Starting phenix.real_space_refine on Wed Aug 5 18:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mcb_63798/08_2026/9mcb_63798_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mcb_63798/08_2026/9mcb_63798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mcb_63798/08_2026/9mcb_63798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mcb_63798/08_2026/9mcb_63798.map" model { file = "/net/cci-nas-00/data/ceres_data/9mcb_63798/08_2026/9mcb_63798_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mcb_63798/08_2026/9mcb_63798_neut.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.982 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 6820 2.51 5 N 1836 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10729 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7948 Classifications: {'peptide': 1009} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 955} Chain: "B" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2156 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 18, 'TRANS': 250} Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.23 Number of scatterers: 10729 At special positions: 0 Unit cell: (88.776, 106.272, 138.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 1 15.00 O 2020 8.00 N 1836 7.00 C 6820 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: 0.78 Conformation dependent library (CDL) restraints added in 399.3 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 47.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.828A pdb=" N VAL A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N HIS A 64 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N GLU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.525A pdb=" N GLU A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.989A pdb=" N SER A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.934A pdb=" N ILE A 123 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.834A pdb=" N GLY A 158 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.712A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 4.035A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 334 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.897A pdb=" N LEU A 445 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 removed outlier: 4.461A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.887A pdb=" N ASN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.704A pdb=" N VAL A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 561 through 568 removed outlier: 3.562A pdb=" N PHE A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 592 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.529A pdb=" N SER A 620 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 621 " --> pdb=" O TYR A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 621' Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 640 through 657 Processing helix chain 'A' and resid 657 through 669 Processing helix chain 'A' and resid 671 through 678 Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.601A pdb=" N CYS A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 707 " --> pdb=" O TRP A 703 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS A 715 " --> pdb=" O CYS A 711 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 3.735A pdb=" N HIS A 727 " --> pdb=" O ARG A 723 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 777 removed outlier: 3.626A pdb=" N ALA A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 removed outlier: 4.362A pdb=" N VAL A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 822 through 833 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.521A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 915 removed outlier: 3.509A pdb=" N THR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 971 through 982 removed outlier: 3.513A pdb=" N PHE A 979 " --> pdb=" O PHE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1011 Processing helix chain 'A' and resid 1014 through 1024 removed outlier: 3.889A pdb=" N SER A1020 " --> pdb=" O THR A1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 944 removed outlier: 3.853A pdb=" N LYS B 942 " --> pdb=" O HIS B 939 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS B 943 " --> pdb=" O SER B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1060 through 1072 removed outlier: 3.518A pdb=" N ILE B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1088 removed outlier: 3.694A pdb=" N ARG B1088 " --> pdb=" O ASP B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1118 removed outlier: 3.672A pdb=" N VAL B1116 " --> pdb=" O MET B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1131 removed outlier: 4.446A pdb=" N ARG B1128 " --> pdb=" O GLU B1124 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS B1130 " --> pdb=" O GLU B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1140 Processing helix chain 'B' and resid 1143 through 1152 removed outlier: 4.215A pdb=" N GLU B1147 " --> pdb=" O GLU B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1262 through 1283 removed outlier: 3.765A pdb=" N LYS B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B1271 " --> pdb=" O LYS B1267 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.659A pdb=" N TYR C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.752A pdb=" N VAL A 99 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR A 147 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU A 101 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 162 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 189 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A 164 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR A 191 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.688A pdb=" N VAL A 231 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.313A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR A 471 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N THR A 503 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A 473 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 598 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 945 through 947 Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.579A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN A1041 " --> pdb=" O ILE A 987 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 987 " --> pdb=" O ASN A1041 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 990 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.579A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 930 through 932 removed outlier: 3.814A pdb=" N SER B 930 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 977 " --> pdb=" O SER B 930 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 978 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 984 " --> pdb=" O PHE B 978 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 16 removed outlier: 3.989A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3562 1.34 - 1.46: 2383 1.46 - 1.58: 4943 1.58 - 1.70: 1 1.70 - 1.82: 81 Bond restraints: 10970 Sorted by residual: bond pdb=" C4 AMP A1101 " pdb=" C5 AMP A1101 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" CG LEU B1261 " pdb=" CD2 LEU B1261 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.72e-01 bond pdb=" CB MET B 962 " pdb=" CG MET B 962 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.17e-01 bond pdb=" CA MET A 421 " pdb=" C MET A 421 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 6.89e-01 bond pdb=" C TYR B1012 " pdb=" N PRO B1013 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.24e-01 ... (remaining 10965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14725 2.28 - 4.57: 131 4.57 - 6.85: 16 6.85 - 9.14: 2 9.14 - 11.42: 2 Bond angle restraints: 14876 Sorted by residual: angle pdb=" CB MET B 962 " pdb=" CG MET B 962 " pdb=" SD MET B 962 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET A 410 " pdb=" CG MET A 410 " pdb=" SD MET A 410 " ideal model delta sigma weight residual 112.70 122.78 -10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA MET B1103 " pdb=" CB MET B1103 " pdb=" CG MET B1103 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C MET A 421 " pdb=" N GLN A 422 " pdb=" CA GLN A 422 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N PHE B1259 " pdb=" CA PHE B1259 " pdb=" C PHE B1259 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.82e+00 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 6036 17.53 - 35.06: 441 35.06 - 52.59: 101 52.59 - 70.11: 25 70.11 - 87.64: 15 Dihedral angle restraints: 6618 sinusoidal: 2698 harmonic: 3920 Sorted by residual: dihedral pdb=" CA LEU B1258 " pdb=" C LEU B1258 " pdb=" N PHE B1259 " pdb=" CA PHE B1259 " ideal model delta harmonic sigma weight residual 180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LYS A 923 " pdb=" C LYS A 923 " pdb=" N ASN A 924 " pdb=" CA ASN A 924 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PHE B1131 " pdb=" C PHE B1131 " pdb=" N SER B1132 " pdb=" CA SER B1132 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 6615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1125 0.037 - 0.073: 372 0.073 - 0.110: 109 0.110 - 0.146: 31 0.146 - 0.183: 4 Chirality restraints: 1641 Sorted by residual: chirality pdb=" CA PHE B1259 " pdb=" N PHE B1259 " pdb=" C PHE B1259 " pdb=" CB PHE B1259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA MET B1103 " pdb=" N MET B1103 " pdb=" C MET B1103 " pdb=" CB MET B1103 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1638 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1259 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B1260 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B1260 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B1260 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 721 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASN A 721 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN A 721 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 722 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 325 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 326 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " 0.023 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3805 2.88 - 3.38: 9985 3.38 - 3.89: 17451 3.89 - 4.39: 20019 4.39 - 4.90: 33345 Nonbonded interactions: 84605 Sorted by model distance: nonbonded pdb=" SD MET A 67 " pdb=" CD1 LEU A 70 " model vdw 2.372 3.820 nonbonded pdb=" O VAL A 524 " pdb=" OG1 THR A 525 " model vdw 2.577 3.040 nonbonded pdb=" N ASP A 227 " pdb=" O ASP A 227 " model vdw 2.616 2.496 nonbonded pdb=" N ASP B 983 " pdb=" OD1 ASP B 983 " model vdw 2.617 3.120 nonbonded pdb=" O LEU B1138 " pdb=" N ILE B1142 " model vdw 2.623 3.120 ... (remaining 84600 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: 5.890 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.002 0.029 10970 Z= 0.111 Angle : 0.556 11.423 14876 Z= 0.285 Chirality : 0.042 0.183 1641 Planarity : 0.005 0.084 1949 Dihedral : 13.952 87.643 4090 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1348 helix: 0.52 (0.23), residues: 528 sheet: 0.12 (0.36), residues: 216 loop : -0.36 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 450 TYR 0.010 0.001 TYR A 910 PHE 0.017 0.001 PHE B1259 TRP 0.013 0.001 TRP A 423 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10970) covalent geometry : angle 0.55609 / 0.28 (14876) hydrogen bonds : bond 0.13911 / 9.67 ( 484) hydrogen bonds : angle 6.34477 / 4.50 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.314 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.8429 (mmm) cc_final: 0.7974 (mmt) REVERT: A 601 LEU cc_start: 0.8661 (tp) cc_final: 0.8385 (tt) REVERT: A 638 PRO cc_start: 0.6726 (Cg_endo) cc_final: 0.6476 (Cg_exo) REVERT: A 639 ASN cc_start: 0.7454 (p0) cc_final: 0.6983 (t0) REVERT: A 646 GLN cc_start: 0.8715 (tp40) cc_final: 0.8224 (tp-100) REVERT: A 725 LEU cc_start: 0.8213 (mt) cc_final: 0.7928 (tt) REVERT: A 987 ILE cc_start: 0.8581 (mm) cc_final: 0.8230 (mm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1124 time to fit residues: 48.4322 Evaluate side-chains 174 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN A 351 ASN A 454 GLN A 463 GLN A 512 ASN A 721 ASN A 792 GLN A 918 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.113991 restraints weight = 22146.493| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.83 r_work: 0.3585 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10970 Z= 0.147 Angle : 0.621 11.514 14876 Z= 0.321 Chirality : 0.043 0.148 1641 Planarity : 0.005 0.075 1949 Dihedral : 5.284 69.324 1472 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.65 % Allowed : 11.18 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1348 helix: 0.64 (0.23), residues: 529 sheet: 0.26 (0.37), residues: 216 loop : -0.23 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 119 TYR 0.015 0.001 TYR A 776 PHE 0.028 0.002 PHE A1001 TRP 0.022 0.002 TRP A 647 HIS 0.008 0.001 HIS B1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10970) covalent geometry : angle 0.62082 / 0.32 (14876) hydrogen bonds : bond 0.04054 / 2.81 ( 484) hydrogen bonds : angle 5.14014 / 3.64 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.417 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7379 (m-40) REVERT: A 410 MET cc_start: 0.9033 (mmm) cc_final: 0.8493 (mmm) REVERT: A 601 LEU cc_start: 0.8969 (tp) cc_final: 0.8640 (tt) REVERT: A 638 PRO cc_start: 0.5567 (Cg_endo) cc_final: 0.4556 (Cg_exo) REVERT: A 646 GLN cc_start: 0.8706 (tp40) cc_final: 0.8197 (tp-100) REVERT: A 658 GLN cc_start: 0.9441 (tp-100) cc_final: 0.8777 (tp-100) REVERT: A 844 MET cc_start: 0.8659 (tpp) cc_final: 0.8431 (tpp) REVERT: A 873 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.6645 (t80) REVERT: A 987 ILE cc_start: 0.8782 (mm) cc_final: 0.8527 (mm) REVERT: A 1002 MET cc_start: 0.7695 (mpp) cc_final: 0.7223 (mpp) REVERT: A 1040 CYS cc_start: 0.7900 (m) cc_final: 0.7576 (m) REVERT: B 944 ILE cc_start: 0.6418 (tp) cc_final: 0.5734 (pt) REVERT: B 953 LYS cc_start: 0.9437 (mttp) cc_final: 0.9225 (mmtm) REVERT: B 1078 TYR cc_start: 0.5550 (t80) cc_final: 0.5100 (t80) REVERT: B 1112 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7089 (mmt) REVERT: C 51 GLU cc_start: 0.7047 (pm20) cc_final: 0.6591 (pm20) REVERT: C 63 LYS cc_start: 0.8543 (tptt) cc_final: 0.8014 (tppt) outliers start: 31 outliers final: 14 residues processed: 199 average time/residue: 0.1038 time to fit residues: 29.3800 Evaluate side-chains 166 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain B residue 1112 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 GLN A 792 GLN A 950 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.150278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.110636 restraints weight = 22654.683| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.53 r_work: 0.3494 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10970 Z= 0.230 Angle : 0.675 15.007 14876 Z= 0.346 Chirality : 0.045 0.185 1641 Planarity : 0.005 0.071 1949 Dihedral : 5.344 67.775 1472 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.50 % Allowed : 11.95 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1348 helix: 0.54 (0.23), residues: 533 sheet: 0.18 (0.37), residues: 216 loop : -0.38 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 880 TYR 0.047 0.002 TYR B1079 PHE 0.039 0.002 PHE A 790 TRP 0.025 0.002 TRP A 647 HIS 0.008 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (10970) covalent geometry : angle 0.67543 / 0.35 (14876) hydrogen bonds : bond 0.04286 / 2.96 ( 484) hydrogen bonds : angle 5.19712 / 3.68 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.384 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: A 410 MET cc_start: 0.9094 (mmm) cc_final: 0.8581 (mmm) REVERT: A 601 LEU cc_start: 0.9024 (tp) cc_final: 0.8801 (tt) REVERT: A 638 PRO cc_start: 0.5433 (Cg_endo) cc_final: 0.5152 (Cg_exo) REVERT: A 646 GLN cc_start: 0.8751 (tp40) cc_final: 0.8295 (tp-100) REVERT: A 649 ARG cc_start: 0.8807 (tpm170) cc_final: 0.8494 (tpm170) REVERT: A 653 GLU cc_start: 0.9352 (tp30) cc_final: 0.9138 (tp30) REVERT: A 656 PHE cc_start: 0.8989 (m-80) cc_final: 0.8034 (m-80) REVERT: A 844 MET cc_start: 0.8750 (tpp) cc_final: 0.8235 (tpp) REVERT: A 987 ILE cc_start: 0.8872 (mm) cc_final: 0.8554 (mm) REVERT: A 1040 CYS cc_start: 0.7977 (m) cc_final: 0.7332 (m) REVERT: B 944 ILE cc_start: 0.6458 (tp) cc_final: 0.5723 (pt) REVERT: B 976 LYS cc_start: 0.7055 (tttt) cc_final: 0.6790 (ttpt) REVERT: B 1012 TYR cc_start: 0.6646 (t80) cc_final: 0.6408 (t80) REVERT: B 1053 GLU cc_start: 0.6404 (mp0) cc_final: 0.6165 (mp0) REVERT: B 1100 TYR cc_start: 0.8681 (m-10) cc_final: 0.8383 (m-10) REVERT: B 1114 GLN cc_start: 0.8963 (tt0) cc_final: 0.8743 (mm110) outliers start: 41 outliers final: 23 residues processed: 186 average time/residue: 0.0906 time to fit residues: 24.4152 Evaluate side-chains 170 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 512 ASN A 516 GLN A 950 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN B1032 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.151114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109970 restraints weight = 22732.621| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.62 r_work: 0.3521 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10970 Z= 0.143 Angle : 0.612 13.532 14876 Z= 0.311 Chirality : 0.043 0.161 1641 Planarity : 0.004 0.066 1949 Dihedral : 5.127 54.685 1472 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.39 % Allowed : 13.82 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1348 helix: 0.67 (0.23), residues: 537 sheet: 0.15 (0.37), residues: 216 loop : -0.28 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 869 TYR 0.012 0.001 TYR A 947 PHE 0.016 0.001 PHE B1276 TRP 0.013 0.002 TRP B1136 HIS 0.007 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10970) covalent geometry : angle 0.61203 / 0.31 (14876) hydrogen bonds : bond 0.03838 / 2.64 ( 484) hydrogen bonds : angle 5.02090 / 3.56 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.305 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: A 408 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 410 MET cc_start: 0.9024 (mmm) cc_final: 0.8550 (mmm) REVERT: A 489 MET cc_start: 0.8717 (mmp) cc_final: 0.8510 (mmp) REVERT: A 601 LEU cc_start: 0.8980 (tp) cc_final: 0.8778 (tt) REVERT: A 646 GLN cc_start: 0.8725 (tp40) cc_final: 0.8254 (tp-100) REVERT: A 649 ARG cc_start: 0.8811 (tpm170) cc_final: 0.8522 (tpt90) REVERT: A 656 PHE cc_start: 0.8936 (m-80) cc_final: 0.8359 (m-80) REVERT: A 844 MET cc_start: 0.8786 (tpp) cc_final: 0.8328 (tpp) REVERT: A 987 ILE cc_start: 0.8891 (mm) cc_final: 0.8567 (mm) REVERT: A 1040 CYS cc_start: 0.7869 (m) cc_final: 0.7230 (m) REVERT: B 944 ILE cc_start: 0.6531 (tp) cc_final: 0.5766 (pt) REVERT: B 953 LYS cc_start: 0.9489 (mttt) cc_final: 0.9256 (mtmt) REVERT: B 1012 TYR cc_start: 0.6744 (t80) cc_final: 0.6476 (t80) REVERT: B 1285 MET cc_start: 0.1630 (ttt) cc_final: 0.1249 (mtm) outliers start: 28 outliers final: 22 residues processed: 176 average time/residue: 0.0925 time to fit residues: 23.5291 Evaluate side-chains 158 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.150869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107391 restraints weight = 22577.508| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.37 r_work: 0.3527 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10970 Z= 0.141 Angle : 0.605 12.808 14876 Z= 0.307 Chirality : 0.042 0.183 1641 Planarity : 0.004 0.058 1949 Dihedral : 5.031 51.430 1472 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.90 % Allowed : 14.51 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.23), residues: 1348 helix: 0.95 (0.23), residues: 522 sheet: 0.17 (0.38), residues: 216 loop : -0.20 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.021 0.001 TYR B1078 PHE 0.023 0.001 PHE B1276 TRP 0.015 0.002 TRP A 709 HIS 0.005 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10970) covalent geometry : angle 0.60460 / 0.31 (14876) hydrogen bonds : bond 0.03723 / 2.53 ( 484) hydrogen bonds : angle 4.95855 / 3.51 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.443 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: A 408 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6827 (mm-30) REVERT: A 410 MET cc_start: 0.9023 (mmm) cc_final: 0.8573 (mmm) REVERT: A 489 MET cc_start: 0.8738 (mmp) cc_final: 0.8523 (mmp) REVERT: A 601 LEU cc_start: 0.9014 (tp) cc_final: 0.8812 (tt) REVERT: A 646 GLN cc_start: 0.8815 (tp40) cc_final: 0.8367 (tp-100) REVERT: A 649 ARG cc_start: 0.8913 (tpm170) cc_final: 0.8595 (tpt90) REVERT: A 656 PHE cc_start: 0.8980 (m-80) cc_final: 0.8001 (m-80) REVERT: A 844 MET cc_start: 0.8867 (tpp) cc_final: 0.8422 (tpp) REVERT: A 987 ILE cc_start: 0.8919 (mm) cc_final: 0.8669 (mm) REVERT: A 1040 CYS cc_start: 0.7867 (m) cc_final: 0.7632 (m) REVERT: B 944 ILE cc_start: 0.6593 (tp) cc_final: 0.5825 (pt) REVERT: B 976 LYS cc_start: 0.7217 (tttt) cc_final: 0.6757 (ttpt) REVERT: B 990 LYS cc_start: 0.8508 (mttt) cc_final: 0.8177 (tppt) REVERT: B 1012 TYR cc_start: 0.6754 (t80) cc_final: 0.6405 (t80) REVERT: B 1285 MET cc_start: 0.1167 (ttt) cc_final: 0.0832 (mtm) outliers start: 34 outliers final: 25 residues processed: 176 average time/residue: 0.0949 time to fit residues: 24.3197 Evaluate side-chains 162 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 24 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN C 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.151095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110473 restraints weight = 22740.107| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.50 r_work: 0.3536 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 10970 Z= 0.131 Angle : 0.626 13.198 14876 Z= 0.315 Chirality : 0.042 0.203 1641 Planarity : 0.004 0.051 1949 Dihedral : 4.965 51.901 1472 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.39 % Allowed : 15.78 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.23), residues: 1348 helix: 0.80 (0.23), residues: 543 sheet: 0.20 (0.38), residues: 214 loop : -0.24 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 869 TYR 0.022 0.001 TYR B1078 PHE 0.021 0.001 PHE B1276 TRP 0.026 0.002 TRP A 709 HIS 0.006 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10970) covalent geometry : angle 0.62635 / 0.31 (14876) hydrogen bonds : bond 0.03626 / 2.48 ( 484) hydrogen bonds : angle 4.94496 / 3.51 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.418 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: A 408 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6806 (mm-30) REVERT: A 410 MET cc_start: 0.8974 (mmm) cc_final: 0.8551 (mmm) REVERT: A 639 ASN cc_start: 0.6856 (p0) cc_final: 0.6518 (t0) REVERT: A 646 GLN cc_start: 0.8817 (tp40) cc_final: 0.8354 (tp-100) REVERT: A 649 ARG cc_start: 0.8882 (tpm170) cc_final: 0.8527 (tpt90) REVERT: A 652 PHE cc_start: 0.9017 (t80) cc_final: 0.8604 (m-80) REVERT: A 656 PHE cc_start: 0.8884 (m-80) cc_final: 0.8142 (m-80) REVERT: A 844 MET cc_start: 0.8938 (tpp) cc_final: 0.8528 (tpp) REVERT: A 987 ILE cc_start: 0.8910 (mm) cc_final: 0.8671 (mm) REVERT: A 1040 CYS cc_start: 0.7826 (m) cc_final: 0.7583 (m) REVERT: B 1012 TYR cc_start: 0.6725 (t80) cc_final: 0.6320 (t80) REVERT: B 1071 LEU cc_start: 0.8483 (mt) cc_final: 0.8226 (pp) REVERT: B 1285 MET cc_start: 0.1174 (ttt) cc_final: 0.0919 (mtm) outliers start: 28 outliers final: 26 residues processed: 170 average time/residue: 0.0798 time to fit residues: 20.0850 Evaluate side-chains 162 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 18 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 ASN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.148466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104888 restraints weight = 22971.569| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.29 r_work: 0.3493 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10970 Z= 0.191 Angle : 0.646 12.530 14876 Z= 0.328 Chirality : 0.043 0.169 1641 Planarity : 0.004 0.051 1949 Dihedral : 5.126 53.642 1472 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.56 % Allowed : 16.64 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1348 helix: 0.79 (0.23), residues: 539 sheet: 0.16 (0.38), residues: 214 loop : -0.32 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 981 TYR 0.046 0.002 TYR B1079 PHE 0.019 0.002 PHE B1276 TRP 0.028 0.002 TRP A 709 HIS 0.004 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (10970) covalent geometry : angle 0.64587 / 0.33 (14876) hydrogen bonds : bond 0.03945 / 2.67 ( 484) hydrogen bonds : angle 5.08305 / 3.60 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.265 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: A 408 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6744 (mm-30) REVERT: A 410 MET cc_start: 0.8999 (mmm) cc_final: 0.8598 (mmm) REVERT: A 646 GLN cc_start: 0.8872 (tp40) cc_final: 0.8415 (tp-100) REVERT: A 649 ARG cc_start: 0.8920 (tpm170) cc_final: 0.8558 (tpt90) REVERT: A 652 PHE cc_start: 0.9058 (t80) cc_final: 0.8665 (m-80) REVERT: A 656 PHE cc_start: 0.8920 (m-80) cc_final: 0.7929 (m-80) REVERT: A 844 MET cc_start: 0.8942 (tpp) cc_final: 0.8557 (tpp) REVERT: A 987 ILE cc_start: 0.8953 (mm) cc_final: 0.8684 (mm) REVERT: A 1040 CYS cc_start: 0.7893 (m) cc_final: 0.7627 (m) REVERT: B 953 LYS cc_start: 0.9492 (mttt) cc_final: 0.9038 (mmtt) REVERT: B 990 LYS cc_start: 0.8448 (mttt) cc_final: 0.8127 (tppt) REVERT: B 1012 TYR cc_start: 0.6661 (t80) cc_final: 0.6211 (t80) REVERT: B 1071 LEU cc_start: 0.8605 (mt) cc_final: 0.8324 (pp) REVERT: B 1285 MET cc_start: 0.1350 (ttt) cc_final: 0.0975 (mtm) outliers start: 30 outliers final: 24 residues processed: 166 average time/residue: 0.0817 time to fit residues: 19.8286 Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 122 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 107 optimal weight: 0.0030 chunk 59 optimal weight: 0.4980 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.150736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.107461 restraints weight = 22597.455| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.31 r_work: 0.3546 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 10970 Z= 0.121 Angle : 0.629 12.705 14876 Z= 0.314 Chirality : 0.042 0.228 1641 Planarity : 0.004 0.047 1949 Dihedral : 5.003 51.558 1472 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.71 % Allowed : 18.09 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1348 helix: 0.92 (0.23), residues: 534 sheet: 0.15 (0.37), residues: 214 loop : -0.32 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1058 TYR 0.023 0.001 TYR B1078 PHE 0.015 0.001 PHE B1276 TRP 0.041 0.002 TRP B1145 HIS 0.003 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10970) covalent geometry : angle 0.62877 / 0.31 (14876) hydrogen bonds : bond 0.03576 / 2.43 ( 484) hydrogen bonds : angle 4.94089 / 3.51 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.419 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: A 408 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 410 MET cc_start: 0.8959 (mmm) cc_final: 0.8561 (mmm) REVERT: A 646 GLN cc_start: 0.8863 (tp40) cc_final: 0.8404 (tp-100) REVERT: A 649 ARG cc_start: 0.8892 (tpm170) cc_final: 0.8569 (tpt90) REVERT: A 652 PHE cc_start: 0.9017 (t80) cc_final: 0.8669 (m-80) REVERT: A 656 PHE cc_start: 0.8847 (m-80) cc_final: 0.7870 (m-80) REVERT: A 844 MET cc_start: 0.8997 (tpp) cc_final: 0.8591 (tpp) REVERT: A 987 ILE cc_start: 0.8951 (mm) cc_final: 0.8689 (mm) REVERT: A 1015 MET cc_start: 0.7890 (mtt) cc_final: 0.7655 (mtt) REVERT: A 1040 CYS cc_start: 0.7847 (m) cc_final: 0.7549 (m) REVERT: B 953 LYS cc_start: 0.9500 (mttt) cc_final: 0.9059 (mmtt) REVERT: B 990 LYS cc_start: 0.8380 (mttt) cc_final: 0.8074 (tppt) REVERT: B 1012 TYR cc_start: 0.6655 (t80) cc_final: 0.6201 (t80) REVERT: B 1071 LEU cc_start: 0.8623 (mt) cc_final: 0.8400 (pp) REVERT: B 1100 TYR cc_start: 0.8930 (m-10) cc_final: 0.8719 (m-80) outliers start: 20 outliers final: 18 residues processed: 163 average time/residue: 0.0936 time to fit residues: 22.2456 Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 0.0000 chunk 67 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN A 698 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.150694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.110696 restraints weight = 22663.447| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.89 r_work: 0.3523 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 10970 Z= 0.138 Angle : 0.649 12.056 14876 Z= 0.322 Chirality : 0.043 0.203 1641 Planarity : 0.005 0.073 1949 Dihedral : 4.989 51.771 1472 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.88 % Allowed : 18.34 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1348 helix: 0.88 (0.23), residues: 535 sheet: 0.25 (0.37), residues: 211 loop : -0.33 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1058 TYR 0.052 0.001 TYR B1079 PHE 0.015 0.001 PHE A 857 TRP 0.046 0.003 TRP B1145 HIS 0.004 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10970) covalent geometry : angle 0.64941 / 0.32 (14876) hydrogen bonds : bond 0.03626 / 2.44 ( 484) hydrogen bonds : angle 4.91994 / 3.47 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.320 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: A 408 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6777 (mm-30) REVERT: A 410 MET cc_start: 0.8950 (mmm) cc_final: 0.8556 (mmm) REVERT: A 508 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7833 (pt) REVERT: A 523 ASP cc_start: 0.7125 (m-30) cc_final: 0.6356 (t0) REVERT: A 646 GLN cc_start: 0.8966 (tp40) cc_final: 0.8550 (tp-100) REVERT: A 649 ARG cc_start: 0.8925 (tpm170) cc_final: 0.8502 (tpt90) REVERT: A 652 PHE cc_start: 0.9012 (t80) cc_final: 0.8675 (m-80) REVERT: A 656 PHE cc_start: 0.8842 (m-80) cc_final: 0.7881 (m-80) REVERT: A 766 MET cc_start: 0.9003 (ptt) cc_final: 0.8634 (tpp) REVERT: A 844 MET cc_start: 0.8979 (tpp) cc_final: 0.8594 (tpp) REVERT: A 987 ILE cc_start: 0.8964 (mm) cc_final: 0.8710 (mm) REVERT: A 1040 CYS cc_start: 0.7946 (m) cc_final: 0.7666 (m) REVERT: B 953 LYS cc_start: 0.9512 (mttt) cc_final: 0.9032 (mmtt) REVERT: B 964 LEU cc_start: 0.9373 (mm) cc_final: 0.9144 (mm) REVERT: B 990 LYS cc_start: 0.8342 (mttt) cc_final: 0.8047 (tppt) REVERT: B 1012 TYR cc_start: 0.6729 (t80) cc_final: 0.6256 (t80) REVERT: B 1063 GLN cc_start: 0.8329 (mp10) cc_final: 0.8084 (mp10) REVERT: B 1071 LEU cc_start: 0.8646 (mt) cc_final: 0.8418 (pp) outliers start: 22 outliers final: 20 residues processed: 156 average time/residue: 0.0822 time to fit residues: 18.9198 Evaluate side-chains 156 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 10 optimal weight: 0.0570 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 0.0050 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 99 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.5532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.151639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110733 restraints weight = 22614.597| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.52 r_work: 0.3547 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 10970 Z= 0.125 Angle : 0.649 12.431 14876 Z= 0.324 Chirality : 0.043 0.184 1641 Planarity : 0.005 0.080 1949 Dihedral : 4.968 51.454 1472 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.62 % Allowed : 18.69 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.23), residues: 1348 helix: 0.91 (0.23), residues: 536 sheet: 0.31 (0.37), residues: 211 loop : -0.32 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1029 TYR 0.025 0.001 TYR B1078 PHE 0.014 0.001 PHE A 857 TRP 0.066 0.003 TRP A 709 HIS 0.004 0.001 HIS B1130 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (10970) covalent geometry : angle 0.64945 / 0.32 (14876) hydrogen bonds : bond 0.03523 / 2.36 ( 484) hydrogen bonds : angle 4.89418 / 3.45 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.278 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: A 408 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6713 (mm-30) REVERT: A 410 MET cc_start: 0.8974 (mmm) cc_final: 0.8574 (mmm) REVERT: A 523 ASP cc_start: 0.7050 (m-30) cc_final: 0.6451 (t0) REVERT: A 646 GLN cc_start: 0.8959 (tp40) cc_final: 0.8534 (tp-100) REVERT: A 649 ARG cc_start: 0.8911 (tpm170) cc_final: 0.8470 (tpt90) REVERT: A 652 PHE cc_start: 0.8971 (t80) cc_final: 0.8651 (m-80) REVERT: A 656 PHE cc_start: 0.8837 (m-80) cc_final: 0.7894 (m-80) REVERT: A 766 MET cc_start: 0.9004 (ptt) cc_final: 0.8646 (tpp) REVERT: A 844 MET cc_start: 0.9002 (tpp) cc_final: 0.8606 (tpp) REVERT: A 987 ILE cc_start: 0.8960 (mm) cc_final: 0.8700 (mm) REVERT: A 1040 CYS cc_start: 0.7892 (m) cc_final: 0.7591 (m) REVERT: B 953 LYS cc_start: 0.9508 (mttt) cc_final: 0.9024 (mmtt) REVERT: B 964 LEU cc_start: 0.9381 (mm) cc_final: 0.9146 (mm) REVERT: B 1012 TYR cc_start: 0.6826 (t80) cc_final: 0.6361 (t80) REVERT: B 1063 GLN cc_start: 0.8420 (mp10) cc_final: 0.8167 (mp10) REVERT: B 1071 LEU cc_start: 0.8694 (mt) cc_final: 0.8449 (pp) outliers start: 19 outliers final: 19 residues processed: 155 average time/residue: 0.0864 time to fit residues: 19.8210 Evaluate side-chains 160 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 748 CYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1003 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 ASN ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.149435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105979 restraints weight = 22666.603| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.26 r_work: 0.3528 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 10970 Z= 0.173 Angle : 0.669 12.027 14876 Z= 0.334 Chirality : 0.044 0.226 1641 Planarity : 0.005 0.063 1949 Dihedral : 5.041 52.497 1472 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.71 % Allowed : 18.52 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1348 helix: 0.80 (0.23), residues: 539 sheet: 0.28 (0.37), residues: 211 loop : -0.38 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1029 TYR 0.051 0.002 TYR B1079 PHE 0.017 0.001 PHE B1276 TRP 0.059 0.003 TRP A 709 HIS 0.004 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (10970) covalent geometry : angle 0.66911 / 0.33 (14876) hydrogen bonds : bond 0.03753 / 2.51 ( 484) hydrogen bonds : angle 4.98701 / 3.51 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.12 seconds wall clock time: 45 minutes 4.09 seconds (2704.09 seconds total)