Starting phenix.real_space_refine on Thu Mar 14 21:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox5_17257/03_2024/8ox5_17257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox5_17257/03_2024/8ox5_17257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox5_17257/03_2024/8ox5_17257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox5_17257/03_2024/8ox5_17257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox5_17257/03_2024/8ox5_17257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox5_17257/03_2024/8ox5_17257_updated.pdb" } resolution = 2.9 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= 1.000 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 6305 2.51 5 N 1609 2.21 5 O 1782 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9751 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 7008 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 20, 'TRANS': 848} Chain breaks: 4 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.60 Number of scatterers: 9751 At special positions: 0 Unit cell: (91.0976, 93.168, 166.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 47 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1782 8.00 N 1609 7.00 C 6305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 6 sheets defined 49.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.649A pdb=" N PHE A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.521A pdb=" N TYR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 141 through 172 removed outlier: 5.380A pdb=" N VAL A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.698A pdb=" N VAL A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 151 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL A 154 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 155 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 158 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL A 161 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A 172 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 354 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.686A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.674A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.845A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.859A pdb=" N GLY A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.626A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 533 removed outlier: 3.679A pdb=" N PHE A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 628 removed outlier: 4.911A pdb=" N ARG A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.733A pdb=" N ALA A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 645 " --> pdb=" O ASP A 641 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 677 removed outlier: 4.005A pdb=" N GLU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 673 " --> pdb=" O TRP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.678A pdb=" N GLU A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.765A pdb=" N PHE A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 removed outlier: 3.640A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 810 removed outlier: 3.562A pdb=" N ASN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 858 Processing helix chain 'A' and resid 870 through 883 removed outlier: 3.687A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.604A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 901 " --> pdb=" O VAL A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 929 through 936 removed outlier: 3.544A pdb=" N ARG A 934 " --> pdb=" O TYR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 970 removed outlier: 3.592A pdb=" N ASN A 958 " --> pdb=" O PHE A 954 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1016 through 1024 removed outlier: 3.685A pdb=" N VAL A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A1023 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A1024 " --> pdb=" O VAL A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 3.563A pdb=" N PHE A1034 " --> pdb=" O TYR A1030 " (cutoff:3.500A) Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1089 Processing helix chain 'A' and resid 1097 through 1118 removed outlier: 3.817A pdb=" N ASP A1116 " --> pdb=" O GLY A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 removed outlier: 3.843A pdb=" N VAL A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1120 through 1125' Processing helix chain 'A' and resid 1135 through 1139 Processing helix chain 'A' and resid 1143 through 1170 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1179 Processing helix chain 'B' and resid 32 through 35 No H-bonds generated for 'chain 'B' and resid 32 through 35' Processing helix chain 'B' and resid 47 through 58 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.208A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 155 through 160 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 323 through 349 removed outlier: 3.614A pdb=" N LEU B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.848A pdb=" N THR A 465 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A 707 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 467 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 606 " --> pdb=" O ALA A 592 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 592 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 730 through 732 removed outlier: 3.597A pdb=" N CYS A 865 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 866 " --> pdb=" O ILE A 801 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 889 through 892 removed outlier: 6.838A pdb=" N ILE A 906 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY A 892 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 908 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 924 " --> pdb=" O GLY A 909 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 77 through 81 removed outlier: 4.140A pdb=" N ILE B 311 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.155A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 123 through 125 365 hydrogen bonds defined for protein. 975 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: 3.00 Time building geometry restraints manager: 4.32 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: 3054 1.34 - 1.46: 2248 1.46 - 1.58: 4598 1.58 - 1.70: 5 1.70 - 1.82: 78 Bond restraints: 9983 Sorted by residual: bond pdb=" C3' ADP A1201 " pdb=" C4' ADP A1201 " ideal model delta sigma weight residual 1.524 1.282 0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C1' ADP A1201 " pdb=" C2' ADP A1201 " ideal model delta sigma weight residual 1.524 1.287 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C4' ADP A1201 " pdb=" O4' ADP A1201 " ideal model delta sigma weight residual 1.426 1.565 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C6 ADP A1201 " pdb=" N6 ADP A1201 " ideal model delta sigma weight residual 1.355 1.490 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C2' ADP A1201 " pdb=" C3' ADP A1201 " ideal model delta sigma weight residual 1.524 1.652 -0.128 2.00e-02 2.50e+03 4.13e+01 ... (remaining 9978 not shown) Histogram of bond angle deviations from ideal: 88.37 - 106.47: 246 106.47 - 124.57: 13106 124.57 - 142.67: 192 142.67 - 160.76: 0 160.76 - 178.86: 2 Bond angle restraints: 13546 Sorted by residual: angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F2 ALF A1202 " ideal model delta sigma weight residual 108.68 178.61 -69.93 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F3 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 109.63 178.86 -69.23 3.00e+00 1.11e-01 5.33e+02 angle pdb=" F1 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.69 88.37 21.32 3.00e+00 1.11e-01 5.05e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F4 ALF A1202 " ideal model delta sigma weight residual 110.21 90.70 19.51 3.00e+00 1.11e-01 4.23e+01 angle pdb=" F2 ALF A1202 " pdb="AL ALF A1202 " pdb=" F3 ALF A1202 " ideal model delta sigma weight residual 109.59 90.26 19.33 3.00e+00 1.11e-01 4.15e+01 ... (remaining 13541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5576 21.62 - 43.23: 319 43.23 - 64.85: 47 64.85 - 86.46: 16 86.46 - 108.08: 5 Dihedral angle restraints: 5963 sinusoidal: 2458 harmonic: 3505 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual -86.00 -45.94 -40.06 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA TYR B 121 " pdb=" C TYR B 121 " pdb=" N TYR B 122 " pdb=" CA TYR B 122 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU A 692 " pdb=" C GLU A 692 " pdb=" N GLU A 693 " pdb=" CA GLU A 693 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1326 0.062 - 0.123: 178 0.123 - 0.185: 19 0.185 - 0.247: 0 0.247 - 0.308: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CG LEU A1027 " pdb=" CB LEU A1027 " pdb=" CD1 LEU A1027 " pdb=" CD2 LEU A1027 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE A 985 " pdb=" CA ILE A 985 " pdb=" CG1 ILE A 985 " pdb=" CG2 ILE A 985 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 1522 not shown) Planarity restraints: 1700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 96 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 97 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 455 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LYS A 455 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A 455 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 456 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 132 " -0.135 9.50e-02 1.11e+02 6.09e-02 2.79e+00 pdb=" NE ARG B 132 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 132 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 132 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 132 " -0.001 2.00e-02 2.50e+03 ... (remaining 1697 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 18 2.12 - 2.82: 3056 2.82 - 3.51: 14725 3.51 - 4.21: 24274 4.21 - 4.90: 42706 Nonbonded interactions: 84779 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" F4 ALF A1202 " model vdw 1.430 2.390 nonbonded pdb=" OD2 ASP A 893 " pdb=" OE2 GLU A 914 " model vdw 1.440 3.040 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1203 " model vdw 1.454 2.170 nonbonded pdb=" OD1 ASP A 454 " pdb="AL ALF A1202 " model vdw 1.818 2.760 nonbonded pdb=" F1 ALF A1202 " pdb="MG MG A1203 " model vdw 1.872 2.120 ... (remaining 84774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.850 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: 3.480 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 29.550 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 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 : 0.006 0.242 9983 Z= 0.453 Angle : 1.127 69.927 13546 Z= 0.443 Chirality : 0.043 0.308 1525 Planarity : 0.005 0.061 1697 Dihedral : 14.359 108.081 3698 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.23), residues: 1185 helix: -0.90 (0.22), residues: 541 sheet: -0.53 (0.47), residues: 135 loop : -1.70 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 805 HIS 0.008 0.001 HIS B 131 PHE 0.016 0.001 PHE B 108 TYR 0.026 0.002 TYR A 992 ARG 0.013 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 1144 TYR cc_start: 0.7649 (m-80) cc_final: 0.7421 (m-10) REVERT: B 121 TYR cc_start: 0.6083 (m-10) cc_final: 0.5736 (m-10) REVERT: B 132 ARG cc_start: 0.4478 (ttp80) cc_final: 0.3151 (ttp80) REVERT: B 244 ASP cc_start: 0.4249 (t70) cc_final: 0.4016 (m-30) REVERT: B 262 ARG cc_start: 0.7581 (ttt90) cc_final: 0.6538 (ttp80) outliers start: 0 outliers final: 1 residues processed: 153 average time/residue: 0.9308 time to fit residues: 156.8216 Evaluate side-chains 120 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9983 Z= 0.234 Angle : 0.875 33.451 13546 Z= 0.386 Chirality : 0.045 0.224 1525 Planarity : 0.005 0.036 1697 Dihedral : 8.309 73.836 1422 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.43 % Allowed : 9.26 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.24), residues: 1185 helix: -0.67 (0.20), residues: 576 sheet: 0.11 (0.50), residues: 126 loop : -1.58 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 669 HIS 0.006 0.001 HIS A 535 PHE 0.018 0.002 PHE A 113 TYR 0.018 0.002 TYR A 142 ARG 0.005 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: B 244 ASP cc_start: 0.4463 (t70) cc_final: 0.4127 (m-30) REVERT: B 262 ARG cc_start: 0.7757 (ttt90) cc_final: 0.6660 (ttp80) REVERT: B 274 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6590 (mtt-85) outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 0.9878 time to fit residues: 147.2878 Evaluate side-chains 115 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 0.0570 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN A 633 ASN A1070 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9983 Z= 0.358 Angle : 0.896 31.738 13546 Z= 0.401 Chirality : 0.046 0.236 1525 Planarity : 0.005 0.044 1697 Dihedral : 7.199 55.712 1422 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.39 % Allowed : 13.26 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.98 (0.23), residues: 1185 helix: -1.06 (0.20), residues: 591 sheet: -0.06 (0.49), residues: 126 loop : -1.86 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 967 HIS 0.008 0.001 HIS A 535 PHE 0.015 0.002 PHE B 54 TYR 0.024 0.002 TYR A 992 ARG 0.004 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 603 MET cc_start: 0.6903 (ttp) cc_final: 0.6570 (ttt) REVERT: A 1147 LEU cc_start: 0.7622 (tp) cc_final: 0.7297 (mt) REVERT: B 244 ASP cc_start: 0.4727 (t70) cc_final: 0.4411 (m-30) REVERT: B 262 ARG cc_start: 0.7997 (ttt90) cc_final: 0.6817 (ttp80) REVERT: B 274 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6725 (mtt-85) outliers start: 25 outliers final: 6 residues processed: 139 average time/residue: 0.8548 time to fit residues: 131.6144 Evaluate side-chains 112 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.0050 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 0.0070 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9983 Z= 0.196 Angle : 0.840 31.845 13546 Z= 0.363 Chirality : 0.043 0.255 1525 Planarity : 0.004 0.038 1697 Dihedral : 6.474 56.152 1422 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.72 % Allowed : 15.65 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.23), residues: 1185 helix: -0.81 (0.20), residues: 591 sheet: -0.12 (0.49), residues: 126 loop : -1.65 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 967 HIS 0.010 0.001 HIS A 535 PHE 0.016 0.001 PHE A 113 TYR 0.024 0.001 TYR A 361 ARG 0.004 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 603 MET cc_start: 0.6871 (ttp) cc_final: 0.6500 (ttt) REVERT: A 1114 MET cc_start: 0.5614 (ttp) cc_final: 0.5397 (ttp) REVERT: B 244 ASP cc_start: 0.4684 (t70) cc_final: 0.4309 (m-30) REVERT: B 262 ARG cc_start: 0.7735 (ttt90) cc_final: 0.6673 (ttp80) outliers start: 18 outliers final: 9 residues processed: 129 average time/residue: 0.8476 time to fit residues: 121.1795 Evaluate side-chains 115 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 772 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9983 Z= 0.296 Angle : 0.866 31.641 13546 Z= 0.380 Chirality : 0.045 0.237 1525 Planarity : 0.005 0.044 1697 Dihedral : 6.388 55.843 1422 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.29 % Allowed : 17.27 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.23), residues: 1185 helix: -0.98 (0.20), residues: 593 sheet: -0.12 (0.48), residues: 126 loop : -1.80 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 207 HIS 0.013 0.001 HIS A 535 PHE 0.014 0.002 PHE A 113 TYR 0.020 0.002 TYR A 142 ARG 0.005 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.925 Fit side-chains REVERT: A 603 MET cc_start: 0.6874 (ttp) cc_final: 0.6557 (ttt) REVERT: B 244 ASP cc_start: 0.4855 (t70) cc_final: 0.4529 (m-30) REVERT: B 262 ARG cc_start: 0.7929 (ttt90) cc_final: 0.6805 (ttp80) REVERT: B 274 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6342 (mtt-85) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.8062 time to fit residues: 111.4409 Evaluate side-chains 117 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.0020 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN B 92 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9983 Z= 0.330 Angle : 0.882 31.644 13546 Z= 0.390 Chirality : 0.045 0.253 1525 Planarity : 0.005 0.049 1697 Dihedral : 6.354 56.381 1422 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.67 % Allowed : 18.13 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.11 (0.23), residues: 1185 helix: -1.17 (0.19), residues: 595 sheet: -0.12 (0.48), residues: 126 loop : -1.93 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 260 HIS 0.006 0.001 HIS A 535 PHE 0.026 0.002 PHE A 124 TYR 0.023 0.002 TYR A 450 ARG 0.009 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.033 Fit side-chains REVERT: A 603 MET cc_start: 0.6850 (ttp) cc_final: 0.6460 (ttt) REVERT: B 244 ASP cc_start: 0.4907 (t70) cc_final: 0.4592 (m-30) REVERT: B 262 ARG cc_start: 0.8031 (ttt90) cc_final: 0.6874 (ttp80) outliers start: 28 outliers final: 18 residues processed: 131 average time/residue: 0.7698 time to fit residues: 112.9019 Evaluate side-chains 119 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 0.0020 chunk 65 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9983 Z= 0.202 Angle : 0.842 32.202 13546 Z= 0.363 Chirality : 0.043 0.244 1525 Planarity : 0.004 0.037 1697 Dihedral : 5.983 55.930 1422 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.48 % Allowed : 19.47 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.76 (0.23), residues: 1185 helix: -0.85 (0.20), residues: 591 sheet: -0.18 (0.48), residues: 127 loop : -1.73 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 207 HIS 0.004 0.001 HIS A 905 PHE 0.024 0.001 PHE A 124 TYR 0.017 0.002 TYR A 476 ARG 0.007 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.018 Fit side-chains REVERT: A 603 MET cc_start: 0.6880 (ttp) cc_final: 0.6571 (ttt) REVERT: B 244 ASP cc_start: 0.4843 (t70) cc_final: 0.4561 (m-30) REVERT: B 262 ARG cc_start: 0.7819 (ttt90) cc_final: 0.6854 (ttp80) outliers start: 26 outliers final: 11 residues processed: 124 average time/residue: 0.7921 time to fit residues: 110.1203 Evaluate side-chains 112 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 103 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 461 GLN A 633 ASN A 648 ASN B 74 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9983 Z= 0.187 Angle : 0.844 31.733 13546 Z= 0.359 Chirality : 0.043 0.250 1525 Planarity : 0.004 0.052 1697 Dihedral : 5.822 55.914 1422 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.19 % Allowed : 19.47 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.23), residues: 1185 helix: -0.68 (0.20), residues: 591 sheet: 0.03 (0.50), residues: 116 loop : -1.72 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 729 HIS 0.005 0.001 HIS A 535 PHE 0.035 0.001 PHE A 966 TYR 0.016 0.001 TYR B 82 ARG 0.007 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.197 Fit side-chains REVERT: A 554 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5484 (m-30) REVERT: A 603 MET cc_start: 0.6870 (ttp) cc_final: 0.6553 (ttt) REVERT: B 244 ASP cc_start: 0.4869 (t70) cc_final: 0.4583 (m-30) REVERT: B 262 ARG cc_start: 0.7751 (ttt90) cc_final: 0.6854 (ttp80) REVERT: B 310 MET cc_start: 0.6667 (tmm) cc_final: 0.6375 (ttp) outliers start: 23 outliers final: 14 residues processed: 128 average time/residue: 0.7924 time to fit residues: 113.0406 Evaluate side-chains 116 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 274 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9983 Z= 0.204 Angle : 0.852 31.182 13546 Z= 0.364 Chirality : 0.043 0.282 1525 Planarity : 0.004 0.038 1697 Dihedral : 5.770 55.752 1422 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.81 % Allowed : 20.04 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.23), residues: 1185 helix: -0.63 (0.21), residues: 591 sheet: -0.11 (0.47), residues: 129 loop : -1.74 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.003 0.001 HIS A 905 PHE 0.034 0.002 PHE A 966 TYR 0.015 0.001 TYR B 82 ARG 0.006 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.840 Fit side-chains REVERT: A 554 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5576 (m-30) REVERT: A 603 MET cc_start: 0.6885 (ttp) cc_final: 0.6559 (ttt) REVERT: B 82 TYR cc_start: 0.6498 (p90) cc_final: 0.6150 (p90) REVERT: B 244 ASP cc_start: 0.5069 (t70) cc_final: 0.4639 (m-30) REVERT: B 262 ARG cc_start: 0.7790 (ttt90) cc_final: 0.6869 (ttp80) REVERT: B 310 MET cc_start: 0.6599 (tmm) cc_final: 0.6345 (ttp) outliers start: 19 outliers final: 15 residues processed: 124 average time/residue: 0.8435 time to fit residues: 116.0025 Evaluate side-chains 116 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9983 Z= 0.188 Angle : 0.864 31.075 13546 Z= 0.365 Chirality : 0.043 0.285 1525 Planarity : 0.004 0.042 1697 Dihedral : 5.711 55.911 1422 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.53 % Allowed : 20.90 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.23), residues: 1185 helix: -0.58 (0.21), residues: 590 sheet: -0.05 (0.47), residues: 129 loop : -1.74 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 729 HIS 0.004 0.001 HIS B 131 PHE 0.034 0.002 PHE A 966 TYR 0.016 0.001 TYR A1110 ARG 0.008 0.001 ARG B 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2370 Ramachandran restraints generated. 1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.050 Fit side-chains REVERT: A 554 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5439 (m-30) REVERT: A 603 MET cc_start: 0.6876 (ttp) cc_final: 0.6498 (ttt) REVERT: B 82 TYR cc_start: 0.6534 (p90) cc_final: 0.6117 (p90) REVERT: B 244 ASP cc_start: 0.5078 (t70) cc_final: 0.4655 (m-30) REVERT: B 262 ARG cc_start: 0.7678 (ttt90) cc_final: 0.6808 (ttp80) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.8215 time to fit residues: 113.1495 Evaluate side-chains 120 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 956 TYR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 7.9990 chunk 86 optimal weight: 0.0370 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS A 633 ASN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.244782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.201847 restraints weight = 10186.761| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.23 r_work: 0.4303 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9983 Z= 0.195 Angle : 0.859 30.602 13546 Z= 0.363 Chirality : 0.043 0.285 1525 Planarity : 0.004 0.040 1697 Dihedral : 5.647 55.864 1422 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.34 % Allowed : 21.47 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.23), residues: 1185 helix: -0.54 (0.21), residues: 589 sheet: -0.02 (0.47), residues: 129 loop : -1.72 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 983 HIS 0.003 0.001 HIS A 905 PHE 0.033 0.002 PHE A 966 TYR 0.015 0.001 TYR B 329 ARG 0.007 0.001 ARG B 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3144.05 seconds wall clock time: 56 minutes 41.51 seconds (3401.51 seconds total)