Starting phenix.real_space_refine on Sat Aug 23 18:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9w_36117/08_2025/8j9w_36117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9w_36117/08_2025/8j9w_36117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2025/8j9w_36117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2025/8j9w_36117_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2025/8j9w_36117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2025/8j9w_36117.map" } resolution = 2.76 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8693 2.51 5 N 2373 2.21 5 O 2661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 13841 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6283 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 30, 'TRANS': 744} Chain: "B" Number of atoms: 6283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6283 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 30, 'TRANS': 744} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 255 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'EVP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.97, per 1000 atoms: 0.21 Number of scatterers: 13841 At special positions: 0 Unit cell: (122.01, 104.58, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 56 15.00 Mg 2 11.99 O 2661 8.00 N 2373 7.00 C 8693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 437.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 50.9% alpha, 9.2% beta 15 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 439 through 453 removed outlier: 4.374A pdb=" N GLY A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.803A pdb=" N ASN A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.983A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.521A pdb=" N ALA A 619 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.928A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.818A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 removed outlier: 4.322A pdb=" N GLU A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.805A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 730 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 755 through 767 Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.076A pdb=" N LEU A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 944 through 951 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.642A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.841A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.634A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1109 through 1118 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.705A pdb=" N GLU A1132 " --> pdb=" O GLN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1166 through 1187 removed outlier: 3.638A pdb=" N TRP A1170 " --> pdb=" O GLY A1166 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A1187 " --> pdb=" O LYS A1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.710A pdb=" N LEU B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.696A pdb=" N ASN B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.535A pdb=" N ARG B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.891A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.568A pdb=" N ALA B 619 " --> pdb=" O GLY B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.772A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.695A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 665 removed outlier: 3.753A pdb=" N ARG B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 662 " --> pdb=" O GLU B 658 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.808A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 755 through 767 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 821 removed outlier: 4.022A pdb=" N LEU B 821 " --> pdb=" O GLU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 953 through 958 removed outlier: 4.275A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 990 removed outlier: 3.636A pdb=" N GLU B 988 " --> pdb=" O ASN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.860A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.462A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1109 through 1118 Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.705A pdb=" N GLU B1132 " --> pdb=" O GLN B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.957A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 468 through 469 removed outlier: 5.687A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 577 through 580 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.844A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 852 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.545A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.471A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AA9, first strand: chain 'B' and resid 468 through 469 removed outlier: 5.757A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 577 through 580 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.862A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 850 through 852 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.548A pdb=" N HIS B 909 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.523A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 926 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 931 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016 566 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2121 1.31 - 1.44: 4227 1.44 - 1.56: 7739 1.56 - 1.68: 112 1.68 - 1.81: 88 Bond restraints: 14287 Sorted by residual: bond pdb=" N VAL B 941 " pdb=" CA VAL B 941 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.94e+01 bond pdb=" CA TRP A1189 " pdb=" C TRP A1189 " ideal model delta sigma weight residual 1.525 1.457 0.068 1.63e-02 3.76e+03 1.72e+01 bond pdb=" C CYS B 545 " pdb=" O CYS B 545 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" CA LEU B 542 " pdb=" C LEU B 542 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" C LEU B 542 " pdb=" O LEU B 542 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.18e-02 7.18e+03 1.28e+01 ... (remaining 14282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 19079 2.31 - 4.62: 395 4.62 - 6.93: 63 6.93 - 9.24: 23 9.24 - 11.55: 7 Bond angle restraints: 19567 Sorted by residual: angle pdb=" N ARG B 940 " pdb=" CA ARG B 940 " pdb=" C ARG B 940 " ideal model delta sigma weight residual 111.52 120.84 -9.32 1.40e+00 5.10e-01 4.43e+01 angle pdb=" C LEU A1047 " pdb=" N MET A1048 " pdb=" CA MET A1048 " ideal model delta sigma weight residual 121.14 109.59 11.55 1.75e+00 3.27e-01 4.36e+01 angle pdb=" N CYS B 545 " pdb=" CA CYS B 545 " pdb=" C CYS B 545 " ideal model delta sigma weight residual 109.46 99.17 10.29 1.66e+00 3.63e-01 3.84e+01 angle pdb=" N GLU B1041 " pdb=" CA GLU B1041 " pdb=" CB GLU B1041 " ideal model delta sigma weight residual 110.39 119.34 -8.95 1.66e+00 3.63e-01 2.91e+01 angle pdb=" N GLU A1041 " pdb=" CA GLU A1041 " pdb=" CB GLU A1041 " ideal model delta sigma weight residual 110.39 119.32 -8.93 1.66e+00 3.63e-01 2.89e+01 ... (remaining 19562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 8170 35.78 - 71.56: 330 71.56 - 107.34: 17 107.34 - 143.12: 6 143.12 - 178.90: 2 Dihedral angle restraints: 8525 sinusoidal: 3981 harmonic: 4544 Sorted by residual: dihedral pdb=" CA PRO A 938 " pdb=" C PRO A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta harmonic sigma weight residual -180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" N HIS A1192 " pdb=" C HIS A1192 " pdb=" CA HIS A1192 " pdb=" CB HIS A1192 " ideal model delta harmonic sigma weight residual 122.80 133.62 -10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA VAL A 941 " pdb=" C VAL A 941 " pdb=" N PRO A 942 " pdb=" CA PRO A 942 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1873 0.074 - 0.148: 239 0.148 - 0.222: 25 0.222 - 0.296: 3 0.296 - 0.370: 3 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA HIS A1192 " pdb=" N HIS A1192 " pdb=" C HIS A1192 " pdb=" CB HIS A1192 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C9 EVP D 101 " pdb=" C10 EVP D 101 " pdb=" C6 EVP D 101 " pdb=" C8 EVP D 101 " both_signs ideal model delta sigma weight residual False 2.49 2.83 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ARG B 940 " pdb=" N ARG B 940 " pdb=" C ARG B 940 " pdb=" CB ARG B 940 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2140 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1190 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS A1190 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS A1190 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A1191 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1044 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" CD GLN A1044 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A1044 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN A1044 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1169 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C VAL B1169 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B1169 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B1170 " -0.014 2.00e-02 2.50e+03 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 622 2.72 - 3.26: 13561 3.26 - 3.81: 24019 3.81 - 4.35: 29180 4.35 - 4.90: 47198 Nonbonded interactions: 114580 Sorted by model distance: nonbonded pdb=" OD2 ASP B 541 " pdb="MG MG B1201 " model vdw 2.175 2.170 nonbonded pdb=" OD2 ASP A 541 " pdb="MG MG A1201 " model vdw 2.202 2.170 nonbonded pdb=" O PRO A1095 " pdb=" OH TYR A1124 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 580 " pdb=" OE1 GLU B 624 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 751 " pdb=" OP2 DA E 12 " model vdw 2.286 3.040 ... (remaining 114575 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 12 or (resid 13 and (name P or name OP1 or name \ OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' or n \ ame C2' or name C1')))) selection = chain 'E' } ncs_group { reference = (chain 'D' and resid 1 through 17) selection = chain 'F' } 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: 6.950 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.190 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.068 14287 Z= 0.241 Angle : 0.839 11.552 19567 Z= 0.454 Chirality : 0.052 0.370 2143 Planarity : 0.006 0.084 2279 Dihedral : 18.058 178.896 5613 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.21 % 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: -1.21 (0.21), residues: 1546 helix: -0.51 (0.19), residues: 714 sheet: -1.17 (0.38), residues: 190 loop : -0.82 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 863 TYR 0.031 0.002 TYR B1067 PHE 0.015 0.002 PHE A1107 TRP 0.016 0.002 TRP A 560 HIS 0.004 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00456 (14287) covalent geometry : angle 0.83888 (19567) hydrogen bonds : bond 0.16105 ( 601) hydrogen bonds : angle 6.77115 ( 1693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 601 LYS cc_start: 0.9365 (mmpt) cc_final: 0.9160 (pptt) REVERT: B 966 TYR cc_start: 0.8595 (m-80) cc_final: 0.8311 (m-10) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.6790 time to fit residues: 83.8305 Evaluate side-chains 69 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1114 ASN B1186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.095676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.080056 restraints weight = 53205.588| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.65 r_work: 0.3589 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14287 Z= 0.176 Angle : 0.672 9.142 19567 Z= 0.351 Chirality : 0.044 0.279 2143 Planarity : 0.004 0.050 2279 Dihedral : 18.290 177.623 2515 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.54 % Allowed : 9.93 % Favored : 88.53 % 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: -0.67 (0.21), residues: 1546 helix: 0.10 (0.19), residues: 724 sheet: -1.11 (0.36), residues: 204 loop : -0.68 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 929 TYR 0.021 0.002 TYR A 698 PHE 0.023 0.001 PHE B1107 TRP 0.009 0.001 TRP A 820 HIS 0.005 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00395 (14287) covalent geometry : angle 0.67165 (19567) hydrogen bonds : bond 0.04484 ( 601) hydrogen bonds : angle 4.93169 ( 1693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.532 Fit side-chains REVERT: A 924 ASP cc_start: 0.8645 (m-30) cc_final: 0.8363 (t0) REVERT: B 593 GLU cc_start: 0.8406 (pm20) cc_final: 0.8132 (pp20) REVERT: B 601 LYS cc_start: 0.9374 (mmpt) cc_final: 0.9152 (pptt) REVERT: B 966 TYR cc_start: 0.8830 (m-80) cc_final: 0.8479 (m-10) REVERT: B 1048 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7564 (mpp) outliers start: 21 outliers final: 5 residues processed: 90 average time/residue: 0.6134 time to fit residues: 60.5955 Evaluate side-chains 70 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1048 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN B 928 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.094986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.079477 restraints weight = 53430.581| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.54 r_work: 0.3586 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14287 Z= 0.157 Angle : 0.638 9.507 19567 Z= 0.331 Chirality : 0.043 0.250 2143 Planarity : 0.004 0.042 2279 Dihedral : 18.023 175.247 2515 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.43 % Allowed : 13.38 % Favored : 84.19 % 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: -0.40 (0.22), residues: 1546 helix: 0.38 (0.20), residues: 728 sheet: -0.94 (0.37), residues: 200 loop : -0.66 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 929 TYR 0.021 0.001 TYR A 698 PHE 0.022 0.001 PHE A 596 TRP 0.008 0.001 TRP A 861 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00353 (14287) covalent geometry : angle 0.63808 (19567) hydrogen bonds : bond 0.04023 ( 601) hydrogen bonds : angle 4.66887 ( 1693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.499 Fit side-chains REVERT: A 601 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8977 (ptpt) REVERT: A 799 ARG cc_start: 0.8497 (mtm110) cc_final: 0.7656 (mtm110) REVERT: A 924 ASP cc_start: 0.8680 (m-30) cc_final: 0.8385 (t0) REVERT: A 1173 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 593 GLU cc_start: 0.8373 (pm20) cc_final: 0.8167 (pp20) REVERT: B 739 PHE cc_start: 0.8409 (t80) cc_final: 0.8192 (t80) REVERT: B 966 TYR cc_start: 0.8737 (m-80) cc_final: 0.8415 (m-10) REVERT: B 1048 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: B 1173 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7856 (mp0) outliers start: 33 outliers final: 9 residues processed: 91 average time/residue: 0.6177 time to fit residues: 61.6778 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 800 TYR Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.092038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.075964 restraints weight = 52096.930| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.65 r_work: 0.3487 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14287 Z= 0.245 Angle : 0.710 10.924 19567 Z= 0.371 Chirality : 0.046 0.269 2143 Planarity : 0.005 0.049 2279 Dihedral : 18.311 170.961 2515 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.65 % Allowed : 16.40 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.48 (0.22), residues: 1546 helix: 0.33 (0.20), residues: 714 sheet: -1.18 (0.36), residues: 204 loop : -0.61 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 863 TYR 0.035 0.002 TYR A1028 PHE 0.032 0.002 PHE A1107 TRP 0.009 0.002 TRP A1035 HIS 0.007 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00554 (14287) covalent geometry : angle 0.71033 (19567) hydrogen bonds : bond 0.04558 ( 601) hydrogen bonds : angle 4.89767 ( 1693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8734 (m-80) cc_final: 0.8001 (m-80) REVERT: A 599 TRP cc_start: 0.8652 (t60) cc_final: 0.8351 (t60) REVERT: A 608 ASN cc_start: 0.8955 (t0) cc_final: 0.8643 (t0) REVERT: A 799 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7595 (mtm110) REVERT: A 924 ASP cc_start: 0.8754 (m-30) cc_final: 0.8399 (t0) REVERT: A 1048 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7663 (pmm) REVERT: A 1173 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: B 599 TRP cc_start: 0.8588 (t60) cc_final: 0.8323 (t60) REVERT: B 966 TYR cc_start: 0.8878 (m-80) cc_final: 0.8471 (m-10) REVERT: B 1048 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7500 (mpp) REVERT: B 1173 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7734 (mp0) outliers start: 36 outliers final: 13 residues processed: 98 average time/residue: 0.5591 time to fit residues: 60.4843 Evaluate side-chains 80 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 0.0770 chunk 122 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN B 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.094420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078785 restraints weight = 52874.789| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.53 r_work: 0.3563 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14287 Z= 0.136 Angle : 0.633 11.044 19567 Z= 0.325 Chirality : 0.042 0.225 2143 Planarity : 0.004 0.070 2279 Dihedral : 17.963 175.059 2513 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.65 % Allowed : 18.60 % Favored : 78.75 % 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: -0.19 (0.22), residues: 1546 helix: 0.54 (0.20), residues: 716 sheet: -0.99 (0.37), residues: 204 loop : -0.44 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 428 TYR 0.020 0.001 TYR A 698 PHE 0.016 0.001 PHE A1107 TRP 0.008 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00304 (14287) covalent geometry : angle 0.63266 (19567) hydrogen bonds : bond 0.03815 ( 601) hydrogen bonds : angle 4.69771 ( 1693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8677 (m-80) cc_final: 0.8021 (m-80) REVERT: A 599 TRP cc_start: 0.8644 (t60) cc_final: 0.8373 (t60) REVERT: A 608 ASN cc_start: 0.8952 (t0) cc_final: 0.8626 (t0) REVERT: A 799 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7641 (mtm110) REVERT: A 924 ASP cc_start: 0.8768 (m-30) cc_final: 0.8455 (t0) REVERT: A 966 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: A 993 THR cc_start: 0.9614 (OUTLIER) cc_final: 0.9389 (p) REVERT: A 1173 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: B 599 TRP cc_start: 0.8628 (t60) cc_final: 0.8379 (t60) REVERT: B 846 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8306 (mpp) REVERT: B 966 TYR cc_start: 0.8834 (m-80) cc_final: 0.8414 (m-10) REVERT: B 1048 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7603 (mpp) REVERT: B 1173 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8089 (mt-10) outliers start: 36 outliers final: 10 residues processed: 96 average time/residue: 0.4759 time to fit residues: 51.0576 Evaluate side-chains 78 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 799 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 966 TYR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 10 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.094379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.078720 restraints weight = 52524.426| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.55 r_work: 0.3569 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14287 Z= 0.138 Angle : 0.627 11.682 19567 Z= 0.318 Chirality : 0.042 0.220 2143 Planarity : 0.004 0.038 2279 Dihedral : 17.740 174.319 2513 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.43 % Allowed : 19.19 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.22), residues: 1546 helix: 0.69 (0.20), residues: 716 sheet: -0.88 (0.37), residues: 204 loop : -0.35 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.020 0.001 TYR A 698 PHE 0.019 0.001 PHE B1107 TRP 0.008 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00310 (14287) covalent geometry : angle 0.62691 (19567) hydrogen bonds : bond 0.03629 ( 601) hydrogen bonds : angle 4.53441 ( 1693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8670 (m-80) cc_final: 0.7976 (m-80) REVERT: A 599 TRP cc_start: 0.8646 (t60) cc_final: 0.8373 (t60) REVERT: A 608 ASN cc_start: 0.8963 (t0) cc_final: 0.8637 (t0) REVERT: A 924 ASP cc_start: 0.8796 (m-30) cc_final: 0.8469 (t0) REVERT: A 993 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9388 (p) REVERT: A 1121 CYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6275 (p) REVERT: A 1173 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 599 TRP cc_start: 0.8614 (t60) cc_final: 0.8374 (t60) REVERT: B 846 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8670 (mpp) REVERT: B 848 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.6111 (p90) REVERT: B 966 TYR cc_start: 0.8816 (m-80) cc_final: 0.8385 (m-10) REVERT: B 1048 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7594 (mpp) REVERT: B 1173 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8116 (mt-10) outliers start: 33 outliers final: 12 residues processed: 94 average time/residue: 0.4781 time to fit residues: 50.1270 Evaluate side-chains 84 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1121 CYS Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 864 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.091974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.075987 restraints weight = 52272.152| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.62 r_work: 0.3505 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14287 Z= 0.224 Angle : 0.695 11.981 19567 Z= 0.356 Chirality : 0.045 0.268 2143 Planarity : 0.004 0.039 2279 Dihedral : 17.989 170.273 2513 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 3.01 % Allowed : 18.90 % Favored : 78.09 % 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: -0.19 (0.22), residues: 1546 helix: 0.53 (0.20), residues: 716 sheet: -0.98 (0.38), residues: 204 loop : -0.42 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.022 0.002 TYR A 698 PHE 0.031 0.002 PHE B1107 TRP 0.009 0.001 TRP A 861 HIS 0.006 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00510 (14287) covalent geometry : angle 0.69473 (19567) hydrogen bonds : bond 0.04192 ( 601) hydrogen bonds : angle 4.70395 ( 1693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8681 (m-80) cc_final: 0.7971 (m-80) REVERT: A 599 TRP cc_start: 0.8646 (t60) cc_final: 0.8365 (t60) REVERT: A 608 ASN cc_start: 0.8972 (t0) cc_final: 0.8650 (t0) REVERT: A 993 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9370 (p) REVERT: A 1031 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 1048 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7777 (pmm) REVERT: A 1097 LEU cc_start: 0.6986 (pt) cc_final: 0.5950 (tt) REVERT: A 1173 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: B 599 TRP cc_start: 0.8625 (t60) cc_final: 0.8365 (t60) REVERT: B 846 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8786 (mtp) REVERT: B 848 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.6355 (p90) REVERT: B 966 TYR cc_start: 0.8875 (m-80) cc_final: 0.8463 (m-10) REVERT: B 1173 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8091 (mt-10) outliers start: 41 outliers final: 18 residues processed: 99 average time/residue: 0.4047 time to fit residues: 45.1255 Evaluate side-chains 87 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1121 CYS Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.093588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.077881 restraints weight = 52142.996| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.61 r_work: 0.3546 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14287 Z= 0.148 Angle : 0.660 12.544 19567 Z= 0.334 Chirality : 0.042 0.204 2143 Planarity : 0.004 0.046 2279 Dihedral : 17.837 171.885 2513 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.50 % Allowed : 19.71 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.22), residues: 1546 helix: 0.67 (0.20), residues: 716 sheet: -0.83 (0.37), residues: 212 loop : -0.34 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.020 0.001 TYR A 698 PHE 0.019 0.001 PHE A1107 TRP 0.009 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00335 (14287) covalent geometry : angle 0.66000 (19567) hydrogen bonds : bond 0.03774 ( 601) hydrogen bonds : angle 4.62774 ( 1693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8712 (m-80) cc_final: 0.7998 (m-80) REVERT: A 599 TRP cc_start: 0.8636 (t60) cc_final: 0.8358 (t60) REVERT: A 608 ASN cc_start: 0.8962 (t0) cc_final: 0.8629 (t0) REVERT: A 993 THR cc_start: 0.9609 (OUTLIER) cc_final: 0.9364 (p) REVERT: A 1031 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8595 (mm) REVERT: A 1048 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7762 (pmm) REVERT: A 1097 LEU cc_start: 0.6907 (pt) cc_final: 0.5910 (tt) REVERT: A 1173 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: B 599 TRP cc_start: 0.8600 (t60) cc_final: 0.8330 (t60) REVERT: B 714 MET cc_start: 0.8430 (ptt) cc_final: 0.8214 (ptt) REVERT: B 739 PHE cc_start: 0.8931 (t80) cc_final: 0.8585 (m-80) REVERT: B 846 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8814 (mtp) REVERT: B 848 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6254 (p90) REVERT: B 924 ASP cc_start: 0.8854 (m-30) cc_final: 0.8640 (m-30) REVERT: B 966 TYR cc_start: 0.8847 (m-80) cc_final: 0.8393 (m-10) REVERT: B 1061 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7295 (tp30) REVERT: B 1173 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8169 (mt-10) outliers start: 34 outliers final: 17 residues processed: 100 average time/residue: 0.4197 time to fit residues: 47.0933 Evaluate side-chains 88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.092422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.076337 restraints weight = 52496.529| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.68 r_work: 0.3497 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14287 Z= 0.194 Angle : 0.697 12.726 19567 Z= 0.355 Chirality : 0.044 0.261 2143 Planarity : 0.004 0.042 2279 Dihedral : 17.853 170.120 2513 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 2.43 % Allowed : 20.07 % Favored : 77.50 % 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: -0.11 (0.22), residues: 1546 helix: 0.59 (0.20), residues: 716 sheet: -0.74 (0.37), residues: 208 loop : -0.46 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.022 0.001 TYR A 698 PHE 0.028 0.002 PHE A1107 TRP 0.008 0.001 TRP A 861 HIS 0.005 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00443 (14287) covalent geometry : angle 0.69680 (19567) hydrogen bonds : bond 0.04040 ( 601) hydrogen bonds : angle 4.70425 ( 1693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8760 (m-80) cc_final: 0.8004 (m-80) REVERT: A 467 MET cc_start: 0.7661 (mmm) cc_final: 0.7340 (mtm) REVERT: A 599 TRP cc_start: 0.8599 (t60) cc_final: 0.8307 (t60) REVERT: A 608 ASN cc_start: 0.8967 (t0) cc_final: 0.8648 (t0) REVERT: A 993 THR cc_start: 0.9618 (OUTLIER) cc_final: 0.9332 (p) REVERT: A 1048 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7643 (pmm) REVERT: A 1097 LEU cc_start: 0.7034 (pt) cc_final: 0.5999 (tt) REVERT: A 1173 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: B 599 TRP cc_start: 0.8583 (t60) cc_final: 0.8305 (t60) REVERT: B 846 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8866 (mtm) REVERT: B 848 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6220 (p90) REVERT: B 966 TYR cc_start: 0.8901 (m-80) cc_final: 0.8430 (m-10) REVERT: B 1061 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7192 (tp30) outliers start: 33 outliers final: 18 residues processed: 92 average time/residue: 0.4608 time to fit residues: 47.3362 Evaluate side-chains 85 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 110 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 HIS B 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.093442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.077665 restraints weight = 51917.263| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.70 r_work: 0.3534 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14287 Z= 0.140 Angle : 0.676 13.212 19567 Z= 0.343 Chirality : 0.042 0.227 2143 Planarity : 0.004 0.063 2279 Dihedral : 17.654 171.852 2513 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 1.76 % Allowed : 20.66 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.22), residues: 1546 helix: 0.73 (0.20), residues: 716 sheet: -0.79 (0.37), residues: 212 loop : -0.32 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.020 0.001 TYR A 698 PHE 0.018 0.001 PHE A1107 TRP 0.010 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.00317 (14287) covalent geometry : angle 0.67600 (19567) hydrogen bonds : bond 0.03722 ( 601) hydrogen bonds : angle 4.61850 ( 1693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8790 (m-80) cc_final: 0.8045 (m-80) REVERT: A 467 MET cc_start: 0.7664 (mmm) cc_final: 0.7340 (mtm) REVERT: A 586 MET cc_start: 0.8754 (mmp) cc_final: 0.8535 (tpp) REVERT: A 599 TRP cc_start: 0.8621 (t60) cc_final: 0.8332 (t60) REVERT: A 608 ASN cc_start: 0.8974 (t0) cc_final: 0.8617 (t0) REVERT: A 993 THR cc_start: 0.9583 (OUTLIER) cc_final: 0.9315 (p) REVERT: A 1048 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7649 (pmm) REVERT: A 1173 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: B 599 TRP cc_start: 0.8579 (t60) cc_final: 0.8317 (t60) REVERT: B 714 MET cc_start: 0.8434 (ptt) cc_final: 0.8231 (ptt) REVERT: B 846 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8715 (mtm) REVERT: B 848 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6117 (p90) REVERT: B 966 TYR cc_start: 0.8814 (m-80) cc_final: 0.8341 (m-10) REVERT: B 1048 MET cc_start: 0.8099 (mtm) cc_final: 0.7771 (pmm) REVERT: B 1173 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7998 (mt-10) outliers start: 24 outliers final: 12 residues processed: 82 average time/residue: 0.5203 time to fit residues: 47.2419 Evaluate side-chains 78 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 1 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.093624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.077862 restraints weight = 52405.518| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.71 r_work: 0.3537 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14287 Z= 0.139 Angle : 0.664 13.256 19567 Z= 0.335 Chirality : 0.042 0.212 2143 Planarity : 0.004 0.056 2279 Dihedral : 17.537 171.778 2513 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 1.91 % Allowed : 20.59 % Favored : 77.50 % 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 (0.22), residues: 1546 helix: 0.78 (0.20), residues: 716 sheet: -0.76 (0.38), residues: 204 loop : -0.28 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 929 TYR 0.020 0.001 TYR A 698 PHE 0.019 0.001 PHE A1107 TRP 0.010 0.001 TRP A 820 HIS 0.003 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00315 (14287) covalent geometry : angle 0.66417 (19567) hydrogen bonds : bond 0.03613 ( 601) hydrogen bonds : angle 4.59656 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.88 seconds wall clock time: 67 minutes 8.25 seconds (4028.25 seconds total)