Starting phenix.real_space_refine on Thu Sep 26 03:30:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/09_2024/6nmd_0447.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/09_2024/6nmd_0447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/09_2024/6nmd_0447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/09_2024/6nmd_0447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/09_2024/6nmd_0447.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/09_2024/6nmd_0447.cif" } resolution = 3.49 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= 0.005 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: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 7451 2.51 5 N 1934 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11779 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9931 Classifications: {'peptide': 1202} Link IDs: {'PTRANS': 26, 'TRANS': 1175} Chain breaks: 3 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 8, 'rna3p': 16} Chain: "B" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1305 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 6.93, per 1000 atoms: 0.59 Number of scatterers: 11779 At special positions: 0 Unit cell: (130.68, 109.08, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 25 15.00 Mg 2 11.99 O 2332 8.00 N 1934 7.00 C 7451 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: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 51.9% alpha, 4.9% beta 1 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 66 removed outlier: 5.043A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 83 removed outlier: 4.073A pdb=" N LEU A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.737A pdb=" N GLU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 4.474A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.881A pdb=" N ILE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 124' Processing helix chain 'A' and resid 136 through 142 removed outlier: 4.147A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.162A pdb=" N GLY A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.846A pdb=" N ARG A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.927A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.169A pdb=" N ASP A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A 195 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 197 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.855A pdb=" N PHE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.719A pdb=" N LYS A 265 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.143A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 409 through 433 removed outlier: 4.363A pdb=" N LYS A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.623A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.702A pdb=" N ALA A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 560 through 563 removed outlier: 4.068A pdb=" N ALA A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 628 through 646 removed outlier: 4.445A pdb=" N LYS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.940A pdb=" N ASN A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.882A pdb=" N TYR A 663 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.799A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 4.058A pdb=" N ARG A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 886 removed outlier: 3.710A pdb=" N GLU A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.443A pdb=" N VAL A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 Processing helix chain 'A' and resid 953 through 956 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 4.398A pdb=" N LYS A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.182A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1169 removed outlier: 4.165A pdb=" N ALA A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 3.774A pdb=" N ILE A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.508A pdb=" N GLU B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.287A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.528A pdb=" N GLU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 124 through 162 removed outlier: 4.589A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.853A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.642A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 746 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.658A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 759 removed outlier: 3.691A pdb=" N HIS A 759 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 783 " --> pdb=" O HIS A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA8, first strand: chain 'A' and resid 828 through 833 removed outlier: 3.594A pdb=" N VAL A 842 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 839 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER A 855 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 862 removed outlier: 4.332A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.708A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 3.844A pdb=" N LEU A1047 " --> pdb=" O TRP A1063 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB4, first strand: chain 'A' and resid 1138 through 1140 455 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 3834 1.36 - 1.51: 4532 1.51 - 1.66: 3643 1.66 - 1.81: 19 1.81 - 1.96: 40 Bond restraints: 12068 Sorted by residual: bond pdb=" SD MET A 626 " pdb=" CE MET A 626 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.71e+01 bond pdb=" SD MET A 531 " pdb=" CE MET A 531 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.71e+01 bond pdb=" CG MET A 531 " pdb=" SD MET A 531 " ideal model delta sigma weight residual 1.803 1.964 -0.161 2.50e-02 1.60e+03 4.13e+01 bond pdb=" CG MET A 626 " pdb=" SD MET A 626 " ideal model delta sigma weight residual 1.803 1.963 -0.160 2.50e-02 1.60e+03 4.09e+01 bond pdb=" SD MET A 603 " pdb=" CE MET A 603 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.05e+01 ... (remaining 12063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 15278 2.10 - 4.20: 911 4.20 - 6.30: 112 6.30 - 8.39: 24 8.39 - 10.49: 11 Bond angle restraints: 16336 Sorted by residual: angle pdb=" N MET A 626 " pdb=" CA MET A 626 " pdb=" C MET A 626 " ideal model delta sigma weight residual 113.16 105.11 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 220 " pdb=" CA PHE A 220 " pdb=" CB PHE A 220 " ideal model delta sigma weight residual 109.29 119.28 -9.99 1.82e+00 3.02e-01 3.01e+01 angle pdb=" CA TRP B 100 " pdb=" C TRP B 100 " pdb=" O TRP B 100 " ideal model delta sigma weight residual 121.10 115.55 5.55 1.10e+00 8.26e-01 2.54e+01 angle pdb=" C GLU A 88 " pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 122.07 129.02 -6.95 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C LYS A 265 " pdb=" N THR A 266 " pdb=" CA THR A 266 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 ... (remaining 16331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 6974 32.09 - 64.19: 322 64.19 - 96.28: 23 96.28 - 128.37: 0 128.37 - 160.46: 1 Dihedral angle restraints: 7320 sinusoidal: 3287 harmonic: 4033 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 71.54 160.46 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" C ASP A 625 " pdb=" N ASP A 625 " pdb=" CA ASP A 625 " pdb=" CB ASP A 625 " ideal model delta harmonic sigma weight residual -122.60 -137.60 15.00 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" CA PHE A 863 " pdb=" C PHE A 863 " pdb=" N ASN A 864 " pdb=" CA ASN A 864 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1514 0.098 - 0.196: 213 0.196 - 0.294: 15 0.294 - 0.392: 3 0.392 - 0.490: 2 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA ASP A 625 " pdb=" N ASP A 625 " pdb=" C ASP A 625 " pdb=" CB ASP A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE A 798 " pdb=" CA ILE A 798 " pdb=" CG1 ILE A 798 " pdb=" CG2 ILE A 798 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE B 113 " pdb=" CA ILE B 113 " pdb=" CG1 ILE B 113 " pdb=" CG2 ILE B 113 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 1744 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 932 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LYS A 932 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS A 932 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 933 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 717 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C PRO A 717 " -0.046 2.00e-02 2.50e+03 pdb=" O PRO A 717 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 718 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 129 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.037 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 218 2.59 - 3.17: 10101 3.17 - 3.75: 18647 3.75 - 4.32: 24597 4.32 - 4.90: 39086 Nonbonded interactions: 92649 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.014 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 203 " model vdw 2.031 2.170 nonbonded pdb=" OP2 A G 19 " pdb="MG MG A1301 " model vdw 2.033 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.035 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 205 " model vdw 2.045 2.170 ... (remaining 92644 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 ========== 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=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: 0.210 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.930 Find NCS groups from input model: 0.120 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4586 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 : 0.013 0.172 12068 Z= 0.842 Angle : 1.111 10.494 16336 Z= 0.648 Chirality : 0.071 0.490 1747 Planarity : 0.007 0.066 1999 Dihedral : 17.366 160.463 4720 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.70 % Favored : 88.86 % Rotamer: Outliers : 2.43 % Allowed : 13.30 % Favored : 84.27 % Cbeta Deviations : 0.38 % 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: -4.62 (0.17), residues: 1346 helix: -2.71 (0.14), residues: 634 sheet: -3.20 (0.44), residues: 112 loop : -3.38 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 100 HIS 0.007 0.002 HIS B 42 PHE 0.034 0.003 PHE A1161 TYR 0.029 0.003 TYR A 237 ARG 0.005 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 322 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.5928 (p) cc_final: 0.5474 (m) REVERT: A 189 ILE cc_start: 0.5144 (mm) cc_final: 0.4892 (tp) REVERT: A 230 THR cc_start: 0.5349 (t) cc_final: 0.4344 (p) REVERT: A 278 LYS cc_start: 0.6765 (ttmt) cc_final: 0.6405 (ttmm) REVERT: A 412 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6395 (tp30) REVERT: A 419 ILE cc_start: 0.7046 (tp) cc_final: 0.6729 (pt) REVERT: A 456 MET cc_start: 0.8104 (mtp) cc_final: 0.7698 (mtp) REVERT: A 525 PHE cc_start: 0.5230 (m-10) cc_final: 0.4614 (m-80) REVERT: A 796 LEU cc_start: 0.4979 (tt) cc_final: 0.4708 (tt) REVERT: A 899 LEU cc_start: 0.6186 (tp) cc_final: 0.5780 (tt) REVERT: A 1060 ILE cc_start: 0.5195 (mm) cc_final: 0.4111 (tt) REVERT: A 1088 GLU cc_start: 0.1620 (tm-30) cc_final: 0.0468 (tp30) REVERT: A 1131 MET cc_start: 0.6605 (mmm) cc_final: 0.6281 (mmm) REVERT: A 1174 ILE cc_start: 0.0898 (OUTLIER) cc_final: 0.0071 (mt) REVERT: A 1211 ILE cc_start: 0.3251 (OUTLIER) cc_final: 0.2971 (mp) REVERT: B 3 LYS cc_start: 0.6807 (tppt) cc_final: 0.6137 (tptp) REVERT: B 87 TYR cc_start: 0.5847 (m-80) cc_final: 0.5488 (m-80) outliers start: 30 outliers final: 6 residues processed: 347 average time/residue: 0.2947 time to fit residues: 136.6843 Evaluate side-chains 184 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 179 ASN A 509 ASN A 577 ASN A 633 HIS A 735 GLN A 849 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 ASN B 20 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12068 Z= 0.192 Angle : 0.681 10.935 16336 Z= 0.358 Chirality : 0.043 0.178 1747 Planarity : 0.004 0.059 1999 Dihedral : 12.245 152.969 1863 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.92 % Allowed : 17.60 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.84 (0.21), residues: 1346 helix: -0.93 (0.19), residues: 634 sheet: -2.85 (0.47), residues: 105 loop : -2.75 (0.22), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 602 HIS 0.007 0.001 HIS A 67 PHE 0.039 0.002 PHE A 931 TYR 0.018 0.002 TYR A 403 ARG 0.005 0.001 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.5454 (m-80) cc_final: 0.5245 (m-80) REVERT: A 120 LYS cc_start: 0.7560 (mmmt) cc_final: 0.7067 (ptpp) REVERT: A 162 PHE cc_start: 0.7684 (m-80) cc_final: 0.7454 (m-80) REVERT: A 178 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8124 (tp30) REVERT: A 187 MET cc_start: 0.1675 (ttt) cc_final: 0.1441 (tpp) REVERT: A 230 THR cc_start: 0.5411 (t) cc_final: 0.5184 (p) REVERT: A 272 LYS cc_start: 0.6409 (mttp) cc_final: 0.6115 (ttmm) REVERT: A 412 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6766 (tp30) REVERT: A 448 LYS cc_start: 0.8738 (mmtm) cc_final: 0.7875 (tmtt) REVERT: A 494 TYR cc_start: 0.5525 (t80) cc_final: 0.5277 (t80) REVERT: A 523 LEU cc_start: 0.7419 (tp) cc_final: 0.7158 (tp) REVERT: A 559 ASP cc_start: 0.7077 (m-30) cc_final: 0.5336 (m-30) REVERT: A 645 ARG cc_start: 0.6787 (mtp180) cc_final: 0.6283 (ttp80) REVERT: A 735 GLN cc_start: 0.5550 (OUTLIER) cc_final: 0.5328 (mp-120) REVERT: A 746 MET cc_start: 0.6289 (tpt) cc_final: 0.6074 (tpt) REVERT: B 3 LYS cc_start: 0.6959 (tppt) cc_final: 0.6296 (tptp) REVERT: B 15 LYS cc_start: 0.8331 (tppt) cc_final: 0.7994 (tppt) REVERT: B 100 TRP cc_start: 0.6063 (OUTLIER) cc_final: 0.5529 (p90) REVERT: B 155 ARG cc_start: 0.6210 (mmm-85) cc_final: 0.5162 (tpp80) outliers start: 36 outliers final: 16 residues processed: 263 average time/residue: 0.2498 time to fit residues: 92.1722 Evaluate side-chains 198 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1217 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 513 GLN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 1.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 12068 Z= 0.466 Angle : 0.932 13.008 16336 Z= 0.493 Chirality : 0.052 0.202 1747 Planarity : 0.006 0.097 1999 Dihedral : 12.959 158.116 1854 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 5.19 % Allowed : 18.57 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.06 (0.21), residues: 1346 helix: -0.99 (0.19), residues: 621 sheet: -3.44 (0.42), residues: 108 loop : -2.86 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 355 HIS 0.018 0.003 HIS A 633 PHE 0.024 0.003 PHE A 474 TYR 0.030 0.003 TYR A 403 ARG 0.015 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 265 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7572 (ptmm) REVERT: A 187 MET cc_start: 0.3874 (ttt) cc_final: 0.2831 (ppp) REVERT: A 188 ASP cc_start: 0.7379 (t0) cc_final: 0.6898 (t70) REVERT: A 191 GLU cc_start: 0.7378 (mp0) cc_final: 0.6770 (mm-30) REVERT: A 220 PHE cc_start: 0.7368 (m-80) cc_final: 0.6950 (m-80) REVERT: A 238 ASN cc_start: 0.7683 (m-40) cc_final: 0.7152 (m110) REVERT: A 325 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6475 (t80) REVERT: A 423 ASP cc_start: 0.8436 (p0) cc_final: 0.8174 (p0) REVERT: A 433 GLU cc_start: 0.7980 (pm20) cc_final: 0.7319 (pm20) REVERT: A 448 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8444 (mppt) REVERT: A 466 PHE cc_start: 0.8415 (t80) cc_final: 0.7804 (t80) REVERT: A 467 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 471 LYS cc_start: 0.7849 (tppt) cc_final: 0.7377 (mtpp) REVERT: A 494 TYR cc_start: 0.6669 (t80) cc_final: 0.6260 (t80) REVERT: A 645 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7445 (ttm-80) REVERT: A 653 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6467 (m-10) REVERT: A 654 ASP cc_start: 0.8129 (t0) cc_final: 0.7902 (m-30) REVERT: A 692 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7947 (tptt) REVERT: A 693 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 755 GLU cc_start: 0.8085 (pm20) cc_final: 0.7826 (pm20) REVERT: A 795 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 867 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8124 (mtp85) REVERT: A 894 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7622 (tp30) REVERT: A 945 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6796 (tttm) REVERT: A 999 TRP cc_start: 0.7454 (m-10) cc_final: 0.7135 (m-10) REVERT: A 1064 LYS cc_start: 0.7084 (mttm) cc_final: 0.6577 (tptp) REVERT: A 1149 PHE cc_start: 0.6693 (p90) cc_final: 0.6430 (p90) REVERT: A 1217 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: B 15 LYS cc_start: 0.8351 (tppt) cc_final: 0.7989 (tppt) REVERT: B 29 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: B 56 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 100 TRP cc_start: 0.7538 (OUTLIER) cc_final: 0.6686 (p90) REVERT: B 121 ASP cc_start: 0.6979 (t70) cc_final: 0.6691 (p0) REVERT: B 129 GLU cc_start: 0.7686 (pt0) cc_final: 0.7263 (mp0) REVERT: B 148 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7292 (mm110) REVERT: B 155 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.6924 (ttp-170) REVERT: B 156 ARG cc_start: 0.7034 (tmm-80) cc_final: 0.6680 (ttt180) outliers start: 64 outliers final: 20 residues processed: 316 average time/residue: 0.2849 time to fit residues: 125.9976 Evaluate side-chains 220 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1162 TYR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1217 GLU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A 861 ASN A1172 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 1.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12068 Z= 0.200 Angle : 0.657 11.736 16336 Z= 0.346 Chirality : 0.043 0.215 1747 Planarity : 0.004 0.041 1999 Dihedral : 12.130 163.816 1849 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.97 % Allowed : 23.11 % Favored : 72.91 % 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: -2.40 (0.22), residues: 1346 helix: -0.36 (0.21), residues: 632 sheet: -2.93 (0.41), residues: 121 loop : -2.68 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 100 HIS 0.005 0.001 HIS B 31 PHE 0.020 0.002 PHE A 621 TYR 0.022 0.002 TYR A 616 ARG 0.004 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7483 (mp0) cc_final: 0.7088 (mm-30) REVERT: A 325 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6253 (t80) REVERT: A 350 ASP cc_start: 0.8368 (m-30) cc_final: 0.8053 (t0) REVERT: A 418 ILE cc_start: 0.7311 (mt) cc_final: 0.7006 (mp) REVERT: A 423 ASP cc_start: 0.8482 (p0) cc_final: 0.8187 (p0) REVERT: A 448 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8500 (mppt) REVERT: A 466 PHE cc_start: 0.8493 (t80) cc_final: 0.7871 (t80) REVERT: A 467 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 471 LYS cc_start: 0.7877 (tppt) cc_final: 0.7473 (mtpp) REVERT: A 562 TYR cc_start: 0.7664 (m-80) cc_final: 0.7360 (m-80) REVERT: A 584 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7577 (mttt) REVERT: A 708 ASP cc_start: 0.8546 (t70) cc_final: 0.8089 (t0) REVERT: A 755 GLU cc_start: 0.8111 (pm20) cc_final: 0.7773 (pm20) REVERT: A 795 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 852 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: A 861 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6895 (p0) REVERT: A 867 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7864 (mtp85) REVERT: A 894 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7344 (pp20) REVERT: A 914 LEU cc_start: 0.7956 (tp) cc_final: 0.7675 (mm) REVERT: A 949 MET cc_start: 0.7849 (tpp) cc_final: 0.7568 (tpp) REVERT: A 1086 TRP cc_start: 0.6464 (t60) cc_final: 0.6243 (t60) REVERT: B 15 LYS cc_start: 0.8234 (tppt) cc_final: 0.7952 (tppt) REVERT: B 16 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5755 (mtpp) REVERT: B 17 MET cc_start: 0.7641 (mmm) cc_final: 0.7388 (mmm) REVERT: B 100 TRP cc_start: 0.7364 (OUTLIER) cc_final: 0.6157 (p90) REVERT: B 121 ASP cc_start: 0.6843 (t70) cc_final: 0.6552 (p0) REVERT: B 128 TYR cc_start: 0.7475 (t80) cc_final: 0.7117 (t80) REVERT: B 129 GLU cc_start: 0.7791 (pt0) cc_final: 0.7173 (mp0) REVERT: B 132 TYR cc_start: 0.8196 (t80) cc_final: 0.7977 (t80) REVERT: B 155 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.7218 (mtp180) REVERT: B 156 ARG cc_start: 0.6896 (tmm-80) cc_final: 0.6601 (ttt180) outliers start: 49 outliers final: 24 residues processed: 255 average time/residue: 0.2712 time to fit residues: 96.0244 Evaluate side-chains 213 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1162 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 113 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A1139 ASN A1172 ASN A1197 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 1.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12068 Z= 0.210 Angle : 0.655 11.961 16336 Z= 0.342 Chirality : 0.043 0.272 1747 Planarity : 0.004 0.045 1999 Dihedral : 12.011 169.146 1849 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.65 % Allowed : 24.82 % Favored : 71.53 % 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: -2.05 (0.22), residues: 1346 helix: -0.12 (0.21), residues: 639 sheet: -2.69 (0.46), residues: 108 loop : -2.51 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1193 HIS 0.006 0.001 HIS A 733 PHE 0.018 0.001 PHE A1198 TYR 0.018 0.001 TYR A 616 ARG 0.006 0.001 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 206 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7500 (ptpp) REVERT: A 178 GLU cc_start: 0.7970 (tp30) cc_final: 0.7604 (tp30) REVERT: A 181 THR cc_start: 0.7303 (t) cc_final: 0.7033 (t) REVERT: A 182 ARG cc_start: 0.7729 (mmt90) cc_final: 0.7441 (mtp85) REVERT: A 224 PHE cc_start: 0.7362 (m-80) cc_final: 0.6805 (m-80) REVERT: A 307 THR cc_start: 0.8656 (t) cc_final: 0.8351 (p) REVERT: A 325 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6202 (t80) REVERT: A 350 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8048 (t0) REVERT: A 359 ARG cc_start: 0.8073 (tmt-80) cc_final: 0.7703 (tpt90) REVERT: A 399 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 423 ASP cc_start: 0.8476 (p0) cc_final: 0.8202 (p0) REVERT: A 448 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8517 (mppt) REVERT: A 466 PHE cc_start: 0.8579 (t80) cc_final: 0.7959 (t80) REVERT: A 467 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 531 MET cc_start: 0.8398 (mtp) cc_final: 0.8032 (mtp) REVERT: A 562 TYR cc_start: 0.7782 (m-80) cc_final: 0.7221 (m-80) REVERT: A 621 PHE cc_start: 0.6238 (p90) cc_final: 0.5822 (p90) REVERT: A 626 MET cc_start: 0.5510 (mmp) cc_final: 0.5307 (mmt) REVERT: A 795 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 836 ARG cc_start: 0.7608 (tpp-160) cc_final: 0.7295 (tpp-160) REVERT: A 852 GLU cc_start: 0.7819 (tt0) cc_final: 0.7111 (tt0) REVERT: A 854 TYR cc_start: 0.8687 (p90) cc_final: 0.8165 (p90) REVERT: A 867 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.7955 (mtp85) REVERT: A 913 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 914 LEU cc_start: 0.7903 (tp) cc_final: 0.7366 (mm) REVERT: A 957 MET cc_start: 0.8353 (ttt) cc_final: 0.8098 (ttt) REVERT: A 1104 ILE cc_start: 0.7593 (mm) cc_final: 0.7011 (tp) REVERT: A 1128 MET cc_start: 0.6065 (ttm) cc_final: 0.5687 (ppp) REVERT: A 1217 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 32 ASP cc_start: 0.7900 (p0) cc_final: 0.7645 (p0) REVERT: B 100 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.5818 (p90) REVERT: B 121 ASP cc_start: 0.7046 (t70) cc_final: 0.6716 (p0) REVERT: B 148 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7704 (mm110) REVERT: B 155 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.7270 (mtp180) outliers start: 45 outliers final: 27 residues processed: 240 average time/residue: 0.2622 time to fit residues: 87.4888 Evaluate side-chains 216 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 861 ASN A 862 ASN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 1.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 12068 Z= 0.354 Angle : 0.757 12.084 16336 Z= 0.398 Chirality : 0.047 0.238 1747 Planarity : 0.005 0.075 1999 Dihedral : 12.217 172.808 1849 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.62 % Allowed : 24.66 % Favored : 70.72 % 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: -2.16 (0.22), residues: 1346 helix: -0.28 (0.21), residues: 640 sheet: -2.80 (0.42), residues: 130 loop : -2.42 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A1193 HIS 0.007 0.002 HIS A 502 PHE 0.034 0.002 PHE A1198 TYR 0.032 0.002 TYR A1068 ARG 0.005 0.001 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7923 (ttt90) REVERT: A 63 ASN cc_start: 0.7932 (t0) cc_final: 0.7723 (m-40) REVERT: A 116 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8779 (pttp) REVERT: A 120 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7627 (ptpp) REVERT: A 238 ASN cc_start: 0.7902 (m-40) cc_final: 0.7256 (m110) REVERT: A 325 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6554 (t80) REVERT: A 359 ARG cc_start: 0.8037 (tmt-80) cc_final: 0.7763 (tpt90) REVERT: A 362 TRP cc_start: 0.6961 (t60) cc_final: 0.6491 (t60) REVERT: A 399 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7869 (tm-30) REVERT: A 423 ASP cc_start: 0.8524 (p0) cc_final: 0.8278 (p0) REVERT: A 448 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8597 (mppt) REVERT: A 467 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 471 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7555 (mtpt) REVERT: A 494 TYR cc_start: 0.7712 (t80) cc_final: 0.7501 (t80) REVERT: A 531 MET cc_start: 0.8811 (mtp) cc_final: 0.8115 (mtp) REVERT: A 539 GLU cc_start: 0.7043 (pm20) cc_final: 0.6831 (tt0) REVERT: A 562 TYR cc_start: 0.7847 (m-80) cc_final: 0.7360 (m-80) REVERT: A 571 LYS cc_start: 0.7582 (tmtt) cc_final: 0.7321 (tmtt) REVERT: A 638 PHE cc_start: 0.7885 (t80) cc_final: 0.7667 (t80) REVERT: A 653 TYR cc_start: 0.6759 (m-10) cc_final: 0.6366 (m-10) REVERT: A 656 ASN cc_start: 0.8425 (m-40) cc_final: 0.8177 (p0) REVERT: A 688 LYS cc_start: 0.6987 (pttt) cc_final: 0.6210 (tppt) REVERT: A 691 ASP cc_start: 0.8814 (m-30) cc_final: 0.8551 (m-30) REVERT: A 795 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 836 ARG cc_start: 0.7753 (tpp-160) cc_final: 0.7421 (tpp-160) REVERT: A 861 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7265 (p0) REVERT: A 914 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7535 (mm) REVERT: A 965 CYS cc_start: 0.7504 (t) cc_final: 0.7298 (p) REVERT: A 992 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.4894 (t80) REVERT: A 1054 ARG cc_start: 0.7162 (mmt90) cc_final: 0.6505 (mmm-85) REVERT: A 1056 ASP cc_start: 0.7014 (t0) cc_final: 0.6114 (t0) REVERT: A 1102 TYR cc_start: 0.6941 (m-80) cc_final: 0.6712 (m-10) REVERT: A 1128 MET cc_start: 0.6886 (ttm) cc_final: 0.5391 (ppp) REVERT: A 1131 MET cc_start: 0.8074 (mmm) cc_final: 0.7511 (tpp) REVERT: B 16 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5698 (mtpp) REVERT: B 25 THR cc_start: 0.6198 (m) cc_final: 0.5971 (p) REVERT: B 85 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 100 TRP cc_start: 0.7559 (OUTLIER) cc_final: 0.5921 (p90) REVERT: B 109 LEU cc_start: 0.8311 (pp) cc_final: 0.8097 (tp) REVERT: B 148 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7931 (mm110) REVERT: B 151 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 160 GLU cc_start: 0.7737 (tp30) cc_final: 0.7225 (tt0) outliers start: 57 outliers final: 34 residues processed: 265 average time/residue: 0.2527 time to fit residues: 94.1823 Evaluate side-chains 229 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 861 ASN A1197 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 1.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12068 Z= 0.176 Angle : 0.669 12.610 16336 Z= 0.345 Chirality : 0.043 0.212 1747 Planarity : 0.003 0.040 1999 Dihedral : 11.920 174.534 1849 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.68 % Allowed : 27.66 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.77 (0.23), residues: 1346 helix: -0.03 (0.21), residues: 645 sheet: -2.39 (0.46), residues: 117 loop : -2.21 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1193 HIS 0.003 0.001 HIS A 502 PHE 0.024 0.001 PHE A 638 TYR 0.020 0.001 TYR A 605 ARG 0.008 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.7930 (ttt90) REVERT: A 63 ASN cc_start: 0.7915 (t0) cc_final: 0.7538 (m-40) REVERT: A 116 LYS cc_start: 0.9323 (mmmt) cc_final: 0.8738 (pttp) REVERT: A 167 LYS cc_start: 0.6048 (mmmt) cc_final: 0.5812 (mmmt) REVERT: A 182 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7192 (mtp85) REVERT: A 238 ASN cc_start: 0.7779 (m-40) cc_final: 0.7154 (m110) REVERT: A 257 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8216 (pt0) REVERT: A 307 THR cc_start: 0.8907 (t) cc_final: 0.8463 (p) REVERT: A 325 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6023 (t80) REVERT: A 399 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 423 ASP cc_start: 0.8499 (p0) cc_final: 0.8255 (p0) REVERT: A 448 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8638 (mppt) REVERT: A 466 PHE cc_start: 0.8640 (t80) cc_final: 0.8095 (t80) REVERT: A 467 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 471 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7479 (mmmm) REVERT: A 531 MET cc_start: 0.8404 (mtp) cc_final: 0.8168 (mtp) REVERT: A 562 TYR cc_start: 0.7765 (m-80) cc_final: 0.7225 (m-80) REVERT: A 571 LYS cc_start: 0.7545 (tmtt) cc_final: 0.7272 (tmtt) REVERT: A 603 MET cc_start: 0.7366 (mtm) cc_final: 0.7129 (mtm) REVERT: A 626 MET cc_start: 0.7171 (mmm) cc_final: 0.6962 (mmt) REVERT: A 653 TYR cc_start: 0.6506 (m-10) cc_final: 0.6306 (m-10) REVERT: A 656 ASN cc_start: 0.8527 (m-40) cc_final: 0.7893 (p0) REVERT: A 670 TYR cc_start: 0.8602 (m-10) cc_final: 0.8264 (m-10) REVERT: A 795 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 835 GLU cc_start: 0.7268 (pm20) cc_final: 0.6740 (pm20) REVERT: A 836 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.7387 (tpp-160) REVERT: A 861 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7246 (p0) REVERT: A 867 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7751 (mtp85) REVERT: A 914 LEU cc_start: 0.7919 (tp) cc_final: 0.7672 (mm) REVERT: A 949 MET cc_start: 0.7886 (tpp) cc_final: 0.7502 (mmt) REVERT: A 957 MET cc_start: 0.8379 (ttt) cc_final: 0.8137 (ttt) REVERT: A 965 CYS cc_start: 0.7263 (t) cc_final: 0.7050 (p) REVERT: A 1054 ARG cc_start: 0.7133 (mmt90) cc_final: 0.6471 (mmm-85) REVERT: A 1102 TYR cc_start: 0.6766 (m-80) cc_final: 0.6531 (m-10) REVERT: A 1126 SER cc_start: 0.8923 (t) cc_final: 0.8602 (p) REVERT: A 1128 MET cc_start: 0.6542 (ttm) cc_final: 0.6239 (ppp) REVERT: A 1134 MET cc_start: 0.8049 (tpp) cc_final: 0.7720 (tpp) REVERT: B 16 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5784 (mtpp) REVERT: B 25 THR cc_start: 0.6211 (m) cc_final: 0.5974 (p) REVERT: B 83 GLU cc_start: 0.7651 (mp0) cc_final: 0.7394 (mm-30) REVERT: B 100 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.5520 (p90) REVERT: B 148 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7704 (mm110) REVERT: B 151 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8164 (mm-30) REVERT: B 155 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7373 (ttt-90) REVERT: B 160 GLU cc_start: 0.7704 (tp30) cc_final: 0.7287 (tt0) outliers start: 33 outliers final: 22 residues processed: 238 average time/residue: 0.2654 time to fit residues: 88.3689 Evaluate side-chains 206 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 0.1980 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A1139 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 1.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12068 Z= 0.166 Angle : 0.658 12.869 16336 Z= 0.337 Chirality : 0.043 0.230 1747 Planarity : 0.003 0.040 1999 Dihedral : 11.882 177.263 1849 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.27 % Allowed : 27.01 % Favored : 70.72 % 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: -1.55 (0.23), residues: 1346 helix: 0.16 (0.21), residues: 645 sheet: -2.15 (0.51), residues: 108 loop : -2.17 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A1193 HIS 0.002 0.000 HIS B 31 PHE 0.021 0.001 PHE A 638 TYR 0.016 0.001 TYR B 136 ARG 0.007 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.7877 (ttt90) REVERT: A 116 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8747 (pttp) REVERT: A 167 LYS cc_start: 0.6165 (mmmt) cc_final: 0.5960 (mmmt) REVERT: A 257 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8195 (pt0) REVERT: A 307 THR cc_start: 0.8776 (t) cc_final: 0.8464 (p) REVERT: A 325 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5903 (t80) REVERT: A 423 ASP cc_start: 0.8525 (p0) cc_final: 0.8097 (m-30) REVERT: A 448 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8637 (mppt) REVERT: A 466 PHE cc_start: 0.8610 (t80) cc_final: 0.8093 (t80) REVERT: A 467 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 471 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7586 (mmmm) REVERT: A 531 MET cc_start: 0.8391 (mtp) cc_final: 0.8183 (mtp) REVERT: A 562 TYR cc_start: 0.7674 (m-80) cc_final: 0.7079 (m-80) REVERT: A 656 ASN cc_start: 0.8385 (m-40) cc_final: 0.7905 (p0) REVERT: A 670 TYR cc_start: 0.8519 (m-10) cc_final: 0.8283 (m-10) REVERT: A 722 MET cc_start: 0.7443 (ttm) cc_final: 0.7163 (mtt) REVERT: A 795 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7081 (mt-10) REVERT: A 808 ASN cc_start: 0.7791 (t0) cc_final: 0.7219 (t0) REVERT: A 811 LYS cc_start: 0.7827 (ttmm) cc_final: 0.7531 (tttm) REVERT: A 835 GLU cc_start: 0.7329 (pm20) cc_final: 0.7077 (pm20) REVERT: A 836 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.7407 (tpp-160) REVERT: A 852 GLU cc_start: 0.7478 (tt0) cc_final: 0.7234 (tt0) REVERT: A 913 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 914 LEU cc_start: 0.7925 (tp) cc_final: 0.7584 (mm) REVERT: A 949 MET cc_start: 0.7710 (tpp) cc_final: 0.7365 (mmt) REVERT: A 1054 ARG cc_start: 0.6993 (mmt90) cc_final: 0.6370 (mmm-85) REVERT: A 1097 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7789 (tm-30) REVERT: A 1110 ASP cc_start: 0.6998 (t0) cc_final: 0.6058 (m-30) REVERT: A 1126 SER cc_start: 0.8877 (t) cc_final: 0.8564 (p) REVERT: A 1128 MET cc_start: 0.6828 (ttm) cc_final: 0.6477 (ppp) REVERT: B 16 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5760 (mtpp) REVERT: B 25 THR cc_start: 0.6191 (m) cc_final: 0.5983 (p) REVERT: B 92 ILE cc_start: 0.8768 (mm) cc_final: 0.8503 (mm) REVERT: B 142 GLU cc_start: 0.7460 (pm20) cc_final: 0.7124 (pm20) REVERT: B 148 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7627 (mm110) REVERT: B 151 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 155 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7593 (ttt-90) REVERT: B 160 GLU cc_start: 0.7787 (tp30) cc_final: 0.7331 (tt0) outliers start: 28 outliers final: 16 residues processed: 225 average time/residue: 0.2482 time to fit residues: 78.3207 Evaluate side-chains 202 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 1.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12068 Z= 0.311 Angle : 0.753 13.989 16336 Z= 0.387 Chirality : 0.047 0.259 1747 Planarity : 0.004 0.038 1999 Dihedral : 12.083 177.160 1849 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.92 % Allowed : 26.76 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.82 (0.23), residues: 1346 helix: -0.06 (0.21), residues: 650 sheet: -2.29 (0.46), residues: 118 loop : -2.32 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A1193 HIS 0.005 0.001 HIS B 31 PHE 0.017 0.002 PHE A1161 TYR 0.027 0.002 TYR A1068 ARG 0.004 0.001 ARG A 747 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8280 (mmm-85) REVERT: A 116 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8760 (pttp) REVERT: A 159 GLU cc_start: 0.7451 (tp30) cc_final: 0.7048 (tp30) REVERT: A 167 LYS cc_start: 0.6509 (mmmt) cc_final: 0.6231 (mmmt) REVERT: A 238 ASN cc_start: 0.7856 (m-40) cc_final: 0.7240 (m110) REVERT: A 307 THR cc_start: 0.8790 (t) cc_final: 0.8491 (p) REVERT: A 325 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6841 (t80) REVERT: A 423 ASP cc_start: 0.8516 (p0) cc_final: 0.8090 (m-30) REVERT: A 436 PHE cc_start: 0.7249 (m-80) cc_final: 0.7039 (m-10) REVERT: A 448 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8606 (mppt) REVERT: A 467 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 471 LYS cc_start: 0.8011 (mtpt) cc_final: 0.7412 (mmmm) REVERT: A 571 LYS cc_start: 0.7485 (tmtt) cc_final: 0.7192 (tptt) REVERT: A 603 MET cc_start: 0.7615 (mtm) cc_final: 0.7218 (mtm) REVERT: A 656 ASN cc_start: 0.8392 (m-40) cc_final: 0.8128 (p0) REVERT: A 688 LYS cc_start: 0.6963 (pttt) cc_final: 0.6670 (tppt) REVERT: A 795 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 808 ASN cc_start: 0.8007 (t0) cc_final: 0.7111 (t0) REVERT: A 836 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7410 (tpp-160) REVERT: A 858 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 914 LEU cc_start: 0.7880 (tp) cc_final: 0.7559 (mm) REVERT: A 947 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7812 (tt0) REVERT: A 952 ASP cc_start: 0.7772 (m-30) cc_final: 0.7107 (m-30) REVERT: A 992 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.5283 (t80) REVERT: A 1054 ARG cc_start: 0.7346 (mmt90) cc_final: 0.6720 (mmm-85) REVERT: A 1097 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7866 (tm-30) REVERT: A 1126 SER cc_start: 0.9013 (t) cc_final: 0.8556 (p) REVERT: A 1128 MET cc_start: 0.6706 (ttm) cc_final: 0.5491 (ppp) REVERT: A 1207 ASP cc_start: 0.7829 (p0) cc_final: 0.7125 (t70) REVERT: B 16 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.5792 (mtpp) REVERT: B 100 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.5564 (p90) REVERT: B 142 GLU cc_start: 0.7551 (pm20) cc_final: 0.7231 (pm20) REVERT: B 148 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7888 (mm110) REVERT: B 151 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 155 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7332 (ttt180) REVERT: B 160 GLU cc_start: 0.7809 (tp30) cc_final: 0.7573 (tt0) outliers start: 36 outliers final: 25 residues processed: 218 average time/residue: 0.2690 time to fit residues: 82.2702 Evaluate side-chains 205 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.0170 chunk 90 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 1.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 12068 Z= 0.196 Angle : 0.692 13.648 16336 Z= 0.353 Chirality : 0.044 0.223 1747 Planarity : 0.003 0.041 1999 Dihedral : 11.921 179.432 1849 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.19 % Allowed : 27.33 % Favored : 70.48 % 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: -1.55 (0.23), residues: 1346 helix: 0.15 (0.21), residues: 649 sheet: -2.08 (0.48), residues: 118 loop : -2.18 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1193 HIS 0.003 0.001 HIS B 31 PHE 0.018 0.001 PHE A 638 TYR 0.020 0.001 TYR B 136 ARG 0.005 0.000 ARG A 645 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.7904 (ttt90) REVERT: A 102 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7283 (mpp80) REVERT: A 116 LYS cc_start: 0.9264 (mmmt) cc_final: 0.8735 (pttp) REVERT: A 159 GLU cc_start: 0.7396 (tp30) cc_final: 0.7017 (tp30) REVERT: A 238 ASN cc_start: 0.7738 (m-40) cc_final: 0.7148 (m110) REVERT: A 257 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8154 (pt0) REVERT: A 307 THR cc_start: 0.8749 (t) cc_final: 0.8436 (p) REVERT: A 325 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6488 (t80) REVERT: A 423 ASP cc_start: 0.8567 (p0) cc_final: 0.8147 (m-30) REVERT: A 466 PHE cc_start: 0.8573 (t80) cc_final: 0.8324 (t80) REVERT: A 467 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 471 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7495 (mmmm) REVERT: A 603 MET cc_start: 0.7617 (mtm) cc_final: 0.7215 (mtm) REVERT: A 656 ASN cc_start: 0.8336 (m-40) cc_final: 0.8029 (p0) REVERT: A 688 LYS cc_start: 0.6881 (pttt) cc_final: 0.6622 (tppt) REVERT: A 795 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 808 ASN cc_start: 0.8034 (t0) cc_final: 0.7173 (t0) REVERT: A 836 ARG cc_start: 0.7748 (tpp-160) cc_final: 0.7325 (tpp-160) REVERT: A 852 GLU cc_start: 0.7469 (tt0) cc_final: 0.7217 (tt0) REVERT: A 867 ARG cc_start: 0.8214 (ptp-110) cc_final: 0.7860 (mtp85) REVERT: A 913 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 914 LEU cc_start: 0.7952 (tp) cc_final: 0.7462 (mm) REVERT: A 947 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7718 (tt0) REVERT: A 992 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.4864 (t80) REVERT: A 1026 LYS cc_start: 0.8423 (mttp) cc_final: 0.8079 (ttpt) REVERT: A 1054 ARG cc_start: 0.7328 (mmt90) cc_final: 0.6715 (mmm-85) REVERT: A 1097 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7903 (tm-30) REVERT: A 1126 SER cc_start: 0.8961 (t) cc_final: 0.8586 (p) REVERT: A 1128 MET cc_start: 0.6667 (ttm) cc_final: 0.6423 (ppp) REVERT: B 16 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.5959 (mtpp) REVERT: B 142 GLU cc_start: 0.7306 (pm20) cc_final: 0.7084 (pm20) REVERT: B 148 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7821 (mm110) REVERT: B 151 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 155 ARG cc_start: 0.7870 (mmm-85) cc_final: 0.7447 (ttt180) REVERT: B 160 GLU cc_start: 0.7721 (tp30) cc_final: 0.7402 (tt0) outliers start: 27 outliers final: 19 residues processed: 208 average time/residue: 0.2768 time to fit residues: 81.5158 Evaluate side-chains 197 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 849 ASN Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A 861 ASN A1197 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113852 restraints weight = 19481.760| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.17 r_work: 0.3323 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 1.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 12068 Z= 0.325 Angle : 0.761 13.339 16336 Z= 0.393 Chirality : 0.047 0.240 1747 Planarity : 0.004 0.037 1999 Dihedral : 12.094 178.185 1849 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.84 % Allowed : 27.17 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.78 (0.23), residues: 1346 helix: -0.07 (0.21), residues: 661 sheet: -2.11 (0.48), residues: 118 loop : -2.31 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1193 HIS 0.005 0.001 HIS A 502 PHE 0.023 0.002 PHE A 244 TYR 0.026 0.002 TYR A1068 ARG 0.011 0.001 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.60 seconds wall clock time: 53 minutes 16.08 seconds (3196.08 seconds total)