Starting phenix.real_space_refine on Sun Apr 5 13:29:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mc6_63790/04_2026/9mc6_63790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mc6_63790/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mc6_63790/04_2026/9mc6_63790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mc6_63790/04_2026/9mc6_63790_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mc6_63790/04_2026/9mc6_63790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mc6_63790/04_2026/9mc6_63790.map" } 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-2.1rc1-6017/lib/python3.9/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: 2.21, per 1000 atoms: 0.21 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: 0.87 Conformation dependent library (CDL) restraints added in 451.1 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: 0.33 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: 2.44 Time building geometry restraints manager: 1.19 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: 13323 1.91 - 3.81: 960 3.81 - 5.72: 146 5.72 - 7.63: 23 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: 5824 17.98 - 35.95: 456 35.95 - 53.93: 101 53.93 - 71.91: 25 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: 1240 0.062 - 0.124: 277 0.124 - 0.186: 62 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: 7.730 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 1.048 9.534 14455 Z= 0.644 Chirality : 0.059 0.310 1597 Planarity : 0.009 0.148 1892 Dihedral : 14.761 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 covalent geometry : bond 0.00654 (10660) covalent geometry : angle 1.04817 (14455) hydrogen bonds : bond 0.14182 ( 479) hydrogen bonds : angle 6.76816 ( 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 : 0.389 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: 0.1157 time to fit residues: 22.6992 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 : 0.374 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4627 r_free = 0.4627 target = 0.210674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4072 r_free = 0.4072 target = 0.152998 restraints weight = 13425.709| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.87 r_work: 0.3659 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10660 Z= 0.123 Angle : 0.628 7.684 14455 Z= 0.320 Chirality : 0.043 0.192 1597 Planarity : 0.005 0.043 1892 Dihedral : 5.511 59.629 1431 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.23 % Allowed : 9.84 % Favored : 88.93 % 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: 0.43 (0.23), residues: 1306 helix: 1.06 (0.22), residues: 531 sheet: 0.14 (0.36), residues: 194 loop : -0.29 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 450 TYR 0.014 0.001 TYR A 910 PHE 0.021 0.001 PHE B1256 TRP 0.018 0.002 TRP A 647 HIS 0.006 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00253 (10660) covalent geometry : angle 0.62817 (14455) hydrogen bonds : bond 0.04483 ( 479) hydrogen bonds : angle 4.97898 ( 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 135 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.343 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: 0.7882 (p0) cc_final: 0.7568 (p0) REVERT: A 1027 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 974 MET cc_start: 0.6793 (mtp) cc_final: 0.6538 (mtp) REVERT: B 990 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8316 (mmtm) REVERT: B 1103 MET cc_start: 0.8470 (pmm) cc_final: 0.8241 (pmm) REVERT: B 1114 GLN cc_start: 0.8056 (tt0) cc_final: 0.7766 (tt0) REVERT: C 60 ASN cc_start: 0.8776 (t0) cc_final: 0.8177 (t0) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.1050 time to fit residues: 19.3454 Evaluate side-chains 123 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 1015 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 27 optimal weight: 0.0170 chunk 1 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.209929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.155821 restraints weight = 13389.422| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.74 r_work: 0.3676 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10660 Z= 0.125 Angle : 0.592 8.256 14455 Z= 0.298 Chirality : 0.042 0.157 1597 Planarity : 0.004 0.047 1892 Dihedral : 5.238 59.622 1430 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.76 % Allowed : 10.90 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.23), residues: 1306 helix: 1.24 (0.22), residues: 539 sheet: 0.14 (0.36), residues: 194 loop : -0.34 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1141 TYR 0.013 0.001 TYR A 910 PHE 0.015 0.001 PHE B1256 TRP 0.015 0.001 TRP A 647 HIS 0.007 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00276 (10660) covalent geometry : angle 0.59175 (14455) hydrogen bonds : bond 0.04011 ( 479) hydrogen bonds : angle 4.66510 ( 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 149 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7835 (p0) cc_final: 0.7517 (p0) REVERT: A 557 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7952 (tp30) REVERT: A 1027 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 974 MET cc_start: 0.6806 (mtp) cc_final: 0.6561 (mtp) REVERT: B 990 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8343 (mmtp) REVERT: B 1055 TRP cc_start: 0.7844 (t-100) cc_final: 0.7591 (t-100) REVERT: B 1114 GLN cc_start: 0.8005 (tt0) cc_final: 0.7655 (tt0) REVERT: C 60 ASN cc_start: 0.8764 (t0) cc_final: 0.8143 (t0) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 0.0956 time to fit residues: 19.2344 Evaluate side-chains 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 1002 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 931 VAL Chi-restraints excluded: chain B residue 1015 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 70 optimal weight: 0.0870 chunk 87 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 ASN ** C 41 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 = 0.4673 r_free = 0.4673 target = 0.213393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.158913 restraints weight = 13516.435| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.83 r_work: 0.3751 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10660 Z= 0.117 Angle : 0.585 9.146 14455 Z= 0.294 Chirality : 0.042 0.148 1597 Planarity : 0.004 0.048 1892 Dihedral : 5.105 59.932 1430 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.11 % Allowed : 11.51 % Favored : 86.38 % 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: 1.31 (0.22), residues: 539 sheet: 0.23 (0.37), residues: 193 loop : -0.26 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1141 TYR 0.012 0.001 TYR A 910 PHE 0.015 0.001 PHE B1256 TRP 0.050 0.002 TRP B1145 HIS 0.007 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00256 (10660) covalent geometry : angle 0.58493 (14455) hydrogen bonds : bond 0.03873 ( 479) hydrogen bonds : angle 4.52956 ( 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 144 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.363 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: 0.7748 (p0) cc_final: 0.7465 (p0) REVERT: A 368 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6995 (ttm170) REVERT: A 557 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8044 (tp30) REVERT: A 977 ASP cc_start: 0.8397 (m-30) cc_final: 0.8190 (t0) REVERT: A 1027 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 974 MET cc_start: 0.6961 (mtp) cc_final: 0.6761 (mtp) REVERT: C 60 ASN cc_start: 0.8816 (t0) cc_final: 0.8189 (t0) outliers start: 24 outliers final: 15 residues processed: 138 average time/residue: 0.1028 time to fit residues: 19.7360 Evaluate side-chains 136 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 916 HIS 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 = 0.4588 r_free = 0.4588 target = 0.206390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.145622 restraints weight = 13360.346| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.77 r_work: 0.3615 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10660 Z= 0.198 Angle : 0.653 14.047 14455 Z= 0.324 Chirality : 0.044 0.160 1597 Planarity : 0.004 0.050 1892 Dihedral : 5.274 59.404 1430 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.67 % Allowed : 12.57 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.23), residues: 1306 helix: 1.19 (0.22), residues: 538 sheet: 0.12 (0.38), residues: 188 loop : -0.34 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1025 TYR 0.013 0.001 TYR A 117 PHE 0.021 0.002 PHE B1256 TRP 0.063 0.003 TRP B1145 HIS 0.011 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00478 (10660) covalent geometry : angle 0.65329 (14455) hydrogen bonds : bond 0.04226 ( 479) hydrogen bonds : angle 4.66481 ( 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 136 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 557 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8042 (tp30) REVERT: A 1027 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8369 (mp) REVERT: B 974 MET cc_start: 0.6570 (mtp) cc_final: 0.6357 (mtp) REVERT: B 990 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8647 (mmmt) REVERT: B 1100 TYR cc_start: 0.8265 (t80) cc_final: 0.8019 (t80) REVERT: B 1103 MET cc_start: 0.8554 (pmm) cc_final: 0.8142 (pmm) REVERT: C 60 ASN cc_start: 0.8769 (t0) cc_final: 0.8125 (t0) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.0935 time to fit residues: 17.5021 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 559 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 1261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 0.0050 chunk 99 optimal weight: 0.6980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4664 r_free = 0.4664 target = 0.212696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.4147 r_free = 0.4147 target = 0.158617 restraints weight = 13500.612| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.79 r_work: 0.3737 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2139 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= 0.115 Angle : 0.597 12.237 14455 Z= 0.296 Chirality : 0.042 0.213 1597 Planarity : 0.004 0.049 1892 Dihedral : 5.037 58.344 1430 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.67 % Allowed : 13.09 % Favored : 85.24 % 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: 0.60 (0.23), residues: 1306 helix: 1.33 (0.22), residues: 531 sheet: 0.10 (0.38), residues: 190 loop : -0.29 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1025 TYR 0.010 0.001 TYR A 910 PHE 0.017 0.001 PHE B1256 TRP 0.059 0.002 TRP B1145 HIS 0.008 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00252 (10660) covalent geometry : angle 0.59682 (14455) hydrogen bonds : bond 0.03796 ( 479) hydrogen bonds : angle 4.43881 ( 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 139 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7848 (p0) cc_final: 0.7606 (p0) REVERT: A 368 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6999 (ttm170) REVERT: A 557 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8068 (tp30) REVERT: A 1027 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 990 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8622 (mmmt) REVERT: B 1024 GLN cc_start: 0.6057 (tp-100) cc_final: 0.5575 (tp-100) REVERT: B 1100 TYR cc_start: 0.8205 (t80) cc_final: 0.8001 (t80) REVERT: B 1103 MET cc_start: 0.8307 (pmm) cc_final: 0.8062 (pmm) REVERT: C 60 ASN cc_start: 0.8847 (t0) cc_final: 0.8227 (t0) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.1006 time to fit residues: 18.8376 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain A residue 618 TYR 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 1145 TRP 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: 3.9990 chunk 17 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 ASN ** B1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.205053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146373 restraints weight = 13412.800| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.62 r_work: 0.3626 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10660 Z= 0.238 Angle : 0.684 11.574 14455 Z= 0.340 Chirality : 0.045 0.191 1597 Planarity : 0.004 0.051 1892 Dihedral : 5.334 59.597 1430 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.67 % Allowed : 13.97 % 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: 0.38 (0.23), residues: 1306 helix: 1.15 (0.23), residues: 538 sheet: -0.12 (0.39), residues: 188 loop : -0.39 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1025 TYR 0.014 0.002 TYR A1052 PHE 0.019 0.002 PHE A 116 TRP 0.052 0.002 TRP B1145 HIS 0.012 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00578 (10660) covalent geometry : angle 0.68373 (14455) hydrogen bonds : bond 0.04325 ( 479) hydrogen bonds : angle 4.71363 ( 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 137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.385 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: 0.8292 (tm-30) cc_final: 0.7937 (mm-30) REVERT: A 977 ASP cc_start: 0.8365 (m-30) cc_final: 0.8118 (t0) REVERT: A 1027 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 1024 GLN cc_start: 0.6140 (tp-100) cc_final: 0.5721 (tp40) REVERT: B 1103 MET cc_start: 0.8336 (pmm) cc_final: 0.8107 (pmm) REVERT: C 60 ASN cc_start: 0.8832 (t0) cc_final: 0.8218 (t0) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.1020 time to fit residues: 19.1169 Evaluate side-chains 128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 606 ASN 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 1129 GLN Chi-restraints excluded: chain B residue 1145 TRP 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: 0.8980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4586 r_free = 0.4586 target = 0.206647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.146265 restraints weight = 13415.696| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.79 r_work: 0.3631 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10660 Z= 0.168 Angle : 0.641 11.351 14455 Z= 0.319 Chirality : 0.043 0.169 1597 Planarity : 0.004 0.048 1892 Dihedral : 5.208 58.076 1430 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.49 % Allowed : 14.59 % Favored : 83.92 % 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: 0.40 (0.23), residues: 1306 helix: 1.20 (0.23), residues: 530 sheet: -0.19 (0.39), residues: 187 loop : -0.37 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1025 TYR 0.010 0.001 TYR A 117 PHE 0.027 0.002 PHE B1265 TRP 0.054 0.002 TRP B1145 HIS 0.011 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00400 (10660) covalent geometry : angle 0.64111 (14455) hydrogen bonds : bond 0.03938 ( 479) hydrogen bonds : angle 4.56522 ( 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 135 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.301 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: 0.8282 (tm-30) cc_final: 0.7916 (mm-30) REVERT: A 1027 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 1024 GLN cc_start: 0.6163 (tp-100) cc_final: 0.5773 (tp40) REVERT: C 60 ASN cc_start: 0.8836 (t0) cc_final: 0.8244 (t0) outliers start: 17 outliers final: 13 residues processed: 129 average time/residue: 0.0970 time to fit residues: 17.5741 Evaluate side-chains 128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 420 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 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: 0.0170 chunk 13 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 949 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.212417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.159219 restraints weight = 13338.567| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.85 r_work: 0.3738 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2569 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= 0.115 Angle : 0.617 11.648 14455 Z= 0.307 Chirality : 0.042 0.181 1597 Planarity : 0.004 0.048 1892 Dihedral : 4.990 59.812 1430 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.32 % Allowed : 14.59 % Favored : 84.09 % 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: 0.52 (0.24), residues: 1306 helix: 1.31 (0.23), residues: 532 sheet: -0.15 (0.38), residues: 194 loop : -0.30 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1025 TYR 0.024 0.001 TYR B1021 PHE 0.022 0.001 PHE B1259 TRP 0.060 0.002 TRP B1145 HIS 0.010 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00254 (10660) covalent geometry : angle 0.61662 (14455) hydrogen bonds : bond 0.03677 ( 479) hydrogen bonds : angle 4.40786 ( 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 135 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.370 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: 0.8339 (tm-30) cc_final: 0.7959 (mm-30) REVERT: A 1027 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 1024 GLN cc_start: 0.6171 (tp-100) cc_final: 0.5506 (tp-100) REVERT: C 60 ASN cc_start: 0.8895 (t0) cc_final: 0.8334 (t0) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.1098 time to fit residues: 19.8504 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL 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: 0.0970 chunk 18 optimal weight: 0.3980 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 102 optimal weight: 0.0670 chunk 15 optimal weight: 0.0870 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 HIS A 713 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.211685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.157747 restraints weight = 13329.073| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.76 r_work: 0.3723 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2738 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= 0.111 Angle : 0.615 12.159 14455 Z= 0.305 Chirality : 0.042 0.173 1597 Planarity : 0.004 0.048 1892 Dihedral : 4.910 59.335 1430 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.14 % Allowed : 14.67 % Favored : 84.18 % 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: 0.60 (0.23), residues: 1306 helix: 1.33 (0.23), residues: 532 sheet: 0.02 (0.39), residues: 184 loop : -0.25 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1025 TYR 0.023 0.001 TYR B1021 PHE 0.032 0.001 PHE A 242 TRP 0.061 0.002 TRP B1145 HIS 0.009 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00242 (10660) covalent geometry : angle 0.61489 (14455) hydrogen bonds : bond 0.03553 ( 479) hydrogen bonds : angle 4.33232 ( 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 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 1024 GLN cc_start: 0.6116 (tp-100) cc_final: 0.5489 (tp-100) REVERT: B 1285 MET cc_start: 0.4679 (ppp) cc_final: 0.1768 (ptm) REVERT: C 60 ASN cc_start: 0.8883 (t0) cc_final: 0.8332 (t0) outliers start: 13 outliers final: 11 residues processed: 121 average time/residue: 0.0958 time to fit residues: 16.3786 Evaluate side-chains 124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 420 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 696 VAL 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 61 optimal weight: 6.9990 chunk 98 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.210335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155855 restraints weight = 13448.497| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.80 r_work: 0.3698 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10660 Z= 0.137 Angle : 0.627 11.031 14455 Z= 0.312 Chirality : 0.042 0.163 1597 Planarity : 0.004 0.050 1892 Dihedral : 4.916 59.306 1430 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.05 % Allowed : 15.03 % Favored : 83.92 % 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: 0.56 (0.24), residues: 1306 helix: 1.28 (0.22), residues: 544 sheet: -0.01 (0.39), residues: 184 loop : -0.29 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 587 TYR 0.022 0.001 TYR B1021 PHE 0.028 0.001 PHE A 242 TRP 0.057 0.002 TRP B1145 HIS 0.009 0.001 HIS A 858 Details of bonding type rmsd covalent geometry : bond 0.00321 (10660) covalent geometry : angle 0.62733 (14455) hydrogen bonds : bond 0.03671 ( 479) hydrogen bonds : angle 4.36611 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.29 seconds wall clock time: 55 minutes 38.55 seconds (3338.55 seconds total)