 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7751 (mmtp) REVERT: A 750 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7244 (mmp-170) REVERT: A 760 ASP cc_start: 0.6280 (p0) cc_final: 0.6061 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: B 155 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: C 3 MET cc_start: 0.6038 (ttp) cc_final: 0.5757 (tpt) REVERT: C 56 LEU cc_start: 0.7691 (tp) cc_final: 0.7480 (tp) outliers start: 36 outliers final: 14 residues processed: 189 average time/residue: 0.9927 time to fit residues: 203.0256 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 599 HIS A 698 GLN ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8992 Z= 0.289 Angle : 0.623 8.112 12222 Z= 0.330 Chirality : 0.046 0.164 1393 Planarity : 0.004 0.052 1555 Dihedral : 4.625 22.902 1204 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.36 % Allowed : 18.26 % Favored : 77.39 % 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: -1.28 (0.24), residues: 1095 helix: -0.28 (0.22), residues: 522 sheet: -1.08 (0.42), residues: 121 loop : -1.33 (0.27), residues: 452 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 0.018 0.002 PHE A 652 TYR 0.023 0.002 TYR A 867 ARG 0.005 0.001 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 194 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.7899 (mm) cc_final: 0.7598 (tt) REVERT: A 334 PHE cc_start: 0.7904 (m-80) cc_final: 0.7467 (m-80) REVERT: A 508 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8109 (mmtp) REVERT: A 750 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7381 (mmm160) REVERT: A 760 ASP cc_start: 0.6776 (p0) cc_final: 0.6527 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: B 155 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: B 176 ASN cc_start: 0.8452 (t0) cc_final: 0.8130 (t0) REVERT: C 3 MET cc_start: 0.6474 (ttp) cc_final: 0.6187 (tpt) REVERT: C 35 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7283 (mp) outliers start: 42 outliers final: 22 residues processed: 183 average time/residue: 1.0566 time to fit residues: 208.3456 Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 662 VAL 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 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 97 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 408 GLN A 543 ASN A 613 HIS A 872 HIS B 100 ASN B 118 ASN B 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8992 Z= 0.244 Angle : 0.561 9.804 12222 Z= 0.296 Chirality : 0.044 0.141 1393 Planarity : 0.004 0.038 1555 Dihedral : 4.476 22.472 1204 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.36 % Allowed : 19.92 % 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: -1.09 (0.24), residues: 1095 helix: -0.06 (0.23), residues: 516 sheet: -0.95 (0.42), residues: 121 loop : -1.34 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 PHE 0.014 0.002 PHE A 652 TYR 0.023 0.002 TYR A 867 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7947 (m-80) cc_final: 0.7494 (m-80) REVERT: A 508 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8068 (mmtp) REVERT: A 750 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7353 (mmm160) REVERT: A 760 ASP cc_start: 0.6744 (p0) cc_final: 0.6466 (p0) REVERT: B 155 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: B 176 ASN cc_start: 0.8511 (t0) cc_final: 0.8284 (t160) REVERT: C 3 MET cc_start: 0.6532 (ttp) cc_final: 0.6296 (tpt) outliers start: 42 outliers final: 18 residues processed: 165 average time/residue: 1.1389 time to fit residues: 201.7560 Evaluate side-chains 151 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 434 SER 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 680 THR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 698 GLN A 872 HIS B 118 ASN D 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8992 Z= 0.178 Angle : 0.526 8.882 12222 Z= 0.280 Chirality : 0.042 0.131 1393 Planarity : 0.004 0.033 1555 Dihedral : 4.295 22.319 1204 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.36 % Allowed : 20.23 % Favored : 75.41 % 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: -0.85 (0.25), residues: 1095 helix: 0.18 (0.23), residues: 517 sheet: -0.77 (0.42), residues: 121 loop : -1.30 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.013 0.002 PHE A 920 TYR 0.016 0.001 TYR A 867 ARG 0.002 0.000 ARG A 555 *********************** 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 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.7911 (mm) cc_final: 0.7640 (tt) REVERT: A 334 PHE cc_start: 0.7837 (m-80) cc_final: 0.7404 (m-80) REVERT: A 508 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8135 (mmtp) REVERT: A 760 ASP cc_start: 0.6721 (p0) cc_final: 0.6453 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: B 90 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6774 (tmt) REVERT: B 176 ASN cc_start: 0.8431 (t0) cc_final: 0.8206 (t0) REVERT: C 35 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7186 (mt) outliers start: 42 outliers final: 21 residues processed: 157 average time/residue: 1.0828 time to fit residues: 183.7063 Evaluate side-chains 145 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 434 SER 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 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 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 D residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 198 ASN A 224 GLN A 543 ASN A 600 ASN A 752 HIS A 872 HIS B 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8992 Z= 0.409 Angle : 0.656 9.935 12222 Z= 0.348 Chirality : 0.049 0.162 1393 Planarity : 0.005 0.042 1555 Dihedral : 4.885 22.568 1204 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.29 % Allowed : 19.29 % Favored : 75.41 % 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: -1.42 (0.24), residues: 1095 helix: -0.34 (0.22), residues: 527 sheet: -0.99 (0.40), residues: 134 loop : -1.56 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.009 0.002 HIS A 309 PHE 0.017 0.003 PHE A 652 TYR 0.022 0.003 TYR A 546 ARG 0.005 0.001 ARG A 651 *********************** 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 178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.081 Fit side-chains REVERT: A 334 PHE cc_start: 0.8036 (m-80) cc_final: 0.7592 (m-80) REVERT: A 361 LEU cc_start: 0.7084 (mp) cc_final: 0.6696 (tt) REVERT: A 508 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8215 (mmtp) REVERT: A 811 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6761 (mm-30) REVERT: B 90 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6988 (ttt) REVERT: B 176 ASN cc_start: 0.8462 (t0) cc_final: 0.8071 (t0) REVERT: B 180 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6555 (mm) outliers start: 51 outliers final: 28 residues processed: 165 average time/residue: 1.1742 time to fit residues: 208.6358 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 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 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 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 D residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 752 HIS A 872 HIS B 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.003 0.029 8992 Z= 0.169 Angle : 0.528 10.546 12222 Z= 0.281 Chirality : 0.042 0.145 1393 Planarity : 0.004 0.034 1555 Dihedral : 4.382 21.664 1204 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.63 % Allowed : 21.16 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1095 helix: 0.16 (0.23), residues: 515 sheet: -0.75 (0.43), residues: 121 loop : -1.36 (0.27), residues: 459 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 0.017 0.001 TYR A 887 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: 35 poor density : 133 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8007 (mm) cc_final: 0.7738 (tt) REVERT: A 334 PHE cc_start: 0.7940 (m-80) cc_final: 0.7487 (m-80) REVERT: A 411 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7959 (ptmm) REVERT: A 508 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8119 (mmtp) REVERT: A 624 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7891 (mpt-90) REVERT: A 760 ASP cc_start: 0.6802 (p0) cc_final: 0.6500 (OUTLIER) REVERT: A 811 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6625 (mm-30) REVERT: B 90 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6761 (tmt) REVERT: B 180 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6698 (mm) outliers start: 35 outliers final: 20 residues processed: 155 average time/residue: 1.1584 time to fit residues: 192.9580 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 415 PHE Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 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 180 LEU Chi-restraints excluded: chain C residue 8 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 543 ASN A 872 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5421 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= 0.247 Angle : 0.562 10.670 12222 Z= 0.299 Chirality : 0.044 0.127 1393 Planarity : 0.004 0.034 1555 Dihedral : 4.474 20.595 1204 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.42 % Allowed : 21.58 % Favored : 75.00 % 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: -1.02 (0.24), residues: 1095 helix: 0.06 (0.23), residues: 521 sheet: -0.77 (0.43), residues: 121 loop : -1.44 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 PHE 0.013 0.002 PHE A 652 TYR 0.017 0.002 TYR A 606 ARG 0.002 0.000 ARG A 750 *********************** 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 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.866 Fit side-chains REVERT: A 37 ILE cc_start: 0.8076 (mm) cc_final: 0.7817 (tt) REVERT: A 196 MET cc_start: 0.7309 (mtp) cc_final: 0.7049 (mtm) REVERT: A 334 PHE cc_start: 0.7948 (m-80) cc_final: 0.7488 (m-80) REVERT: A 481 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6630 (t0) REVERT: A 508 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8182 (mmtp) REVERT: A 624 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7943 (mpt-90) REVERT: A 811 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: B 90 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6837 (tmt) REVERT: B 180 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6578 (mm) outliers start: 33 outliers final: 21 residues processed: 152 average time/residue: 1.1485 time to fit residues: 187.5399 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 MET 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 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 D residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 58 optimal weight: 0.0670 chunk 42 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.0570 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8992 Z= 0.134 Angle : 0.505 10.648 12222 Z= 0.268 Chirality : 0.041 0.131 1393 Planarity : 0.003 0.036 1555 Dihedral : 4.088 19.320 1204 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 22.72 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1095 helix: 0.43 (0.24), residues: 516 sheet: -0.68 (0.47), residues: 100 loop : -1.19 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 PHE 0.013 0.001 PHE A 920 TYR 0.012 0.001 TYR A 606 ARG 0.002 0.000 ARG B 96 *********************** 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 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.978 Fit side-chains REVERT: A 196 MET cc_start: 0.7245 (mtp) cc_final: 0.6943 (mtm) REVERT: A 334 PHE cc_start: 0.7804 (m-80) cc_final: 0.7367 (m-80) REVERT: A 508 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8060 (mmtp) REVERT: A 624 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7867 (mpt-90) REVERT: A 760 ASP cc_start: 0.6599 (p0) cc_final: 0.6394 (OUTLIER) REVERT: B 90 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6724 (tmt) REVERT: B 180 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6614 (mm) REVERT: C 35 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7205 (mt) outliers start: 23 outliers final: 13 residues processed: 144 average time/residue: 1.0872 time to fit residues: 168.3800 Evaluate side-chains 143 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 477 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 791 ASN A 872 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8992 Z= 0.185 Angle : 0.528 10.865 12222 Z= 0.281 Chirality : 0.043 0.154 1393 Planarity : 0.003 0.036 1555 Dihedral : 4.193 18.944 1204 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.07 % Allowed : 23.76 % Favored : 74.17 % 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: -0.70 (0.25), residues: 1095 helix: 0.33 (0.23), residues: 520 sheet: -0.64 (0.48), residues: 100 loop : -1.27 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 PHE 0.012 0.001 PHE A 753 TYR 0.030 0.001 TYR A 867 ARG 0.002 0.000 ARG A 726 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.042 Fit side-chains REVERT: A 196 MET cc_start: 0.7258 (mtp) cc_final: 0.7021 (mtm) REVERT: A 334 PHE cc_start: 0.7831 (m-80) cc_final: 0.7425 (m-80) REVERT: A 481 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6601 (t0) REVERT: A 508 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8130 (mmtp) REVERT: A 624 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7912 (mpt-90) REVERT: A 760 ASP cc_start: 0.6514 (p0) cc_final: 0.6302 (OUTLIER) REVERT: B 180 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6602 (mm) REVERT: C 35 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7221 (mt) outliers start: 20 outliers final: 12 residues processed: 148 average time/residue: 1.1224 time to fit residues: 179.4324 Evaluate side-chains 142 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS 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 477 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 624 ARG Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 35 LEU 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 79 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 C 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.180388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145728 restraints weight = 10050.574| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.83 r_work: 0.3552 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8992 Z= 0.238 Angle : 0.565 11.046 12222 Z= 0.300 Chirality : 0.044 0.130 1393 Planarity : 0.004 0.037 1555 Dihedral : 4.423 21.739 1204 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.70 % Allowed : 23.13 % Favored : 74.17 % 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: -0.84 (0.25), residues: 1095 helix: 0.20 (0.23), residues: 520 sheet: -0.61 (0.46), residues: 113 loop : -1.35 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 290 HIS 0.008 0.001 HIS A 309 PHE 0.013 0.002 PHE A 753 TYR 0.031 0.002 TYR A 867 ARG 0.002 0.000 ARG A 726 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3499.60 seconds wall clock time: 63 minutes 51.39 seconds (3831.39 seconds total)