Starting phenix.real_space_refine on Fri Jul 3 11:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9w_36117/07_2026/8j9w_36117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9w_36117/07_2026/8j9w_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_36117/07_2026/8j9w_36117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2026/8j9w_36117_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2026/8j9w_36117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2026/8j9w_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-dev-6108/lib/python3.11/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: 2.37, per 1000 atoms: 0.17 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: 1.11 Conformation dependent library (CDL) restraints added in 508.1 milliseconds 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: 1.23 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: 2.15 Time building geometry restraints manager: 1.45 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=" C3' DC C 6 " pdb=" C2' DC C 6 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+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 ... (remaining 14282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 19032 2.31 - 4.62: 441 4.62 - 6.93: 64 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: 1833 0.074 - 0.148: 278 0.148 - 0.222: 24 0.222 - 0.296: 5 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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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= 0.330 Angle : 0.863 11.552 19567 Z= 0.520 Chirality : 0.054 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 are 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/Z covalent geometry : bond 0.00493 / 0.33 (14287) covalent geometry : angle 0.86307 / 0.52 (19567) hydrogen bonds : bond 0.16105 / 10.60 ( 601) hydrogen bonds : angle 6.77115 / 4.77 ( 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 : 0.362 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: 0.6085 time to fit residues: 75.4638 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 : 0.459 ------------------------------------------------------------------------------- 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... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS A1014 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN B1114 ASN B1186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.096510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.080981 restraints weight = 52978.190| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.66 r_work: 0.3604 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1052 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= 0.174 Angle : 0.693 9.619 19567 Z= 0.371 Chirality : 0.046 0.399 2143 Planarity : 0.004 0.046 2279 Dihedral : 18.895 178.844 2515 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.03 % Allowed : 9.85 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.21), residues: 1546 helix: 0.05 (0.19), residues: 716 sheet: -0.96 (0.36), residues: 200 loop : -0.77 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 863 TYR 0.021 0.001 TYR A 698 PHE 0.020 0.001 PHE B1107 TRP 0.010 0.001 TRP A 560 HIS 0.008 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (14287) covalent geometry : angle 0.69332 / 0.37 (19567) hydrogen bonds : bond 0.05682 / 3.87 ( 601) hydrogen bonds : angle 5.27418 / 3.65 ( 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 91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 608 ASN cc_start: 0.8898 (t0) cc_final: 0.8633 (t0) REVERT: A 924 ASP cc_start: 0.8628 (m-30) cc_final: 0.8357 (t0) REVERT: A 1048 MET cc_start: 0.7785 (pmm) cc_final: 0.7517 (pmm) REVERT: A 1172 GLU cc_start: 0.8406 (pm20) cc_final: 0.8183 (pm20) REVERT: B 601 LYS cc_start: 0.9388 (mmpt) cc_final: 0.9155 (pptt) REVERT: B 966 TYR cc_start: 0.8858 (m-80) cc_final: 0.8495 (m-10) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 0.5259 time to fit residues: 48.8846 Evaluate side-chains 74 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 120 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.096077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.080163 restraints weight = 53174.955| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.73 r_work: 0.3590 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14287 Z= 0.158 Angle : 0.656 10.278 19567 Z= 0.344 Chirality : 0.045 0.390 2143 Planarity : 0.004 0.058 2279 Dihedral : 18.458 177.583 2515 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.28 % Allowed : 12.21 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1546 helix: 0.28 (0.20), residues: 720 sheet: -0.90 (0.36), residues: 200 loop : -0.66 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 863 TYR 0.021 0.001 TYR A 698 PHE 0.020 0.001 PHE B1107 TRP 0.009 0.001 TRP B 560 HIS 0.004 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (14287) covalent geometry : angle 0.65557 / 0.34 (19567) hydrogen bonds : bond 0.04622 / 3.16 ( 601) hydrogen bonds : angle 4.91480 / 3.37 ( 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 105 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 924 ASP cc_start: 0.8660 (m-30) cc_final: 0.8338 (t0) REVERT: A 1173 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 593 GLU cc_start: 0.8393 (pm20) cc_final: 0.8169 (OUTLIER) REVERT: B 601 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9167 (pptt) REVERT: B 846 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8167 (mpt) REVERT: B 966 TYR cc_start: 0.8877 (m-80) cc_final: 0.8540 (m-10) REVERT: B 1173 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7979 (mt-10) outliers start: 31 outliers final: 9 residues processed: 90 average time/residue: 0.5600 time to fit residues: 55.7811 Evaluate side-chains 75 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1172 GLU 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 846 MET Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1121 CYS 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: 9.9990 chunk 140 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 864 GLN A1014 ASN B1014 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.093053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.076810 restraints weight = 52620.834| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.70 r_work: 0.3504 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14287 Z= 0.246 Angle : 0.720 9.960 19567 Z= 0.380 Chirality : 0.049 0.465 2143 Planarity : 0.005 0.059 2279 Dihedral : 18.423 175.223 2515 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.24 % Allowed : 14.78 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1546 helix: 0.26 (0.19), residues: 726 sheet: -0.98 (0.37), residues: 204 loop : -0.83 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 929 TYR 0.027 0.002 TYR A1028 PHE 0.032 0.002 PHE B1107 TRP 0.008 0.002 TRP A 861 HIS 0.010 0.002 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (14287) covalent geometry : angle 0.72018 / 0.38 (19567) hydrogen bonds : bond 0.04942 / 3.35 ( 601) hydrogen bonds : angle 4.90194 / 3.38 ( 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 116 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8575 (t60) cc_final: 0.8332 (t60) REVERT: A 608 ASN cc_start: 0.8954 (t0) cc_final: 0.8696 (t0) REVERT: A 799 ARG cc_start: 0.8499 (mtm110) cc_final: 0.7523 (mtm110) REVERT: A 846 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8170 (mmm) REVERT: A 924 ASP cc_start: 0.8736 (m-30) cc_final: 0.8371 (t0) REVERT: A 993 THR cc_start: 0.9706 (OUTLIER) cc_final: 0.9478 (p) REVERT: A 1173 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: B 467 MET cc_start: 0.7697 (tpp) cc_final: 0.7457 (mtm) REVERT: B 593 GLU cc_start: 0.8420 (pm20) cc_final: 0.8132 (pp20) REVERT: B 601 LYS cc_start: 0.9387 (mmpt) cc_final: 0.9182 (pptt) REVERT: B 846 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8176 (mpt) REVERT: B 966 TYR cc_start: 0.8897 (m-80) cc_final: 0.8524 (m-10) REVERT: B 1173 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8029 (mt-10) outliers start: 44 outliers final: 15 residues processed: 106 average time/residue: 0.5174 time to fit residues: 60.9397 Evaluate side-chains 81 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 MET 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 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 993 THR 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 840 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.094260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.078165 restraints weight = 52571.486| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.69 r_work: 0.3541 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14287 Z= 0.153 Angle : 0.657 10.409 19567 Z= 0.341 Chirality : 0.045 0.405 2143 Planarity : 0.004 0.057 2279 Dihedral : 18.259 175.875 2513 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.43 % Allowed : 16.84 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.22), residues: 1546 helix: 0.46 (0.20), residues: 714 sheet: -0.88 (0.37), residues: 204 loop : -0.66 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 799 TYR 0.022 0.001 TYR A 698 PHE 0.020 0.001 PHE B1107 TRP 0.008 0.001 TRP A 861 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (14287) covalent geometry : angle 0.65740 / 0.34 (19567) hydrogen bonds : bond 0.04196 / 2.86 ( 601) hydrogen bonds : angle 4.74916 / 3.26 ( 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 101 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8572 (t60) cc_final: 0.8331 (t60) REVERT: A 608 ASN cc_start: 0.8951 (t0) cc_final: 0.8681 (t0) REVERT: A 635 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7248 (ppp) REVERT: A 799 ARG cc_start: 0.8434 (mtm110) cc_final: 0.7523 (mtm110) REVERT: A 848 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6122 (p90) REVERT: A 924 ASP cc_start: 0.8746 (m-30) cc_final: 0.8356 (t0) REVERT: A 1048 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7709 (pmm) REVERT: A 1097 LEU cc_start: 0.6912 (pt) cc_final: 0.5824 (tt) REVERT: A 1173 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 467 MET cc_start: 0.7527 (tpp) cc_final: 0.7283 (mtm) REVERT: B 593 GLU cc_start: 0.8492 (pm20) cc_final: 0.8279 (pp20) REVERT: B 601 LYS cc_start: 0.9383 (mmpt) cc_final: 0.9180 (pptt) REVERT: B 739 PHE cc_start: 0.8878 (t80) cc_final: 0.8548 (m-80) REVERT: B 966 TYR cc_start: 0.8887 (m-80) cc_final: 0.8498 (m-10) REVERT: B 1173 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7729 (mp0) outliers start: 33 outliers final: 12 residues processed: 92 average time/residue: 0.5162 time to fit residues: 53.2344 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 635 MET 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 1048 MET Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1172 GLU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1121 CYS 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: 2.9990 chunk 157 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.093062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.076881 restraints weight = 52140.110| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.67 r_work: 0.3509 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14287 Z= 0.212 Angle : 0.681 10.789 19567 Z= 0.356 Chirality : 0.046 0.431 2143 Planarity : 0.004 0.043 2279 Dihedral : 18.280 176.835 2513 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.01 % Allowed : 17.72 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1546 helix: 0.34 (0.19), residues: 726 sheet: -0.71 (0.37), residues: 200 loop : -0.65 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 736 TYR 0.025 0.002 TYR A1028 PHE 0.028 0.002 PHE A1107 TRP 0.008 0.001 TRP B1170 HIS 0.007 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (14287) covalent geometry : angle 0.68143 / 0.36 (19567) hydrogen bonds : bond 0.04445 / 3.02 ( 601) hydrogen bonds : angle 4.80436 / 3.31 ( 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 106 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8726 (m-80) cc_final: 0.8047 (m-80) REVERT: A 599 TRP cc_start: 0.8613 (t60) cc_final: 0.8355 (t60) REVERT: A 608 ASN cc_start: 0.8956 (t0) cc_final: 0.8690 (t0) REVERT: A 635 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7236 (ppp) REVERT: A 799 ARG cc_start: 0.8361 (mtm110) cc_final: 0.7523 (mtm110) REVERT: A 924 ASP cc_start: 0.8745 (m-30) cc_final: 0.8360 (t0) REVERT: A 993 THR cc_start: 0.9690 (OUTLIER) cc_final: 0.9455 (p) REVERT: A 1048 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (pmm) REVERT: A 1097 LEU cc_start: 0.7066 (pt) cc_final: 0.5973 (tt) REVERT: A 1173 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: B 467 MET cc_start: 0.7610 (tpp) cc_final: 0.7388 (mtm) REVERT: B 593 GLU cc_start: 0.8514 (pm20) cc_final: 0.8299 (pp20) REVERT: B 601 LYS cc_start: 0.9383 (mmpt) cc_final: 0.9179 (pptt) REVERT: B 739 PHE cc_start: 0.8954 (t80) cc_final: 0.8584 (m-80) REVERT: B 846 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: B 848 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6328 (p90) REVERT: B 966 TYR cc_start: 0.8913 (m-80) cc_final: 0.8490 (m-10) REVERT: B 1061 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7044 (tp30) REVERT: B 1173 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7776 (mp0) outliers start: 41 outliers final: 18 residues processed: 99 average time/residue: 0.4754 time to fit residues: 52.9706 Evaluate side-chains 85 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE 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 635 MET 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 993 THR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1172 GLU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 840 VAL 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 1121 CYS Chi-restraints excluded: chain B residue 1123 THR 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: 3.9990 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.094022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.078049 restraints weight = 52226.707| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.70 r_work: 0.3549 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14287 Z= 0.148 Angle : 0.655 11.319 19567 Z= 0.337 Chirality : 0.044 0.391 2143 Planarity : 0.004 0.039 2279 Dihedral : 18.202 176.484 2513 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 2.43 % Allowed : 19.12 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1546 helix: 0.42 (0.20), residues: 726 sheet: -0.60 (0.37), residues: 200 loop : -0.52 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.022 0.001 TYR A 698 PHE 0.020 0.001 PHE B1107 TRP 0.008 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (14287) covalent geometry : angle 0.65491 / 0.34 (19567) hydrogen bonds : bond 0.04071 / 2.78 ( 601) hydrogen bonds : angle 4.71610 / 3.24 ( 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 100 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8723 (m-80) cc_final: 0.8058 (m-80) REVERT: A 599 TRP cc_start: 0.8618 (t60) cc_final: 0.8365 (t60) REVERT: A 608 ASN cc_start: 0.8937 (t0) cc_final: 0.8652 (t0) REVERT: A 799 ARG cc_start: 0.8387 (mtm110) cc_final: 0.7594 (mtm110) REVERT: A 848 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6127 (p90) REVERT: A 924 ASP cc_start: 0.8782 (m-30) cc_final: 0.8400 (t0) REVERT: A 993 THR cc_start: 0.9673 (OUTLIER) cc_final: 0.9426 (p) REVERT: A 1031 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8565 (mm) REVERT: A 1048 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7723 (pmm) REVERT: A 1097 LEU cc_start: 0.6988 (pt) cc_final: 0.5922 (tt) REVERT: A 1173 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: B 599 TRP cc_start: 0.8577 (t60) cc_final: 0.8324 (t60) REVERT: B 739 PHE cc_start: 0.8934 (t80) cc_final: 0.8612 (m-80) REVERT: B 848 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.6278 (p90) REVERT: B 966 TYR cc_start: 0.8876 (m-80) cc_final: 0.8443 (m-10) REVERT: B 1061 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7056 (tp30) REVERT: B 1173 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7783 (mp0) outliers start: 33 outliers final: 13 residues processed: 96 average time/residue: 0.5032 time to fit residues: 53.8743 Evaluate side-chains 84 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 569 VAL 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 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 1172 GLU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 840 VAL 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: 1.9990 chunk 146 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.094213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.078404 restraints weight = 51763.733| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.65 r_work: 0.3546 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14287 Z= 0.141 Angle : 0.654 11.643 19567 Z= 0.338 Chirality : 0.044 0.379 2143 Planarity : 0.004 0.040 2279 Dihedral : 18.098 177.217 2513 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 2.35 % Allowed : 19.26 % 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 are not related in a simple way. whole: -0.13 (0.22), residues: 1546 helix: 0.47 (0.20), residues: 728 sheet: -0.51 (0.37), residues: 200 loop : -0.45 (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 0.018 0.001 PHE B1107 TRP 0.008 0.001 TRP B 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14287) covalent geometry : angle 0.65398 / 0.34 (19567) hydrogen bonds : bond 0.03958 / 2.71 ( 601) hydrogen bonds : angle 4.68078 / 3.22 ( 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 100 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8732 (m-80) cc_final: 0.8064 (m-80) REVERT: A 599 TRP cc_start: 0.8614 (t60) cc_final: 0.8375 (t60) REVERT: A 608 ASN cc_start: 0.8935 (t0) cc_final: 0.8641 (t0) REVERT: A 799 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7544 (mtm110) REVERT: A 924 ASP cc_start: 0.8794 (m-30) cc_final: 0.8412 (t0) REVERT: A 993 THR cc_start: 0.9663 (OUTLIER) cc_final: 0.9416 (p) REVERT: A 1031 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 1048 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7658 (pmm) REVERT: A 1097 LEU cc_start: 0.6975 (pt) cc_final: 0.5934 (tt) REVERT: A 1173 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: B 599 TRP cc_start: 0.8540 (t60) cc_final: 0.8316 (t60) REVERT: B 635 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6904 (ppp) REVERT: B 714 MET cc_start: 0.8484 (ptt) cc_final: 0.8274 (ptt) REVERT: B 739 PHE cc_start: 0.8925 (t80) cc_final: 0.8599 (m-80) REVERT: B 848 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.6226 (p90) REVERT: B 966 TYR cc_start: 0.8853 (m-80) cc_final: 0.8442 (m-10) REVERT: B 1061 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6960 (tp30) REVERT: B 1173 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7772 (mp0) outliers start: 32 outliers final: 13 residues processed: 96 average time/residue: 0.4731 time to fit residues: 51.0458 Evaluate side-chains 86 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 569 VAL 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 966 TYR 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 542 LEU Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 840 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.093846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.077895 restraints weight = 52446.391| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.70 r_work: 0.3536 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14287 Z= 0.167 Angle : 0.681 12.086 19567 Z= 0.352 Chirality : 0.045 0.391 2143 Planarity : 0.004 0.040 2279 Dihedral : 18.128 179.071 2513 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 1.91 % Allowed : 20.22 % Favored : 77.87 % 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 are not related in a simple way. whole: -0.15 (0.22), residues: 1546 helix: 0.45 (0.20), residues: 728 sheet: -0.55 (0.37), residues: 200 loop : -0.44 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.021 0.001 TYR A 698 PHE 0.022 0.001 PHE B1107 TRP 0.011 0.001 TRP A1170 HIS 0.004 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (14287) covalent geometry : angle 0.68129 / 0.35 (19567) hydrogen bonds : bond 0.04108 / 2.78 ( 601) hydrogen bonds : angle 4.74517 / 3.25 ( 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 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8759 (m-80) cc_final: 0.8081 (m-80) REVERT: A 599 TRP cc_start: 0.8624 (t60) cc_final: 0.8367 (t60) REVERT: A 608 ASN cc_start: 0.8934 (t0) cc_final: 0.8639 (t0) REVERT: A 799 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7511 (mtm110) REVERT: A 924 ASP cc_start: 0.8808 (m-30) cc_final: 0.8416 (t0) REVERT: A 993 THR cc_start: 0.9664 (OUTLIER) cc_final: 0.9408 (p) REVERT: A 1031 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 1048 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7701 (pmm) REVERT: A 1097 LEU cc_start: 0.7017 (pt) cc_final: 0.5973 (tt) REVERT: A 1173 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: B 599 TRP cc_start: 0.8546 (t60) cc_final: 0.8311 (t60) REVERT: B 635 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6907 (ppp) REVERT: B 739 PHE cc_start: 0.8968 (t80) cc_final: 0.8619 (m-80) REVERT: B 848 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.6192 (p90) REVERT: B 966 TYR cc_start: 0.8864 (m-80) cc_final: 0.8452 (m-10) REVERT: B 1061 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7006 (tp30) REVERT: B 1173 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7810 (mp0) outliers start: 26 outliers final: 13 residues processed: 89 average time/residue: 0.5203 time to fit residues: 51.6164 Evaluate side-chains 89 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 840 VAL 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 542 LEU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 840 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 110 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.092248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.076129 restraints weight = 52162.087| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.66 r_work: 0.3502 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14287 Z= 0.244 Angle : 0.766 15.844 19567 Z= 0.395 Chirality : 0.048 0.428 2143 Planarity : 0.005 0.042 2279 Dihedral : 18.274 177.855 2513 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.76 % Rotamer: Outliers : 1.84 % Allowed : 20.44 % Favored : 77.72 % 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 are not related in a simple way. whole: -0.36 (0.22), residues: 1546 helix: 0.32 (0.19), residues: 726 sheet: -0.71 (0.38), residues: 192 loop : -0.59 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1039 TYR 0.022 0.002 TYR A 698 PHE 0.033 0.002 PHE B1107 TRP 0.008 0.001 TRP A 861 HIS 0.008 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (14287) covalent geometry : angle 0.76580 / 0.40 (19567) hydrogen bonds : bond 0.04578 / 3.11 ( 601) hydrogen bonds : angle 4.85069 / 3.34 ( 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 89 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8763 (m-80) cc_final: 0.8091 (m-80) REVERT: A 599 TRP cc_start: 0.8661 (t60) cc_final: 0.8389 (t60) REVERT: A 608 ASN cc_start: 0.8921 (t0) cc_final: 0.8634 (t0) REVERT: A 799 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7457 (mtm110) REVERT: A 848 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.6467 (p90) REVERT: A 993 THR cc_start: 0.9658 (OUTLIER) cc_final: 0.9400 (p) REVERT: A 1048 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7690 (pmm) REVERT: A 1097 LEU cc_start: 0.7144 (pt) cc_final: 0.6065 (tt) REVERT: B 599 TRP cc_start: 0.8594 (t60) cc_final: 0.8374 (t60) REVERT: B 635 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.6912 (ppp) REVERT: B 739 PHE cc_start: 0.9021 (t80) cc_final: 0.8732 (t80) REVERT: B 848 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6315 (p90) REVERT: B 966 TYR cc_start: 0.8874 (m-80) cc_final: 0.8451 (m-10) REVERT: B 1061 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7122 (tp30) REVERT: B 1173 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7842 (mp0) outliers start: 25 outliers final: 15 residues processed: 85 average time/residue: 0.5273 time to fit residues: 49.8514 Evaluate side-chains 84 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 993 THR 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 542 LEU Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1121 CYS 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: 1.9990 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.093549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.077734 restraints weight = 52284.161| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.62 r_work: 0.3543 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2773 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= 0.150 Angle : 0.703 12.526 19567 Z= 0.360 Chirality : 0.045 0.376 2143 Planarity : 0.004 0.041 2279 Dihedral : 18.143 179.501 2513 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 1.84 % Allowed : 20.51 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1546 helix: 0.44 (0.20), residues: 728 sheet: -0.74 (0.38), residues: 196 loop : -0.42 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.021 0.001 TYR A 698 PHE 0.020 0.001 PHE B1107 TRP 0.009 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (14287) covalent geometry : angle 0.70333 / 0.36 (19567) hydrogen bonds : bond 0.04097 / 2.79 ( 601) hydrogen bonds : angle 4.78774 / 3.28 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3784.81 seconds wall clock time: 65 minutes 40.03 seconds (3940.03 seconds total)