Starting phenix.real_space_refine on Sat Nov 16 18:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj6_16906/11_2024/8oj6_16906.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj6_16906/11_2024/8oj6_16906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj6_16906/11_2024/8oj6_16906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj6_16906/11_2024/8oj6_16906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj6_16906/11_2024/8oj6_16906.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj6_16906/11_2024/8oj6_16906.cif" } resolution = 2.41 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= 0.003 sd= 0.047 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 51 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 7271 2.51 5 N 2055 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11650 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8550 Classifications: {'peptide': 1085} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1031} Chain breaks: 2 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2049 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Chain: "C" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 455 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 4} Link IDs: {None: 5} Time building chain proxies: 10.17, per 1000 atoms: 0.87 Number of scatterers: 11650 At special positions: 0 Unit cell: (87.87, 115.14, 148.47, 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 47 16.00 P 51 15.00 Mg 2 11.99 O 2224 8.00 N 2055 7.00 C 7271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 40.3% alpha, 22.8% beta 19 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.647A pdb=" N ALA A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 235 through 239 removed outlier: 4.608A pdb=" N SER A 239 " --> pdb=" O PRO A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.662A pdb=" N ASN A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 420 through 430 Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 567 through 593 Processing helix chain 'A' and resid 593 through 606 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 617 through 632 removed outlier: 3.631A pdb=" N VAL A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 732 through 734 No H-bonds generated for 'chain 'A' and resid 732 through 734' Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.596A pdb=" N ALA A 744 " --> pdb=" O ASP A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 790 Processing helix chain 'A' and resid 796 through 823 removed outlier: 3.852A pdb=" N LEU A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.536A pdb=" N ASP A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 898 through 918 removed outlier: 3.578A pdb=" N LEU A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 959 Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 980 through 991 removed outlier: 4.065A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 993 No H-bonds generated for 'chain 'A' and resid 992 through 993' Processing helix chain 'A' and resid 994 through 1000 Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1022 removed outlier: 3.687A pdb=" N THR A1022 " --> pdb=" O HIS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1032 removed outlier: 3.509A pdb=" N VAL A1032 " --> pdb=" O GLN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1044 removed outlier: 3.646A pdb=" N TYR A1044 " --> pdb=" O PRO A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1061 Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.629A pdb=" N ALA A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1141 Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1157 through 1174 Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1180 through 1190 Processing helix chain 'A' and resid 1199 through 1209 Processing helix chain 'A' and resid 1219 through 1235 removed outlier: 4.245A pdb=" N ASP A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 273 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 79 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 removed outlier: 3.578A pdb=" N ASP A 151 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 187 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL A 149 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 removed outlier: 7.926A pdb=" N ILE A 635 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR A 256 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 440 removed outlier: 8.613A pdb=" N VAL A 436 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 409 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 438 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 411 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE A 440 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER A 413 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 398 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A 409 " --> pdb=" O CYS A 396 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS A 396 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 411 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 394 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 413 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE A 392 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL A 391 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS A 372 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS A 363 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N THR A 463 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET A 365 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL A 462 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 502 Processing sheet with id=AA8, first strand: chain 'A' and resid 707 through 709 removed outlier: 5.176A pdb=" N CYS A 926 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP A 717 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 928 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 884 " --> pdb=" O PHE A 891 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 893 " --> pdb=" O ILE A 882 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE A 882 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ARG A 895 " --> pdb=" O MET A 880 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N MET A 880 " --> pdb=" O ARG A 895 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 707 through 709 removed outlier: 3.851A pdb=" N LYS A 932 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1036 Processing sheet with id=AB3, first strand: chain 'A' and resid 1212 through 1215 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.945A pdb=" N CYS B 31 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.945A pdb=" N CYS B 31 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.683A pdb=" N VAL B 176 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 257 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 256 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 222 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY B 258 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 224 " --> pdb=" O GLY B 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 102 529 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 7.03 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2636 1.33 - 1.46: 4109 1.46 - 1.59: 5107 1.59 - 1.72: 86 1.72 - 1.85: 70 Bond restraints: 12008 Sorted by residual: bond pdb=" CG HIS A 912 " pdb=" CD2 HIS A 912 " ideal model delta sigma weight residual 1.354 1.302 0.052 1.10e-02 8.26e+03 2.24e+01 bond pdb=" CG HIS A 386 " pdb=" CD2 HIS A 386 " ideal model delta sigma weight residual 1.354 1.303 0.051 1.10e-02 8.26e+03 2.19e+01 bond pdb=" C ASN A 307 " pdb=" O ASN A 307 " ideal model delta sigma weight residual 1.246 1.211 0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" CA SER A 513 " pdb=" CB SER A 513 " ideal model delta sigma weight residual 1.529 1.466 0.062 1.66e-02 3.63e+03 1.42e+01 bond pdb=" CA ALA A1035 " pdb=" CB ALA A1035 " ideal model delta sigma weight residual 1.534 1.473 0.061 1.78e-02 3.16e+03 1.16e+01 ... (remaining 12003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 15470 2.58 - 5.15: 977 5.15 - 7.72: 52 7.72 - 10.30: 5 10.30 - 12.87: 4 Bond angle restraints: 16508 Sorted by residual: angle pdb=" N PRO A 920 " pdb=" CA PRO A 920 " pdb=" C PRO A 920 " ideal model delta sigma weight residual 110.70 123.57 -12.87 1.22e+00 6.72e-01 1.11e+02 angle pdb=" O3' DC D 35 " pdb=" P DA D 36 " pdb=" O5' DA D 36 " ideal model delta sigma weight residual 104.00 94.22 9.78 1.50e+00 4.44e-01 4.25e+01 angle pdb=" C ARG A 170 " pdb=" CA ARG A 170 " pdb=" CB ARG A 170 " ideal model delta sigma weight residual 110.68 100.37 10.31 1.70e+00 3.46e-01 3.68e+01 angle pdb=" CA PRO A 920 " pdb=" C PRO A 920 " pdb=" N PRO A 921 " ideal model delta sigma weight residual 117.93 125.08 -7.15 1.20e+00 6.94e-01 3.55e+01 angle pdb=" C PRO A 177 " pdb=" CA PRO A 177 " pdb=" CB PRO A 177 " ideal model delta sigma weight residual 111.56 121.35 -9.79 1.65e+00 3.67e-01 3.52e+01 ... (remaining 16503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 6762 35.87 - 71.74: 244 71.74 - 107.61: 12 107.61 - 143.48: 0 143.48 - 179.35: 3 Dihedral angle restraints: 7021 sinusoidal: 3116 harmonic: 3905 Sorted by residual: dihedral pdb=" CA ARG B 113 " pdb=" C ARG B 113 " pdb=" N ALA B 114 " pdb=" CA ALA B 114 " ideal model delta harmonic sigma weight residual -180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA CYS B 272 " pdb=" C CYS B 272 " pdb=" N SER B 273 " pdb=" CA SER B 273 " ideal model delta harmonic sigma weight residual -180.00 -149.62 -30.38 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N ASN A 518 " pdb=" CA ASN A 518 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1654 0.127 - 0.253: 195 0.253 - 0.380: 12 0.380 - 0.506: 0 0.506 - 0.633: 2 Chirality restraints: 1863 Sorted by residual: chirality pdb=" P DC D 20 " pdb=" OP1 DC D 20 " pdb=" OP2 DC D 20 " pdb=" O5' DC D 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DC C 1 " pdb=" OP1 DC C 1 " pdb=" OP2 DC C 1 " pdb=" O5' DC C 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" CA PRO A 920 " pdb=" N PRO A 920 " pdb=" C PRO A 920 " pdb=" CB PRO A 920 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 1860 not shown) Planarity restraints: 1951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 330 " 0.411 9.50e-02 1.11e+02 1.84e-01 2.12e+01 pdb=" NE ARG A 330 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 330 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 330 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 330 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 611 " -0.369 9.50e-02 1.11e+02 1.66e-01 2.00e+01 pdb=" NE ARG A 611 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 611 " 0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 611 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 611 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C 18 " -0.063 2.00e-02 2.50e+03 2.67e-02 1.95e+01 pdb=" N9 DA C 18 " 0.010 2.00e-02 2.50e+03 pdb=" C8 DA C 18 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DA C 18 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA C 18 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA C 18 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA C 18 " -0.032 2.00e-02 2.50e+03 pdb=" N1 DA C 18 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DA C 18 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA C 18 " 0.033 2.00e-02 2.50e+03 pdb=" C4 DA C 18 " 0.027 2.00e-02 2.50e+03 ... (remaining 1948 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 284 2.69 - 3.24: 11192 3.24 - 3.79: 19080 3.79 - 4.35: 26050 4.35 - 4.90: 40937 Nonbonded interactions: 97543 Sorted by model distance: nonbonded pdb=" OE2 GLU A 370 " pdb=" CD1 ILE A 560 " model vdw 2.137 3.460 nonbonded pdb=" OD2 ASP A 888 " pdb=" O HOH A1401 " model vdw 2.168 3.040 nonbonded pdb=" N2 DG C 19 " pdb=" O2 DC D 30 " model vdw 2.282 3.120 nonbonded pdb=" N2 DG C 17 " pdb=" N3 DC D 32 " model vdw 2.339 2.560 nonbonded pdb=" NZ LYS B 289 " pdb=" OG1 THR B 302 " model vdw 2.349 3.120 ... (remaining 97538 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: 2.400 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 38.560 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.009 0.076 12008 Z= 0.608 Angle : 1.351 12.875 16508 Z= 0.888 Chirality : 0.084 0.633 1863 Planarity : 0.014 0.184 1951 Dihedral : 17.113 179.345 4511 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.01 (0.21), residues: 1341 helix: -0.89 (0.21), residues: 470 sheet: -0.45 (0.29), residues: 251 loop : -0.40 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP A 502 HIS 0.027 0.004 HIS A 729 PHE 0.050 0.008 PHE A1031 TYR 0.059 0.010 TYR A 490 ARG 0.031 0.003 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8927 (tt0) cc_final: 0.8241 (mp0) REVERT: A 228 MET cc_start: 0.8542 (mtm) cc_final: 0.8293 (mtm) REVERT: A 426 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8333 (tt0) REVERT: A 525 MET cc_start: 0.9197 (mmm) cc_final: 0.8908 (mmm) REVERT: A 552 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7120 (pptt) REVERT: A 581 ASP cc_start: 0.8570 (m-30) cc_final: 0.8323 (t0) REVERT: A 700 ARG cc_start: 0.8243 (mtp85) cc_final: 0.8003 (mtt-85) REVERT: A 711 ASN cc_start: 0.9026 (m110) cc_final: 0.8822 (m110) REVERT: A 771 GLU cc_start: 0.8774 (tt0) cc_final: 0.8112 (pm20) REVERT: A 799 GLU cc_start: 0.7989 (tt0) cc_final: 0.7543 (tp30) REVERT: A 860 GLU cc_start: 0.7929 (tp30) cc_final: 0.7407 (mp0) REVERT: A 923 LYS cc_start: 0.9034 (tttp) cc_final: 0.8753 (tptp) REVERT: A 925 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8590 (mt-10) REVERT: A 927 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7498 (mp0) REVERT: A 950 MET cc_start: 0.8700 (tpp) cc_final: 0.8389 (ttm) REVERT: A 981 ASP cc_start: 0.8155 (m-30) cc_final: 0.7763 (t0) REVERT: A 1025 GLU cc_start: 0.8907 (tt0) cc_final: 0.8635 (tm-30) REVERT: A 1156 LEU cc_start: 0.8431 (mm) cc_final: 0.8109 (mt) REVERT: A 1185 GLU cc_start: 0.8287 (tt0) cc_final: 0.7755 (tp30) REVERT: B 85 GLN cc_start: 0.7495 (mm110) cc_final: 0.6993 (mt0) REVERT: B 101 LEU cc_start: 0.7937 (mt) cc_final: 0.7733 (mp) REVERT: B 121 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8144 (mmm160) REVERT: B 282 GLN cc_start: 0.6281 (mp10) cc_final: 0.6035 (mp-120) REVERT: B 313 PHE cc_start: 0.6783 (m-80) cc_final: 0.6258 (m-80) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 1.7126 time to fit residues: 334.0459 Evaluate side-chains 125 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN B 69 HIS B 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12008 Z= 0.242 Angle : 0.662 8.055 16508 Z= 0.364 Chirality : 0.044 0.210 1863 Planarity : 0.005 0.043 1951 Dihedral : 18.598 175.548 2040 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.52 % Allowed : 10.08 % Favored : 88.40 % 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: 0.02 (0.22), residues: 1341 helix: 0.58 (0.23), residues: 481 sheet: -0.39 (0.29), residues: 259 loop : -0.10 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 502 HIS 0.006 0.001 HIS A 197 PHE 0.024 0.002 PHE A 444 TYR 0.017 0.002 TYR A 483 ARG 0.005 0.001 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8863 (tt0) cc_final: 0.8339 (mp0) REVERT: A 552 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7288 (pptt) REVERT: A 581 ASP cc_start: 0.8464 (m-30) cc_final: 0.8085 (t0) REVERT: A 700 ARG cc_start: 0.8252 (mtp85) cc_final: 0.8000 (mtt-85) REVERT: A 771 GLU cc_start: 0.8702 (tt0) cc_final: 0.8006 (pm20) REVERT: A 860 GLU cc_start: 0.8042 (tp30) cc_final: 0.7526 (pm20) REVERT: A 923 LYS cc_start: 0.8986 (tttp) cc_final: 0.8730 (tptp) REVERT: A 925 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8683 (mt-10) REVERT: A 927 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7520 (mp0) REVERT: A 1156 LEU cc_start: 0.8510 (mm) cc_final: 0.8156 (mt) REVERT: A 1159 ASP cc_start: 0.8432 (m-30) cc_final: 0.8221 (OUTLIER) REVERT: A 1185 GLU cc_start: 0.8146 (tt0) cc_final: 0.7714 (tp30) REVERT: B 81 LEU cc_start: 0.6988 (mt) cc_final: 0.6710 (mp) REVERT: B 85 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6793 (mt0) REVERT: B 121 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8177 (mmm160) outliers start: 17 outliers final: 2 residues processed: 135 average time/residue: 1.7286 time to fit residues: 250.0575 Evaluate side-chains 112 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN B 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12008 Z= 0.343 Angle : 0.672 7.997 16508 Z= 0.364 Chirality : 0.045 0.198 1863 Planarity : 0.005 0.066 1951 Dihedral : 18.647 174.382 2040 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.14 % Allowed : 11.24 % Favored : 86.62 % 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: 0.05 (0.22), residues: 1341 helix: 0.73 (0.24), residues: 487 sheet: -0.52 (0.30), residues: 250 loop : -0.14 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 502 HIS 0.007 0.001 HIS A 197 PHE 0.022 0.002 PHE A 444 TYR 0.021 0.002 TYR A 483 ARG 0.008 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8924 (tt0) cc_final: 0.8367 (mp0) REVERT: A 222 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7769 (tpm170) REVERT: A 234 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 291 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8705 (ttpt) REVERT: A 370 GLU cc_start: 0.8222 (tp30) cc_final: 0.7996 (tp30) REVERT: A 552 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7251 (pptt) REVERT: A 581 ASP cc_start: 0.8414 (m-30) cc_final: 0.8056 (t0) REVERT: A 639 THR cc_start: 0.7268 (p) cc_final: 0.7026 (t) REVERT: A 771 GLU cc_start: 0.8729 (tt0) cc_final: 0.8037 (pm20) REVERT: A 860 GLU cc_start: 0.7993 (tp30) cc_final: 0.7515 (pm20) REVERT: A 868 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7512 (mp0) REVERT: A 888 ASP cc_start: 0.8374 (p0) cc_final: 0.8133 (p0) REVERT: A 923 LYS cc_start: 0.9001 (tttp) cc_final: 0.8768 (tptp) REVERT: A 927 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7659 (mp0) REVERT: A 1185 GLU cc_start: 0.8193 (tt0) cc_final: 0.7772 (tp30) REVERT: B 85 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7029 (mt0) REVERT: B 121 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8005 (mmm160) outliers start: 24 outliers final: 6 residues processed: 135 average time/residue: 1.6968 time to fit residues: 244.2764 Evaluate side-chains 117 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 0.0870 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12008 Z= 0.265 Angle : 0.611 8.100 16508 Z= 0.334 Chirality : 0.043 0.231 1863 Planarity : 0.005 0.041 1951 Dihedral : 18.502 173.088 2040 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.14 % Allowed : 12.76 % Favored : 85.10 % 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: 0.20 (0.22), residues: 1341 helix: 1.03 (0.24), residues: 481 sheet: -0.55 (0.30), residues: 251 loop : -0.17 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 502 HIS 0.004 0.001 HIS A 197 PHE 0.018 0.002 PHE A 444 TYR 0.017 0.002 TYR A 483 ARG 0.006 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8916 (tt0) cc_final: 0.8378 (mp0) REVERT: A 234 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: A 370 GLU cc_start: 0.8345 (tp30) cc_final: 0.8131 (tp30) REVERT: A 552 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7208 (pptt) REVERT: A 564 TYR cc_start: 0.8876 (t80) cc_final: 0.8672 (t80) REVERT: A 771 GLU cc_start: 0.8687 (tt0) cc_final: 0.7998 (pm20) REVERT: A 860 GLU cc_start: 0.7957 (tp30) cc_final: 0.7481 (pm20) REVERT: A 868 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7511 (mp0) REVERT: A 888 ASP cc_start: 0.8287 (p0) cc_final: 0.8058 (p0) REVERT: A 923 LYS cc_start: 0.8969 (tttp) cc_final: 0.8746 (tptp) REVERT: A 927 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7677 (mm-30) REVERT: A 1185 GLU cc_start: 0.8202 (tt0) cc_final: 0.7766 (tp30) REVERT: B 85 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7099 (mt0) outliers start: 24 outliers final: 9 residues processed: 138 average time/residue: 1.5247 time to fit residues: 227.3157 Evaluate side-chains 121 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 274 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12008 Z= 0.312 Angle : 0.637 8.077 16508 Z= 0.346 Chirality : 0.044 0.200 1863 Planarity : 0.005 0.054 1951 Dihedral : 18.538 172.622 2040 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.14 % Allowed : 13.20 % Favored : 84.66 % 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: 0.21 (0.23), residues: 1341 helix: 1.06 (0.24), residues: 483 sheet: -0.63 (0.30), residues: 252 loop : -0.14 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 502 HIS 0.005 0.001 HIS A 729 PHE 0.018 0.002 PHE A 590 TYR 0.018 0.002 TYR A 483 ARG 0.006 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8928 (tt0) cc_final: 0.8379 (mp0) REVERT: A 234 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: A 291 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8703 (ttpt) REVERT: A 552 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7244 (pptt) REVERT: A 771 GLU cc_start: 0.8705 (tt0) cc_final: 0.8012 (pm20) REVERT: A 860 GLU cc_start: 0.7964 (tp30) cc_final: 0.7475 (pm20) REVERT: A 868 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7479 (mp0) REVERT: A 882 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 888 ASP cc_start: 0.8262 (p0) cc_final: 0.8051 (p0) REVERT: A 923 LYS cc_start: 0.8940 (tttp) cc_final: 0.8740 (tptp) REVERT: A 927 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7683 (mm-30) REVERT: A 1185 GLU cc_start: 0.8202 (tt0) cc_final: 0.7769 (tp30) REVERT: B 85 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7204 (mt0) outliers start: 24 outliers final: 11 residues processed: 140 average time/residue: 1.5884 time to fit residues: 238.3440 Evaluate side-chains 123 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12008 Z= 0.195 Angle : 0.570 8.123 16508 Z= 0.311 Chirality : 0.042 0.202 1863 Planarity : 0.004 0.040 1951 Dihedral : 18.349 170.993 2040 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.68 % Allowed : 13.56 % Favored : 83.76 % 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: 0.32 (0.23), residues: 1341 helix: 1.24 (0.24), residues: 486 sheet: -0.80 (0.29), residues: 267 loop : -0.02 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 PHE 0.015 0.001 PHE A 444 TYR 0.016 0.001 TYR A 281 ARG 0.008 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8903 (tt0) cc_final: 0.8391 (mp0) REVERT: A 234 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: A 291 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8733 (ttpt) REVERT: A 552 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7275 (pptt) REVERT: A 739 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8188 (mtp85) REVERT: A 771 GLU cc_start: 0.8643 (tt0) cc_final: 0.8118 (mp0) REVERT: A 860 GLU cc_start: 0.7973 (tp30) cc_final: 0.7478 (pm20) REVERT: A 868 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7442 (mp0) REVERT: A 888 ASP cc_start: 0.8254 (p0) cc_final: 0.8045 (p0) REVERT: A 927 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7676 (mm-30) REVERT: A 950 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7393 (ttm) REVERT: A 1185 GLU cc_start: 0.8222 (tt0) cc_final: 0.7742 (tp30) REVERT: B 85 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7246 (mt0) outliers start: 30 outliers final: 13 residues processed: 133 average time/residue: 1.5171 time to fit residues: 216.6914 Evaluate side-chains 126 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN A1197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12008 Z= 0.214 Angle : 0.576 8.067 16508 Z= 0.313 Chirality : 0.042 0.202 1863 Planarity : 0.004 0.042 1951 Dihedral : 18.294 168.546 2040 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.79 % Favored : 98.14 % Rotamer: Outliers : 2.32 % Allowed : 14.01 % Favored : 83.68 % 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: 0.39 (0.23), residues: 1341 helix: 1.31 (0.24), residues: 486 sheet: -0.85 (0.29), residues: 269 loop : 0.07 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 PHE 0.014 0.001 PHE A 444 TYR 0.016 0.002 TYR A 281 ARG 0.008 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8894 (tt0) cc_final: 0.8378 (mp0) REVERT: A 222 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7831 (tpm170) REVERT: A 234 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: A 291 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8719 (ttpt) REVERT: A 532 LYS cc_start: 0.8378 (mttt) cc_final: 0.8116 (mtpp) REVERT: A 552 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7294 (pptt) REVERT: A 771 GLU cc_start: 0.8621 (tt0) cc_final: 0.8114 (mp0) REVERT: A 860 GLU cc_start: 0.7965 (tp30) cc_final: 0.7441 (pm20) REVERT: A 882 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8410 (mt) REVERT: A 888 ASP cc_start: 0.8233 (p0) cc_final: 0.8026 (p0) REVERT: A 927 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 950 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7391 (ttm) REVERT: A 1185 GLU cc_start: 0.8224 (tt0) cc_final: 0.7720 (tp30) REVERT: B 85 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7288 (mt0) outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 1.6176 time to fit residues: 230.5608 Evaluate side-chains 128 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12008 Z= 0.305 Angle : 0.622 7.883 16508 Z= 0.336 Chirality : 0.044 0.201 1863 Planarity : 0.005 0.049 1951 Dihedral : 18.388 163.347 2040 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.91 % Rotamer: Outliers : 2.41 % Allowed : 14.45 % Favored : 83.14 % 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: 0.30 (0.23), residues: 1341 helix: 1.24 (0.24), residues: 483 sheet: -0.87 (0.29), residues: 268 loop : 0.01 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 502 HIS 0.005 0.001 HIS A 729 PHE 0.018 0.002 PHE A 590 TYR 0.018 0.002 TYR A 483 ARG 0.008 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8901 (tt0) cc_final: 0.8377 (mp0) REVERT: A 222 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7820 (tpm170) REVERT: A 291 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8712 (ttpt) REVERT: A 532 LYS cc_start: 0.8374 (mttt) cc_final: 0.8123 (mtpp) REVERT: A 552 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7321 (pptt) REVERT: A 739 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8215 (mtp85) REVERT: A 771 GLU cc_start: 0.8709 (tt0) cc_final: 0.7998 (pm20) REVERT: A 860 GLU cc_start: 0.7948 (tp30) cc_final: 0.7426 (pm20) REVERT: A 868 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6883 (mp0) REVERT: A 882 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 888 ASP cc_start: 0.8279 (p0) cc_final: 0.8073 (p0) REVERT: A 927 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7666 (mm-30) REVERT: A 950 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7397 (ttm) REVERT: A 1185 GLU cc_start: 0.8223 (tt0) cc_final: 0.7764 (tp30) REVERT: B 45 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7606 (mt0) REVERT: B 85 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7324 (mt0) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 1.6161 time to fit residues: 223.2678 Evaluate side-chains 126 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 10.0000 chunk 116 optimal weight: 0.1980 chunk 123 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN B 282 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12008 Z= 0.200 Angle : 0.565 7.760 16508 Z= 0.307 Chirality : 0.042 0.202 1863 Planarity : 0.004 0.043 1951 Dihedral : 18.201 152.536 2040 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 15.08 % Favored : 82.87 % 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: 0.41 (0.23), residues: 1341 helix: 1.36 (0.24), residues: 486 sheet: -0.94 (0.29), residues: 273 loop : 0.12 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 PHE 0.014 0.001 PHE A 444 TYR 0.017 0.002 TYR A 281 ARG 0.006 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8886 (tt0) cc_final: 0.8377 (mp0) REVERT: A 234 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: A 291 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8730 (ttpt) REVERT: A 532 LYS cc_start: 0.8342 (mttt) cc_final: 0.8099 (mtpp) REVERT: A 552 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7327 (pptt) REVERT: A 739 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8295 (mtp85) REVERT: A 771 GLU cc_start: 0.8627 (tt0) cc_final: 0.8119 (mp0) REVERT: A 860 GLU cc_start: 0.7948 (tp30) cc_final: 0.7421 (pm20) REVERT: A 868 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6919 (mp0) REVERT: A 927 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7673 (mm-30) REVERT: A 950 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7399 (ttm) REVERT: A 1010 PHE cc_start: 0.7590 (m-80) cc_final: 0.7292 (m-80) REVERT: A 1185 GLU cc_start: 0.8229 (tt0) cc_final: 0.7720 (tp30) REVERT: B 45 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7591 (mt0) REVERT: B 85 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7366 (mt0) outliers start: 23 outliers final: 10 residues processed: 129 average time/residue: 1.5745 time to fit residues: 217.7244 Evaluate side-chains 120 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 739 ARG Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 313 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12008 Z= 0.266 Angle : 0.604 8.256 16508 Z= 0.326 Chirality : 0.043 0.210 1863 Planarity : 0.005 0.043 1951 Dihedral : 18.176 153.683 2040 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 1.87 % Allowed : 15.34 % Favored : 82.78 % 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: 0.38 (0.23), residues: 1341 helix: 1.31 (0.24), residues: 485 sheet: -0.84 (0.29), residues: 267 loop : 0.04 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 502 HIS 0.004 0.001 HIS A 729 PHE 0.016 0.002 PHE A 590 TYR 0.017 0.002 TYR A 281 ARG 0.007 0.000 ARG B 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8890 (tt0) cc_final: 0.8379 (mp0) REVERT: A 291 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8734 (ttpt) REVERT: A 532 LYS cc_start: 0.8360 (mttt) cc_final: 0.8116 (mtpp) REVERT: A 552 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7328 (pptt) REVERT: A 771 GLU cc_start: 0.8661 (tt0) cc_final: 0.8059 (pm20) REVERT: A 860 GLU cc_start: 0.7954 (tp30) cc_final: 0.7425 (pm20) REVERT: A 868 GLU cc_start: 0.7623 (tm-30) cc_final: 0.6919 (mp0) REVERT: A 882 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8426 (mt) REVERT: A 927 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7683 (mm-30) REVERT: A 950 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7337 (ttm) REVERT: A 1185 GLU cc_start: 0.8239 (tt0) cc_final: 0.7739 (tp30) REVERT: B 45 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7565 (mt0) REVERT: B 85 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7421 (mt0) REVERT: B 282 GLN cc_start: 0.5722 (mp10) cc_final: 0.5518 (mt0) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 1.6043 time to fit residues: 209.7117 Evaluate side-chains 120 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1170 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.0970 chunk 96 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.141130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107599 restraints weight = 17604.817| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.83 r_work: 0.3383 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12008 Z= 0.211 Angle : 0.571 8.580 16508 Z= 0.309 Chirality : 0.042 0.206 1863 Planarity : 0.004 0.044 1951 Dihedral : 18.050 153.832 2040 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.76 % Rotamer: Outliers : 1.52 % Allowed : 15.52 % Favored : 82.96 % 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: 0.46 (0.23), residues: 1341 helix: 1.40 (0.24), residues: 485 sheet: -0.79 (0.30), residues: 267 loop : 0.05 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 502 HIS 0.004 0.001 HIS A 912 PHE 0.014 0.001 PHE A 444 TYR 0.017 0.002 TYR A 281 ARG 0.007 0.000 ARG B 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.50 seconds wall clock time: 89 minutes 10.43 seconds (5350.43 seconds total)