Starting phenix.real_space_refine on Wed Aug 5 17:05:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc6_63790/08_2026/9mc6_63790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc6_63790/08_2026/9mc6_63790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mc6_63790/08_2026/9mc6_63790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc6_63790/08_2026/9mc6_63790.map" model { file = "/net/cci-nas-00/data/ceres_data/9mc6_63790/08_2026/9mc6_63790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc6_63790/08_2026/9mc6_63790_neut.cif" } resolution = 3.32 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= 0.000 sd= 0.010 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 50 5.16 5 C 6632 2.51 5 N 1785 2.21 5 O 1959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 10427 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7712 Classifications: {'peptide': 980} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 928} Chain breaks: 1 Chain: "B" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2090 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 17, 'TRANS': 242} Chain breaks: 1 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: 1.76, per 1000 atoms: 0.17 Number of scatterers: 10427 At special positions: 0 Unit cell: (93.96, 106.272, 127.008, 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 50 16.00 P 1 15.00 O 1959 8.00 N 1785 7.00 C 6632 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: 0.66 Conformation dependent library (CDL) restraints added in 228.3 milliseconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 44.4% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 108 through 114 removed outlier: 3.802A pdb=" N SER A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 4.077A pdb=" N ILE A 123 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 Proline residue: A 133 - end of helix removed outlier: 3.900A pdb=" N GLU A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.842A pdb=" N GLY A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.723A pdb=" N PHE A 323 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 344 removed outlier: 3.825A pdb=" N GLN A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.567A pdb=" N VAL A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N SER A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N ASP A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.822A pdb=" N LEU A 513 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.553A pdb=" N GLU A 557 " --> pdb=" O PRO A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 577 through 592 removed outlier: 4.098A pdb=" N ARG A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 640 through 669 removed outlier: 4.265A pdb=" N PHE A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Proline residue: A 659 - end of helix removed outlier: 3.591A pdb=" N ASP A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.712A pdb=" N ARG A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 702 through 718 removed outlier: 3.606A pdb=" N TYR A 718 " --> pdb=" O TRP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 758 through 776 removed outlier: 3.663A pdb=" N LEU A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.917A pdb=" N VAL A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 833 Processing helix chain 'A' and resid 857 through 870 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 894 through 914 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 4.024A pdb=" N ASP A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1024 Processing helix chain 'B' and resid 950 through 969 removed outlier: 3.719A pdb=" N LEU B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1060 through 1074 removed outlier: 3.901A pdb=" N ILE B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1081 Processing helix chain 'B' and resid 1084 through 1088 Processing helix chain 'B' and resid 1090 through 1118 Processing helix chain 'B' and resid 1123 through 1152 removed outlier: 4.432A pdb=" N THR B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B1136 " --> pdb=" O SER B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1263 through 1283 removed outlier: 3.591A pdb=" N LYS B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 removed outlier: 6.524A pdb=" N VAL A 75 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS A 102 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 77 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER A 74 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 163 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 76 " --> pdb=" O VAL A 163 " (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 218 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.678A pdb=" N MET A 223 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.284A pdb=" N ILE A 500 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS A 548 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 502 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR A 471 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR A 503 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 473 " --> pdb=" O THR A 503 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS A 470 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA A 572 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE A 472 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 571 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N SER A 598 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 573 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR A 600 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 945 through 947 Processing sheet with id=AA8, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.781A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A1035 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN A 992 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A1037 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 990 " --> pdb=" O GLU A1037 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS A1039 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR A 988 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A 999 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 990 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.781A pdb=" N PHE A 958 " --> pdb=" O ARG A1054 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR A1056 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 960 " --> pdb=" O THR A1056 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS A1040 " --> pdb=" O VAL A1048 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 929 through 932 removed outlier: 3.862A pdb=" N PHE B 978 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU B 984 " --> pdb=" O PHE B 978 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 16 removed outlier: 4.286A pdb=" N SER C 65 " --> pdb=" O GLN C 2 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1353 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: 1.38 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3316 1.34 - 1.46: 1986 1.46 - 1.58: 5279 1.58 - 1.70: 1 1.70 - 1.83: 78 Bond restraints: 10660 Sorted by residual: bond pdb=" N LEU A 259 " pdb=" CA LEU A 259 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.40e+01 bond pdb=" C VAL B1015 " pdb=" N PRO B1016 " ideal model delta sigma weight residual 1.331 1.364 -0.032 8.70e-03 1.32e+04 1.38e+01 bond pdb=" N ILE B1254 " pdb=" CA ILE B1254 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.22e-02 6.72e+03 1.10e+01 bond pdb=" N VAL B1041 " pdb=" CA VAL B1041 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ASP B 999 " pdb=" CA ASP B 999 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.87e+00 ... (remaining 10655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13331 1.91 - 3.81: 956 3.81 - 5.72: 144 5.72 - 7.63: 21 7.63 - 9.53: 3 Bond angle restraints: 14455 Sorted by residual: angle pdb=" CB HIS A 240 " pdb=" CG HIS A 240 " pdb=" CD2 HIS A 240 " ideal model delta sigma weight residual 131.20 126.00 5.20 1.30e+00 5.92e-01 1.60e+01 angle pdb=" OE1 GLN A 108 " pdb=" CD GLN A 108 " pdb=" NE2 GLN A 108 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" CA ASN B1101 " pdb=" CB ASN B1101 " pdb=" CG ASN B1101 " ideal model delta sigma weight residual 112.60 108.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" OE1 GLN A 294 " pdb=" CD GLN A 294 " pdb=" NE2 GLN A 294 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" C PHE B1256 " pdb=" N PRO B1257 " pdb=" CA PRO B1257 " ideal model delta sigma weight residual 119.87 123.96 -4.09 1.04e+00 9.25e-01 1.54e+01 ... (remaining 14450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5823 17.98 - 35.95: 457 35.95 - 53.93: 102 53.93 - 71.91: 24 71.91 - 89.88: 15 Dihedral angle restraints: 6421 sinusoidal: 2613 harmonic: 3808 Sorted by residual: dihedral pdb=" CA HIS A 240 " pdb=" C HIS A 240 " pdb=" N GLY A 241 " pdb=" CA GLY A 241 " ideal model delta harmonic sigma weight residual 180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL A 257 " pdb=" C VAL A 257 " pdb=" N GLU A 258 " pdb=" CA GLU A 258 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B1256 " pdb=" C PHE B1256 " pdb=" N PRO B1257 " pdb=" CA PRO B1257 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 6418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1242 0.062 - 0.124: 276 0.124 - 0.186: 61 0.186 - 0.248: 13 0.248 - 0.310: 5 Chirality restraints: 1597 Sorted by residual: 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 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB VAL A 902 " pdb=" CA VAL A 902 " pdb=" CG1 VAL A 902 " pdb=" CG2 VAL A 902 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA HIS A 881 " pdb=" N HIS A 881 " pdb=" C HIS A 881 " pdb=" CB HIS A 881 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1594 not shown) Planarity restraints: 1892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1021 " 0.064 2.00e-02 2.50e+03 4.65e-02 4.32e+01 pdb=" CG TYR B1021 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B1021 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR B1021 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B1021 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B1021 " -0.058 2.00e-02 2.50e+03 pdb=" CZ TYR B1021 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B1021 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 910 " -0.076 2.00e-02 2.50e+03 3.94e-02 3.10e+01 pdb=" CG TYR A 910 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 910 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 910 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 910 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 910 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 910 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 910 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1131 " 0.035 2.00e-02 2.50e+03 3.86e-02 2.61e+01 pdb=" CG PHE B1131 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B1131 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE B1131 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE B1131 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 PHE B1131 " -0.027 2.00e-02 2.50e+03 pdb=" CZ PHE B1131 " 0.004 2.00e-02 2.50e+03 ... (remaining 1889 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 3527 2.87 - 3.38: 10074 3.38 - 3.88: 17306 3.88 - 4.39: 20095 4.39 - 4.90: 33798 Nonbonded interactions: 84800 Sorted by model distance: nonbonded pdb=" O ASN A 377 " pdb=" OD1 ASN A 377 " model vdw 2.359 3.040 nonbonded pdb=" N GLU A 214 " pdb=" OE1 GLU A 214 " model vdw 2.471 3.120 nonbonded pdb=" O GLY B1271 " pdb=" OE1 GLN B1275 " model vdw 2.480 3.040 nonbonded pdb=" N GLN B 947 " pdb=" OE1 GLN B 947 " model vdw 2.500 3.120 nonbonded pdb=" N GLU B1121 " pdb=" OE1 GLU B1121 " model vdw 2.510 3.120 ... (remaining 84795 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 : 0.007 0.048 10660 Z= 0.380 Angle : 1.043 9.534 14455 Z= 0.644 Chirality : 0.059 0.310 1597 Planarity : 0.009 0.148 1892 Dihedral : 14.755 89.882 3963 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.26 % Allowed : 10.46 % Favored : 89.28 % 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: -0.18 (0.22), residues: 1306 helix: 0.33 (0.22), residues: 526 sheet: 0.05 (0.37), residues: 182 loop : -0.46 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 81 TYR 0.083 0.006 TYR B1021 PHE 0.055 0.005 PHE B1131 TRP 0.055 0.006 TRP B1047 HIS 0.012 0.002 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.38 (10660) covalent geometry : angle 1.04280 / 0.64 (14455) hydrogen bonds : bond 0.14182 / 9.43 ( 479) hydrogen bonds : angle 6.76816 / 4.65 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ARG cc_start: 0.7815 (ptp90) cc_final: 0.7277 (ptp90) REVERT: A 766 MET cc_start: 0.7589 (tpt) cc_final: 0.7352 (tmm) REVERT: B 974 MET cc_start: 0.6653 (mtp) cc_final: 0.6396 (mtp) REVERT: B 990 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8275 (mmmm) REVERT: B 997 TYR cc_start: 0.7482 (m-10) cc_final: 0.7234 (m-10) REVERT: B 1145 TRP cc_start: 0.8344 (m-10) cc_final: 0.8045 (m-10) REVERT: B 1285 MET cc_start: 0.4964 (mtm) cc_final: 0.4503 (ttm) REVERT: C 34 GLU cc_start: 0.7956 (tt0) cc_final: 0.7737 (tt0) REVERT: C 60 ASN cc_start: 0.8889 (t0) cc_final: 0.8294 (t0) outliers start: 3 outliers final: 2 residues processed: 145 average time/residue: 0.1113 time to fit residues: 22.0377 Evaluate side-chains 127 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 618 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 949 ASN ** B1275 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 = 0.4624 r_free = 0.4624 target = 0.210552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.152368 restraints weight = 13417.419| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.81 r_work: 0.3665 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10660 Z= 0.121 Angle : 0.628 7.837 14455 Z= 0.322 Chirality : 0.042 0.190 1597 Planarity : 0.005 0.044 1892 Dihedral : 5.626 59.418 1431 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 1.32 % Allowed : 9.84 % Favored : 88.84 % 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: 0.41 (0.23), residues: 1306 helix: 1.05 (0.22), residues: 531 sheet: 0.13 (0.36), residues: 194 loop : -0.30 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 515 TYR 0.013 0.001 TYR A 910 PHE 0.021 0.001 PHE B1256 TRP 0.017 0.002 TRP A 647 HIS 0.007 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (10660) covalent geometry : angle 0.62817 / 0.32 (14455) hydrogen bonds : bond 0.04486 / 3.04 ( 479) hydrogen bonds : angle 5.02932 / 3.47 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7861 (p0) cc_final: 0.7535 (p0) REVERT: A 1027 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 955 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: B 974 MET cc_start: 0.6778 (mtp) cc_final: 0.6516 (mtp) REVERT: B 990 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8333 (mmtm) REVERT: B 1103 MET cc_start: 0.8520 (pmm) cc_final: 0.8265 (pmm) REVERT: B 1114 GLN cc_start: 0.8074 (tt0) cc_final: 0.7791 (tt0) REVERT: C 60 ASN cc_start: 0.8782 (t0) cc_final: 0.8184 (t0) outliers start: 15 outliers final: 7 residues processed: 135 average time/residue: 0.0887 time to fit residues: 17.0676 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 1015 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.208855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4026 r_free = 0.4026 target = 0.149108 restraints weight = 13394.192| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.79 r_work: 0.3657 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10660 Z= 0.143 Angle : 0.603 7.928 14455 Z= 0.306 Chirality : 0.042 0.162 1597 Planarity : 0.004 0.047 1892 Dihedral : 5.426 59.459 1430 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.85 % Allowed : 10.63 % Favored : 87.52 % 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: 0.57 (0.23), residues: 1306 helix: 1.28 (0.22), residues: 531 sheet: 0.13 (0.36), residues: 196 loop : -0.30 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 81 TYR 0.013 0.001 TYR A 910 PHE 0.015 0.001 PHE B1256 TRP 0.013 0.002 TRP A 709 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10660) covalent geometry : angle 0.60344 / 0.31 (14455) hydrogen bonds : bond 0.04124 / 2.81 ( 479) hydrogen bonds : angle 4.70758 / 3.26 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.6960 (mtt-85) REVERT: A 314 ASP cc_start: 0.7866 (p0) cc_final: 0.7542 (p0) REVERT: A 557 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7953 (tp30) REVERT: A 1027 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 955 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6568 (m-80) REVERT: B 974 MET cc_start: 0.6681 (mtp) cc_final: 0.6415 (mtp) REVERT: B 990 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8264 (mmtp) REVERT: B 1055 TRP cc_start: 0.7852 (t-100) cc_final: 0.7601 (t-100) REVERT: B 1114 GLN cc_start: 0.8141 (tt0) cc_final: 0.7772 (tt0) REVERT: C 60 ASN cc_start: 0.8758 (t0) cc_final: 0.8138 (t0) outliers start: 21 outliers final: 11 residues processed: 143 average time/residue: 0.0917 time to fit residues: 18.6509 Evaluate side-chains 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 70 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN A 949 ASN ** C 41 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 = 0.4660 r_free = 0.4660 target = 0.212276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.158172 restraints weight = 13512.447| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.79 r_work: 0.3735 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10660 Z= 0.126 Angle : 0.600 14.492 14455 Z= 0.299 Chirality : 0.042 0.149 1597 Planarity : 0.004 0.047 1892 Dihedral : 5.309 59.564 1430 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.67 % Allowed : 11.78 % Favored : 86.56 % 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: 0.64 (0.23), residues: 1306 helix: 1.37 (0.23), residues: 532 sheet: 0.14 (0.37), residues: 193 loop : -0.28 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1025 TYR 0.012 0.001 TYR A 910 PHE 0.014 0.001 PHE B1256 TRP 0.016 0.001 TRP A 647 HIS 0.007 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10660) covalent geometry : angle 0.60012 / 0.30 (14455) hydrogen bonds : bond 0.03889 / 2.61 ( 479) hydrogen bonds : angle 4.54769 / 3.13 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.249 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 314 ASP cc_start: 0.7837 (p0) cc_final: 0.7533 (p0) REVERT: A 557 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8104 (tp30) REVERT: A 977 ASP cc_start: 0.8466 (m-30) cc_final: 0.8255 (t0) REVERT: A 1027 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8402 (mp) REVERT: B 974 MET cc_start: 0.6946 (mtp) cc_final: 0.6737 (mtp) REVERT: B 1114 GLN cc_start: 0.8003 (tt0) cc_final: 0.7650 (tt0) REVERT: C 60 ASN cc_start: 0.8845 (t0) cc_final: 0.8234 (t0) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.0811 time to fit residues: 15.6725 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1261 LEU Chi-restraints excluded: chain B residue 1275 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 22 optimal weight: 0.0570 chunk 109 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 39 optimal weight: 0.4980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 ASN A 398 ASN A 949 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.212910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.158635 restraints weight = 13358.647| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.74 r_work: 0.3756 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10660 Z= 0.112 Angle : 0.579 12.154 14455 Z= 0.287 Chirality : 0.041 0.138 1597 Planarity : 0.004 0.048 1892 Dihedral : 5.220 59.967 1430 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.67 % Allowed : 12.21 % Favored : 86.12 % 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: 0.73 (0.23), residues: 1306 helix: 1.47 (0.22), residues: 532 sheet: 0.24 (0.38), residues: 190 loop : -0.29 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1025 TYR 0.011 0.001 TYR A 910 PHE 0.022 0.001 PHE B1256 TRP 0.017 0.001 TRP B1055 HIS 0.007 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10660) covalent geometry : angle 0.57912 / 0.29 (14455) hydrogen bonds : bond 0.03681 / 2.48 ( 479) hydrogen bonds : angle 4.41363 / 3.04 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7765 (p0) cc_final: 0.7511 (p0) REVERT: A 368 ARG cc_start: 0.7318 (mtm110) cc_final: 0.7029 (ttm170) REVERT: A 557 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8050 (tp30) REVERT: A 977 ASP cc_start: 0.8425 (m-30) cc_final: 0.8221 (t0) REVERT: A 1027 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8355 (mp) REVERT: B 990 LYS cc_start: 0.8895 (mmtp) cc_final: 0.8658 (mmmt) REVERT: B 1103 MET cc_start: 0.8367 (pmm) cc_final: 0.8040 (pmm) REVERT: B 1114 GLN cc_start: 0.7988 (tt0) cc_final: 0.7581 (tt0) REVERT: C 60 ASN cc_start: 0.8796 (t0) cc_final: 0.8183 (t0) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.0878 time to fit residues: 15.9996 Evaluate side-chains 130 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 916 HIS A 949 ASN ** B1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 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 = 0.4639 r_free = 0.4639 target = 0.210280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154204 restraints weight = 13485.130| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.84 r_work: 0.3683 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10660 Z= 0.172 Angle : 0.619 10.991 14455 Z= 0.308 Chirality : 0.043 0.213 1597 Planarity : 0.004 0.050 1892 Dihedral : 5.311 59.738 1430 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.93 % Allowed : 12.65 % Favored : 85.41 % 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: 0.66 (0.23), residues: 1306 helix: 1.40 (0.23), residues: 533 sheet: 0.23 (0.39), residues: 185 loop : -0.31 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1025 TYR 0.011 0.001 TYR A 117 PHE 0.017 0.002 PHE B1256 TRP 0.014 0.002 TRP B1136 HIS 0.009 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (10660) covalent geometry : angle 0.61927 / 0.31 (14455) hydrogen bonds : bond 0.03967 / 2.77 ( 479) hydrogen bonds : angle 4.51513 / 3.12 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7985 (p0) cc_final: 0.7691 (p0) REVERT: A 368 ARG cc_start: 0.7417 (mtm110) cc_final: 0.7080 (ttm170) REVERT: A 557 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7935 (mm-30) REVERT: A 1027 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 990 LYS cc_start: 0.8876 (mmtp) cc_final: 0.8637 (mmmt) REVERT: B 1100 TYR cc_start: 0.8316 (t80) cc_final: 0.8096 (t80) REVERT: B 1103 MET cc_start: 0.8425 (pmm) cc_final: 0.8156 (pmm) REVERT: B 1114 GLN cc_start: 0.8091 (tt0) cc_final: 0.7698 (tt0) REVERT: C 60 ASN cc_start: 0.8877 (t0) cc_final: 0.8265 (t0) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.0891 time to fit residues: 17.3738 Evaluate side-chains 133 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 1071 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 GLN A 949 ASN ** B1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.205107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147596 restraints weight = 13365.720| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.65 r_work: 0.3618 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10660 Z= 0.240 Angle : 0.667 11.139 14455 Z= 0.334 Chirality : 0.045 0.194 1597 Planarity : 0.005 0.050 1892 Dihedral : 5.516 58.581 1430 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.76 % Allowed : 13.88 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.37 (0.23), residues: 1306 helix: 1.20 (0.23), residues: 538 sheet: -0.18 (0.39), residues: 189 loop : -0.43 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1025 TYR 0.014 0.002 TYR A 117 PHE 0.019 0.002 PHE A 116 TRP 0.012 0.002 TRP A 952 HIS 0.011 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 (10660) covalent geometry : angle 0.66656 / 0.33 (14455) hydrogen bonds : bond 0.04194 / 2.89 ( 479) hydrogen bonds : angle 4.67993 / 3.25 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7908 (mm-30) REVERT: A 1027 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8375 (mp) REVERT: B 1103 MET cc_start: 0.8266 (pmm) cc_final: 0.8062 (pmm) REVERT: B 1114 GLN cc_start: 0.8156 (tt0) cc_final: 0.7903 (tt0) REVERT: C 60 ASN cc_start: 0.8824 (t0) cc_final: 0.8225 (t0) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.0820 time to fit residues: 15.5449 Evaluate side-chains 133 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1129 GLN Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 GLN A 949 ASN ** B1275 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 = 0.4640 r_free = 0.4640 target = 0.210640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.155870 restraints weight = 13375.218| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.80 r_work: 0.3692 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10660 Z= 0.140 Angle : 0.612 11.553 14455 Z= 0.303 Chirality : 0.042 0.183 1597 Planarity : 0.004 0.049 1892 Dihedral : 5.325 58.622 1430 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.49 % Allowed : 14.50 % Favored : 84.01 % 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: 0.50 (0.23), residues: 1306 helix: 1.32 (0.23), residues: 527 sheet: -0.14 (0.39), residues: 187 loop : -0.34 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 587 TYR 0.009 0.001 TYR A 117 PHE 0.018 0.001 PHE B1259 TRP 0.012 0.001 TRP A 647 HIS 0.009 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10660) covalent geometry : angle 0.61174 / 0.30 (14455) hydrogen bonds : bond 0.03721 / 2.54 ( 479) hydrogen bonds : angle 4.47197 / 3.11 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.484 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 557 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7943 (mm-30) REVERT: A 844 MET cc_start: -0.0732 (tpt) cc_final: -0.1243 (tpt) REVERT: A 1027 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 961 GLU cc_start: 0.6730 (mm-30) cc_final: 0.5655 (mm-30) REVERT: B 1114 GLN cc_start: 0.8122 (tt0) cc_final: 0.7876 (tt0) REVERT: C 60 ASN cc_start: 0.8919 (t0) cc_final: 0.8357 (t0) outliers start: 17 outliers final: 14 residues processed: 126 average time/residue: 0.1011 time to fit residues: 18.3459 Evaluate side-chains 131 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 99 optimal weight: 0.4980 chunk 13 optimal weight: 0.0040 chunk 88 optimal weight: 0.4980 chunk 110 optimal weight: 0.0070 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 ASN ** B1275 GLN ** 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 = 0.4660 r_free = 0.4660 target = 0.212571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.159115 restraints weight = 13336.065| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.79 r_work: 0.3734 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10660 Z= 0.109 Angle : 0.587 11.044 14455 Z= 0.290 Chirality : 0.041 0.186 1597 Planarity : 0.004 0.049 1892 Dihedral : 5.172 59.972 1430 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.32 % Allowed : 14.85 % Favored : 83.83 % 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: 0.64 (0.23), residues: 1306 helix: 1.48 (0.23), residues: 525 sheet: -0.00 (0.39), residues: 187 loop : -0.31 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 368 TYR 0.012 0.001 TYR B1251 PHE 0.022 0.001 PHE B1259 TRP 0.011 0.001 TRP A 714 HIS 0.009 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10660) covalent geometry : angle 0.58720 / 0.29 (14455) hydrogen bonds : bond 0.03472 / 2.37 ( 479) hydrogen bonds : angle 4.29042 / 2.98 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.292 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 273 TYR cc_start: 0.8226 (m-80) cc_final: 0.7966 (m-80) REVERT: A 557 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8106 (tp30) REVERT: A 1027 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8240 (mp) REVERT: B 961 GLU cc_start: 0.6586 (mm-30) cc_final: 0.5441 (mm-30) REVERT: C 60 ASN cc_start: 0.8914 (t0) cc_final: 0.8353 (t0) outliers start: 15 outliers final: 12 residues processed: 129 average time/residue: 0.1016 time to fit residues: 18.3621 Evaluate side-chains 130 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 0.0000 chunk 18 optimal weight: 0.2980 chunk 115 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 ASN ** B1275 GLN ** 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 = 0.4656 r_free = 0.4656 target = 0.212599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.159348 restraints weight = 13332.611| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.81 r_work: 0.3744 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10660 Z= 0.105 Angle : 0.591 11.265 14455 Z= 0.290 Chirality : 0.042 0.203 1597 Planarity : 0.004 0.049 1892 Dihedral : 5.110 59.230 1430 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.14 % Allowed : 15.29 % Favored : 83.57 % 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: 0.74 (0.24), residues: 1306 helix: 1.52 (0.23), residues: 531 sheet: -0.01 (0.38), residues: 194 loop : -0.21 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1025 TYR 0.010 0.001 TYR A 910 PHE 0.026 0.001 PHE B1265 TRP 0.016 0.001 TRP B1145 HIS 0.010 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10660) covalent geometry : angle 0.59073 / 0.29 (14455) hydrogen bonds : bond 0.03459 / 2.33 ( 479) hydrogen bonds : angle 4.18799 / 2.90 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.414 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 273 TYR cc_start: 0.8202 (m-80) cc_final: 0.7923 (m-80) REVERT: A 1027 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 961 GLU cc_start: 0.6526 (mm-30) cc_final: 0.5401 (mm-30) REVERT: B 1114 GLN cc_start: 0.8324 (tt0) cc_final: 0.7953 (pt0) REVERT: C 60 ASN cc_start: 0.8893 (t0) cc_final: 0.8335 (t0) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.0933 time to fit residues: 16.8586 Evaluate side-chains 125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain B residue 1256 PHE Chi-restraints excluded: chain B residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 0.0030 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 ASN ** B1275 GLN ** 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 = 0.4642 r_free = 0.4642 target = 0.211279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.156055 restraints weight = 13421.078| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.75 r_work: 0.3706 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10660 Z= 0.136 Angle : 0.614 11.154 14455 Z= 0.304 Chirality : 0.042 0.215 1597 Planarity : 0.004 0.051 1892 Dihedral : 5.122 59.071 1430 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.23 % Allowed : 15.03 % Favored : 83.74 % 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: 0.72 (0.24), residues: 1306 helix: 1.46 (0.23), residues: 532 sheet: 0.10 (0.40), residues: 180 loop : -0.22 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 587 TYR 0.009 0.001 TYR A 910 PHE 0.026 0.001 PHE B1265 TRP 0.038 0.002 TRP B1145 HIS 0.010 0.001 HIS A 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10660) covalent geometry : angle 0.61356 / 0.30 (14455) hydrogen bonds : bond 0.03602 / 2.50 ( 479) hydrogen bonds : angle 4.24509 / 2.93 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.47 seconds wall clock time: 48 minutes 36.71 seconds (2916.71 seconds total)