Starting phenix.real_space_refine on Sat Aug 23 17:59:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isj_35692/08_2025/8isj_35692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isj_35692/08_2025/8isj_35692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8isj_35692/08_2025/8isj_35692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isj_35692/08_2025/8isj_35692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8isj_35692/08_2025/8isj_35692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isj_35692/08_2025/8isj_35692.map" } resolution = 3.0 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= 0.030 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 8611 2.51 5 N 2319 2.21 5 O 2497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13533 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6730 Classifications: {'peptide': 859} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 824} Chain breaks: 5 Chain: "B" Number of atoms: 6717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6717 Classifications: {'peptide': 857} Link IDs: {'PTRANS': 34, 'TRANS': 822} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.09, per 1000 atoms: 0.23 Number of scatterers: 13533 At special positions: 0 Unit cell: (109.65, 125.8, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 2497 8.00 N 2319 7.00 C 8611 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 471.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 19 sheets defined 41.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 removed outlier: 4.015A pdb=" N LYS A 76 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 removed outlier: 4.026A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.586A pdb=" N PHE A 133 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.189A pdb=" N ALA A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.863A pdb=" N ASN A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.834A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.634A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 382 through 398 removed outlier: 4.445A pdb=" N GLU A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 removed outlier: 3.881A pdb=" N MET A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.731A pdb=" N SER A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 497 through 502 removed outlier: 4.012A pdb=" N LEU A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 502' Processing helix chain 'A' and resid 569 through 589 removed outlier: 3.806A pdb=" N MET A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 574 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 789 through 793 Processing helix chain 'A' and resid 814 through 832 removed outlier: 3.666A pdb=" N PHE A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 924 removed outlier: 3.575A pdb=" N ARG A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 906 " --> pdb=" O TYR A 902 " (cutoff:3.500A) Proline residue: A 910 - end of helix Processing helix chain 'A' and resid 927 through 950 Processing helix chain 'A' and resid 952 through 959 removed outlier: 4.161A pdb=" N ILE A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 980 removed outlier: 3.556A pdb=" N GLN A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 988 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1008 through 1026 removed outlier: 4.089A pdb=" N LEU A1012 " --> pdb=" O ASP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1074 Processing helix chain 'A' and resid 1079 through 1096 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 134 through 147 Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 380 through 425 removed outlier: 4.004A pdb=" N GLN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 403 " --> pdb=" O ASN B 399 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.626A pdb=" N GLN B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 569 through 588 removed outlier: 3.701A pdb=" N MET B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.632A pdb=" N PHE B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 removed outlier: 3.715A pdb=" N ARG B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 924 removed outlier: 4.259A pdb=" N LYS B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 927 through 949 removed outlier: 3.555A pdb=" N ARG B 931 " --> pdb=" O GLY B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 970 through 988 removed outlier: 3.797A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS B 984 " --> pdb=" O GLN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 Processing helix chain 'B' and resid 1008 through 1026 Processing helix chain 'B' and resid 1065 through 1073 Processing helix chain 'B' and resid 1080 through 1096 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.508A pdb=" N ALA A 298 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 7.096A pdb=" N VAL A 96 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP A 90 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 98 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.516A pdb=" N VAL A 239 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 458 removed outlier: 6.498A pdb=" N GLY A 484 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 748 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 486 " --> pdb=" O ILE A 748 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.382A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 855 " --> pdb=" O GLU A 835 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 835 " --> pdb=" O VAL A 855 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AA9, first strand: chain 'A' and resid 966 through 969 Processing sheet with id=AB1, first strand: chain 'A' and resid 991 through 994 removed outlier: 5.974A pdb=" N GLN A1032 " --> pdb=" O THR A1060 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.945A pdb=" N LEU B 301 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 99 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 86 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.618A pdb=" N ALA B 241 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU B 255 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 239 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 368 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET B 339 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL B 370 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 337 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS B 372 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 335 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 455 through 460 removed outlier: 3.806A pdb=" N GLY B 507 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 529 through 530 Processing sheet with id=AB6, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.049A pdb=" N PHE B 745 " --> pdb=" O GLN B 757 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 757 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 755 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.324A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 855 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 835 " --> pdb=" O VAL B 855 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 803 through 804 Processing sheet with id=AB9, first strand: chain 'B' and resid 966 through 969 Processing sheet with id=AC1, first strand: chain 'B' and resid 991 through 994 removed outlier: 6.573A pdb=" N ARG B 991 " --> pdb=" O LEU B1033 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL B1035 " --> pdb=" O ARG B 991 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 993 " --> pdb=" O VAL B1035 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ALA B1037 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN B1032 " --> pdb=" O THR B1060 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1905 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: 2.05 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4193 1.34 - 1.46: 2014 1.46 - 1.58: 7405 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 13784 Sorted by residual: bond pdb=" N VAL A1079 " pdb=" CA VAL A1079 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N VAL A 398 " pdb=" CA VAL A 398 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.388 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.389 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.389 0.059 2.00e-02 2.50e+03 8.75e+00 ... (remaining 13779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 18194 2.21 - 4.43: 357 4.43 - 6.64: 42 6.64 - 8.86: 14 8.86 - 11.07: 6 Bond angle restraints: 18613 Sorted by residual: angle pdb=" N TYR A 385 " pdb=" CA TYR A 385 " pdb=" C TYR A 385 " ideal model delta sigma weight residual 114.56 104.47 10.09 1.27e+00 6.20e-01 6.31e+01 angle pdb=" N GLU A 401 " pdb=" CA GLU A 401 " pdb=" C GLU A 401 " ideal model delta sigma weight residual 112.88 105.13 7.75 1.29e+00 6.01e-01 3.61e+01 angle pdb=" C MET A 192 " pdb=" CA MET A 192 " pdb=" CB MET A 192 " ideal model delta sigma weight residual 117.23 109.58 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" N ALA A 386 " pdb=" CA ALA A 386 " pdb=" C ALA A 386 " ideal model delta sigma weight residual 113.28 107.01 6.27 1.22e+00 6.72e-01 2.64e+01 angle pdb=" N LYS A 400 " pdb=" CA LYS A 400 " pdb=" C LYS A 400 " ideal model delta sigma weight residual 113.30 106.67 6.63 1.34e+00 5.57e-01 2.45e+01 ... (remaining 18608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7341 17.90 - 35.81: 843 35.81 - 53.71: 212 53.71 - 71.61: 31 71.61 - 89.52: 12 Dihedral angle restraints: 8439 sinusoidal: 3471 harmonic: 4968 Sorted by residual: dihedral pdb=" CD ARG B 384 " pdb=" NE ARG B 384 " pdb=" CZ ARG B 384 " pdb=" NH1 ARG B 384 " ideal model delta sinusoidal sigma weight residual 0.00 33.18 -33.18 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CA ALA A 428 " pdb=" C ALA A 428 " pdb=" N PRO A 429 " pdb=" CA PRO A 429 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR A 902 " pdb=" C TYR A 902 " pdb=" N ILE A 903 " pdb=" CA ILE A 903 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1753 0.055 - 0.110: 288 0.110 - 0.164: 71 0.164 - 0.219: 7 0.219 - 0.274: 5 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CB VAL A 398 " pdb=" CA VAL A 398 " pdb=" CG1 VAL A 398 " pdb=" CG2 VAL A 398 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL A 338 " pdb=" N VAL A 338 " pdb=" C VAL A 338 " pdb=" CB VAL A 338 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2121 not shown) Planarity restraints: 2368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " -0.133 2.00e-02 2.50e+03 1.45e-01 5.22e+02 pdb=" CAP O6E B1201 " 0.138 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " 0.120 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.067 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " 0.012 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " -0.041 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " -0.027 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " 0.012 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.281 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.267 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.023 2.00e-02 2.50e+03 1.33e-01 4.41e+02 pdb=" CAP O6E A1201 " -0.205 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.009 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.058 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.008 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.013 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.298 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.138 2.00e-02 2.50e+03 9.21e-02 2.12e+02 pdb=" CAO O6E A1201 " -0.023 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " 0.062 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.156 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.054 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.027 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.069 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.011 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.130 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.108 2.00e-02 2.50e+03 ... (remaining 2365 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 480 2.72 - 3.26: 12989 3.26 - 3.81: 20794 3.81 - 4.35: 24898 4.35 - 4.90: 43616 Nonbonded interactions: 102777 Sorted by model distance: nonbonded pdb=" O VAL A1079 " pdb=" OG SER A1080 " model vdw 2.173 3.040 nonbonded pdb=" OG SER B 100 " pdb=" OD1 ASN B 102 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 985 " pdb=" O VAL A 990 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP A1018 " pdb=" OG SER A1085 " model vdw 2.239 3.040 nonbonded pdb=" O SER A 104 " pdb=" OG1 THR A 108 " model vdw 2.270 3.040 ... (remaining 102772 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 588 or resid 742 through 1040 or resid 1050 thr \ ough 1119 or resid 1201)) selection = (chain 'B' and (resid 73 through 110 or resid 121 through 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.004 0.060 13786 Z= 0.226 Angle : 0.722 11.074 18613 Z= 0.403 Chirality : 0.046 0.274 2124 Planarity : 0.009 0.265 2368 Dihedral : 16.090 89.518 5211 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 0.20 % Allowed : 21.08 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.21), residues: 1692 helix: 1.60 (0.21), residues: 665 sheet: 0.34 (0.28), residues: 337 loop : -1.61 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 891 TYR 0.026 0.001 TYR B 478 PHE 0.043 0.001 PHE B 916 TRP 0.012 0.001 TRP B 366 HIS 0.008 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00384 (13784) covalent geometry : angle 0.72205 (18613) hydrogen bonds : bond 0.13271 ( 676) hydrogen bonds : angle 5.99472 ( 1905) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 251 GLU cc_start: 0.7727 (tt0) cc_final: 0.7454 (tt0) REVERT: A 782 MET cc_start: 0.8731 (tpt) cc_final: 0.8510 (tpt) REVERT: B 210 ARG cc_start: 0.7421 (ttm170) cc_final: 0.7153 (ptm160) REVERT: B 474 TRP cc_start: 0.6413 (t60) cc_final: 0.6059 (t60) REVERT: B 548 MET cc_start: 0.3824 (tmm) cc_final: 0.3609 (ttt) REVERT: B 797 MET cc_start: 0.9162 (tpp) cc_final: 0.8923 (tpt) REVERT: B 881 GLN cc_start: 0.8019 (mm110) cc_final: 0.7589 (mt0) REVERT: B 919 LYS cc_start: 0.7056 (tmmt) cc_final: 0.6854 (mttt) outliers start: 3 outliers final: 0 residues processed: 169 average time/residue: 0.5345 time to fit residues: 98.6906 Evaluate side-chains 129 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 399 ASN A 469 GLN A 873 GLN A 941 GLN A 980 GLN A1013 GLN B 330 ASN B 372 HIS B 577 HIS B 757 GLN B 827 ASN B 980 GLN B1013 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.233067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149845 restraints weight = 15658.780| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.92 r_work: 0.3536 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13786 Z= 0.143 Angle : 0.604 7.592 18613 Z= 0.303 Chirality : 0.042 0.160 2124 Planarity : 0.004 0.062 2368 Dihedral : 5.720 89.544 1911 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.56 % Rotamer: Outliers : 3.97 % Allowed : 18.72 % Favored : 77.31 % 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 aren not related in a simple way. whole: 0.14 (0.21), residues: 1692 helix: 1.58 (0.20), residues: 678 sheet: 0.52 (0.29), residues: 327 loop : -1.70 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 891 TYR 0.019 0.001 TYR B 327 PHE 0.027 0.002 PHE B 916 TRP 0.015 0.001 TRP B 366 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00340 (13784) covalent geometry : angle 0.60437 (18613) hydrogen bonds : bond 0.04362 ( 676) hydrogen bonds : angle 4.91483 ( 1905) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 331 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6725 (mmt) REVERT: A 824 VAL cc_start: 0.8675 (t) cc_final: 0.8396 (p) REVERT: A 896 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7178 (ttm170) REVERT: B 105 GLU cc_start: 0.7508 (tp30) cc_final: 0.7199 (tp30) REVERT: B 210 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7251 (ptm160) REVERT: B 474 TRP cc_start: 0.6246 (t60) cc_final: 0.5948 (t60) REVERT: B 576 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7787 (mp) REVERT: B 881 GLN cc_start: 0.8411 (mm110) cc_final: 0.7886 (mt0) outliers start: 59 outliers final: 19 residues processed: 184 average time/residue: 0.4084 time to fit residues: 83.8897 Evaluate side-chains 153 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 152 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN B 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.231244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146992 restraints weight = 15881.200| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 4.03 r_work: 0.3552 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13786 Z= 0.175 Angle : 0.626 7.981 18613 Z= 0.313 Chirality : 0.043 0.159 2124 Planarity : 0.005 0.062 2368 Dihedral : 5.613 88.250 1911 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 4.44 % Allowed : 19.19 % Favored : 76.36 % 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 aren not related in a simple way. whole: 0.10 (0.21), residues: 1692 helix: 1.51 (0.20), residues: 684 sheet: 0.46 (0.29), residues: 331 loop : -1.71 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 891 TYR 0.022 0.002 TYR B 327 PHE 0.022 0.002 PHE A 83 TRP 0.016 0.002 TRP B 366 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00433 (13784) covalent geometry : angle 0.62584 (18613) hydrogen bonds : bond 0.04651 ( 676) hydrogen bonds : angle 4.85396 ( 1905) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6825 (tpp) REVERT: A 824 VAL cc_start: 0.8676 (t) cc_final: 0.8427 (p) REVERT: A 896 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7153 (ttm170) REVERT: A 1096 MET cc_start: 0.5260 (OUTLIER) cc_final: 0.4800 (mmp) REVERT: B 105 GLU cc_start: 0.7613 (tp30) cc_final: 0.7297 (tp30) REVERT: B 210 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7363 (ttt180) REVERT: B 474 TRP cc_start: 0.6099 (t60) cc_final: 0.5800 (t60) REVERT: B 548 MET cc_start: 0.3847 (ttp) cc_final: 0.3217 (tmm) REVERT: B 576 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7652 (mp) REVERT: B 762 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8392 (mp) REVERT: B 881 GLN cc_start: 0.8390 (mm110) cc_final: 0.7981 (mt0) REVERT: B 919 LYS cc_start: 0.7108 (tmmt) cc_final: 0.6849 (mttt) outliers start: 66 outliers final: 32 residues processed: 180 average time/residue: 0.4548 time to fit residues: 90.8556 Evaluate side-chains 168 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 469 GLN A1014 GLN B 469 GLN B 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.239751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151513 restraints weight = 16160.697| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.60 r_work: 0.3687 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13786 Z= 0.134 Angle : 0.588 8.003 18613 Z= 0.294 Chirality : 0.042 0.223 2124 Planarity : 0.004 0.062 2368 Dihedral : 5.355 87.940 1911 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 3.77 % Allowed : 20.13 % Favored : 76.09 % 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 aren not related in a simple way. whole: 0.29 (0.21), residues: 1692 helix: 1.68 (0.20), residues: 684 sheet: 0.61 (0.29), residues: 327 loop : -1.63 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 891 TYR 0.022 0.002 TYR B 327 PHE 0.021 0.002 PHE A 83 TRP 0.014 0.001 TRP B 366 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00318 (13784) covalent geometry : angle 0.58755 (18613) hydrogen bonds : bond 0.04046 ( 676) hydrogen bonds : angle 4.68961 ( 1905) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 0.652 Fit side-chains REVERT: A 331 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: A 896 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: A 1096 MET cc_start: 0.5109 (OUTLIER) cc_final: 0.4633 (mmp) REVERT: B 105 GLU cc_start: 0.7601 (tp30) cc_final: 0.7246 (tp30) REVERT: B 210 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7461 (ttt180) REVERT: B 474 TRP cc_start: 0.6092 (t60) cc_final: 0.5801 (t60) REVERT: B 508 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7444 (ttt) REVERT: B 576 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7880 (mp) REVERT: B 762 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 881 GLN cc_start: 0.8438 (mm110) cc_final: 0.8027 (mt0) REVERT: B 920 MET cc_start: 0.4735 (mmt) cc_final: 0.4523 (mmt) outliers start: 56 outliers final: 30 residues processed: 172 average time/residue: 0.5465 time to fit residues: 104.0577 Evaluate side-chains 165 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 888 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN B 469 GLN B 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.228744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148473 restraints weight = 16079.885| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.92 r_work: 0.3645 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13786 Z= 0.203 Angle : 0.654 8.167 18613 Z= 0.326 Chirality : 0.044 0.167 2124 Planarity : 0.005 0.064 2368 Dihedral : 5.541 87.052 1911 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.91 % Favored : 92.97 % Rotamer: Outliers : 4.44 % Allowed : 20.67 % Favored : 74.88 % 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 aren not related in a simple way. whole: 0.02 (0.21), residues: 1692 helix: 1.40 (0.20), residues: 686 sheet: 0.48 (0.29), residues: 330 loop : -1.74 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 891 TYR 0.023 0.002 TYR B 327 PHE 0.022 0.002 PHE A 83 TRP 0.017 0.002 TRP B 366 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00506 (13784) covalent geometry : angle 0.65352 (18613) hydrogen bonds : bond 0.04881 ( 676) hydrogen bonds : angle 4.83987 ( 1905) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 0.411 Fit side-chains REVERT: A 331 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7138 (mtt) REVERT: A 570 ASP cc_start: 0.7669 (t70) cc_final: 0.7273 (m-30) REVERT: A 824 VAL cc_start: 0.8815 (t) cc_final: 0.8550 (p) REVERT: A 896 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7134 (ttm170) REVERT: A 1096 MET cc_start: 0.5013 (OUTLIER) cc_final: 0.4613 (mpp) REVERT: B 105 GLU cc_start: 0.7639 (tp30) cc_final: 0.7293 (tp30) REVERT: B 210 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7460 (ttt180) REVERT: B 228 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: B 469 GLN cc_start: 0.7311 (mm-40) cc_final: 0.6892 (mm-40) REVERT: B 576 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 762 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8451 (mp) REVERT: B 881 GLN cc_start: 0.8478 (mm110) cc_final: 0.7984 (mt0) REVERT: B 915 MET cc_start: 0.7175 (tpp) cc_final: 0.6726 (tpp) REVERT: B 919 LYS cc_start: 0.7192 (tmmt) cc_final: 0.6880 (mttt) REVERT: B 1022 MET cc_start: 0.4905 (ppp) cc_final: 0.4124 (ppp) outliers start: 66 outliers final: 37 residues processed: 180 average time/residue: 0.4739 time to fit residues: 94.7603 Evaluate side-chains 174 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 983 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A1014 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.230717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147397 restraints weight = 16105.026| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 4.01 r_work: 0.3561 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13786 Z= 0.140 Angle : 0.604 8.449 18613 Z= 0.300 Chirality : 0.042 0.158 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.311 86.638 1911 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.03 % Favored : 93.85 % Rotamer: Outliers : 3.77 % Allowed : 21.75 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1692 helix: 1.55 (0.20), residues: 686 sheet: 0.53 (0.29), residues: 331 loop : -1.64 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 891 TYR 0.023 0.002 TYR B 327 PHE 0.022 0.002 PHE A 83 TRP 0.015 0.001 TRP B 366 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00335 (13784) covalent geometry : angle 0.60364 (18613) hydrogen bonds : bond 0.04074 ( 676) hydrogen bonds : angle 4.66229 ( 1905) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6709 (t0) REVERT: A 331 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6943 (mtt) REVERT: A 570 ASP cc_start: 0.7703 (t70) cc_final: 0.7277 (m-30) REVERT: A 824 VAL cc_start: 0.8727 (t) cc_final: 0.8439 (p) REVERT: A 896 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7122 (ttm170) REVERT: A 1096 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.4489 (mmp) REVERT: B 105 GLU cc_start: 0.7650 (tp30) cc_final: 0.7324 (tp30) REVERT: B 210 ARG cc_start: 0.8336 (ttm170) cc_final: 0.7486 (ttt180) REVERT: B 262 GLU cc_start: 0.7813 (pm20) cc_final: 0.6684 (tm-30) REVERT: B 576 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7864 (mp) REVERT: B 762 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8463 (mp) REVERT: B 881 GLN cc_start: 0.8460 (mm110) cc_final: 0.7932 (mt0) REVERT: B 919 LYS cc_start: 0.7095 (tmmt) cc_final: 0.6846 (mtmt) outliers start: 56 outliers final: 36 residues processed: 173 average time/residue: 0.5162 time to fit residues: 99.0996 Evaluate side-chains 174 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 983 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN B 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.231946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148933 restraints weight = 15939.849| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.99 r_work: 0.3572 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13786 Z= 0.119 Angle : 0.587 8.481 18613 Z= 0.290 Chirality : 0.041 0.156 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.156 86.360 1911 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 3.64 % Allowed : 22.09 % Favored : 74.28 % 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 aren not related in a simple way. whole: 0.31 (0.21), residues: 1692 helix: 1.68 (0.20), residues: 687 sheet: 0.57 (0.29), residues: 321 loop : -1.57 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 891 TYR 0.024 0.002 TYR B 478 PHE 0.021 0.001 PHE A 83 TRP 0.014 0.001 TRP B 366 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00277 (13784) covalent geometry : angle 0.58717 (18613) hydrogen bonds : bond 0.03704 ( 676) hydrogen bonds : angle 4.55039 ( 1905) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 331 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6425 (mtt) REVERT: A 896 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7117 (ttm170) REVERT: A 1096 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4452 (mmp) REVERT: B 105 GLU cc_start: 0.7626 (tp30) cc_final: 0.7310 (tp30) REVERT: B 210 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7474 (ttt180) REVERT: B 262 GLU cc_start: 0.7703 (pm20) cc_final: 0.6599 (tm-30) REVERT: B 469 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6821 (mm-40) REVERT: B 517 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.5989 (m-30) REVERT: B 576 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7890 (mp) REVERT: B 762 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 877 HIS cc_start: 0.7388 (t-90) cc_final: 0.6959 (t70) REVERT: B 881 GLN cc_start: 0.8450 (mm110) cc_final: 0.7937 (mt0) REVERT: B 965 MET cc_start: 0.2467 (OUTLIER) cc_final: 0.2144 (tpt) REVERT: B 1073 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.5600 (t80) outliers start: 54 outliers final: 29 residues processed: 174 average time/residue: 0.5596 time to fit residues: 108.1675 Evaluate side-chains 171 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1073 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 123 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.232615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148904 restraints weight = 15811.782| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.90 r_work: 0.3605 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13786 Z= 0.117 Angle : 0.597 8.395 18613 Z= 0.294 Chirality : 0.041 0.162 2124 Planarity : 0.004 0.063 2368 Dihedral : 5.083 86.639 1911 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 3.50 % Allowed : 22.49 % Favored : 74.01 % 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 aren not related in a simple way. whole: 0.36 (0.21), residues: 1692 helix: 1.68 (0.20), residues: 689 sheet: 0.61 (0.29), residues: 321 loop : -1.51 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 891 TYR 0.024 0.001 TYR B 327 PHE 0.023 0.001 PHE A 83 TRP 0.013 0.001 TRP B 366 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00266 (13784) covalent geometry : angle 0.59706 (18613) hydrogen bonds : bond 0.03596 ( 676) hydrogen bonds : angle 4.51168 ( 1905) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6555 (t0) REVERT: A 896 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7123 (ttm170) REVERT: A 1096 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.4390 (mmp) REVERT: B 105 GLU cc_start: 0.7612 (tp30) cc_final: 0.7287 (tp30) REVERT: B 210 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7457 (ttt180) REVERT: B 262 GLU cc_start: 0.7645 (pm20) cc_final: 0.6569 (tm-30) REVERT: B 508 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7309 (ttt) REVERT: B 517 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.5946 (m-30) REVERT: B 531 ARG cc_start: 0.6169 (mtm-85) cc_final: 0.5812 (mtm-85) REVERT: B 576 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 762 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 877 HIS cc_start: 0.7368 (t-90) cc_final: 0.6940 (t70) REVERT: B 881 GLN cc_start: 0.8455 (mm110) cc_final: 0.7942 (mt0) REVERT: B 919 LYS cc_start: 0.7033 (tmmt) cc_final: 0.6411 (pttm) outliers start: 52 outliers final: 30 residues processed: 181 average time/residue: 0.5851 time to fit residues: 116.8188 Evaluate side-chains 170 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 469 GLN B 469 GLN ** B1014 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 = 0.4693 r_free = 0.4693 target = 0.238650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150719 restraints weight = 16076.860| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.20 r_work: 0.3612 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13786 Z= 0.145 Angle : 0.639 9.045 18613 Z= 0.316 Chirality : 0.042 0.161 2124 Planarity : 0.004 0.061 2368 Dihedral : 5.272 87.058 1911 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 3.43 % Allowed : 22.69 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1692 helix: 1.53 (0.20), residues: 689 sheet: 0.59 (0.29), residues: 327 loop : -1.51 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 891 TYR 0.023 0.001 TYR B 327 PHE 0.023 0.002 PHE A 83 TRP 0.014 0.002 TRP B 366 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00347 (13784) covalent geometry : angle 0.63908 (18613) hydrogen bonds : bond 0.04033 ( 676) hydrogen bonds : angle 4.59971 ( 1905) Misc. bond : bond 0.00313 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 896 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7125 (ttm170) REVERT: A 1096 MET cc_start: 0.4640 (OUTLIER) cc_final: 0.4416 (tpp) REVERT: B 105 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7297 (tp30) REVERT: B 210 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7468 (ttt180) REVERT: B 228 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: B 249 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.5671 (p-80) REVERT: B 262 GLU cc_start: 0.7699 (pm20) cc_final: 0.6645 (tm-30) REVERT: B 469 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6938 (mm-40) REVERT: B 517 ASP cc_start: 0.6474 (OUTLIER) cc_final: 0.5994 (m-30) REVERT: B 576 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7899 (mp) REVERT: B 762 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B 877 HIS cc_start: 0.7410 (t-90) cc_final: 0.6980 (t70) REVERT: B 881 GLN cc_start: 0.8452 (mm110) cc_final: 0.7937 (mt0) REVERT: B 915 MET cc_start: 0.7677 (ttm) cc_final: 0.7477 (ttm) REVERT: B 919 LYS cc_start: 0.7036 (tmmt) cc_final: 0.6818 (mtmt) outliers start: 51 outliers final: 37 residues processed: 171 average time/residue: 0.5729 time to fit residues: 108.7900 Evaluate side-chains 178 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 469 GLN ** B1014 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 = 0.4649 r_free = 0.4649 target = 0.230321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.154282 restraints weight = 15554.792| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.68 r_work: 0.3602 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13786 Z= 0.167 Angle : 0.666 12.235 18613 Z= 0.329 Chirality : 0.043 0.162 2124 Planarity : 0.005 0.061 2368 Dihedral : 5.388 87.439 1911 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.44 % Rotamer: Outliers : 3.23 % Allowed : 23.10 % Favored : 73.67 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1692 helix: 1.36 (0.20), residues: 688 sheet: 0.55 (0.29), residues: 326 loop : -1.54 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 891 TYR 0.026 0.002 TYR B 478 PHE 0.023 0.002 PHE A 83 TRP 0.015 0.002 TRP B 474 HIS 0.009 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00408 (13784) covalent geometry : angle 0.66573 (18613) hydrogen bonds : bond 0.04352 ( 676) hydrogen bonds : angle 4.70121 ( 1905) Misc. bond : bond 0.00217 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 824 VAL cc_start: 0.8759 (t) cc_final: 0.8478 (p) REVERT: A 896 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7103 (ttm170) REVERT: A 1096 MET cc_start: 0.4686 (OUTLIER) cc_final: 0.4364 (tpp) REVERT: B 105 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: B 210 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7476 (ttt180) REVERT: B 228 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: B 249 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.5773 (p-80) REVERT: B 262 GLU cc_start: 0.7732 (pm20) cc_final: 0.6644 (tm-30) REVERT: B 517 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: B 576 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 877 HIS cc_start: 0.7433 (t-90) cc_final: 0.6997 (t70) REVERT: B 881 GLN cc_start: 0.8456 (mm110) cc_final: 0.7943 (mt0) REVERT: B 1087 MET cc_start: 0.8048 (ppp) cc_final: 0.7050 (ptp) outliers start: 48 outliers final: 34 residues processed: 173 average time/residue: 0.5704 time to fit residues: 109.2588 Evaluate side-chains 176 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 106 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN B 326 GLN B 469 GLN ** B1014 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 = 0.4662 r_free = 0.4662 target = 0.232087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148349 restraints weight = 15993.988| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 4.02 r_work: 0.3579 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13786 Z= 0.133 Angle : 0.644 13.167 18613 Z= 0.317 Chirality : 0.042 0.162 2124 Planarity : 0.004 0.062 2368 Dihedral : 5.328 87.210 1911 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 3.23 % Allowed : 23.10 % Favored : 73.67 % 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 aren not related in a simple way. whole: 0.20 (0.21), residues: 1692 helix: 1.41 (0.20), residues: 689 sheet: 0.60 (0.29), residues: 326 loop : -1.48 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 891 TYR 0.024 0.001 TYR B 327 PHE 0.023 0.002 PHE A 83 TRP 0.016 0.002 TRP B 474 HIS 0.007 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00312 (13784) covalent geometry : angle 0.64436 (18613) hydrogen bonds : bond 0.03901 ( 676) hydrogen bonds : angle 4.63990 ( 1905) Misc. bond : bond 0.00141 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4914.58 seconds wall clock time: 84 minutes 36.11 seconds (5076.11 seconds total)