Starting phenix.real_space_refine on Thu Aug 6 06:27:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9w_36117/08_2026/8j9w_36117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9w_36117/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2026/8j9w_36117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2026/8j9w_36117.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2026/8j9w_36117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9w_36117/08_2026/8j9w_36117_neut.cif" } 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-2.2rc3-6140/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: 3.12, per 1000 atoms: 0.23 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: 1.08 Conformation dependent library (CDL) restraints added in 616.9 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: 1.86 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: 2.89 Time building geometry restraints manager: 1.48 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: 440 4.62 - 6.93: 65 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: 8.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.400 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:9.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- 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 : 0.864 11.552 19567 Z= 0.522 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 0.86409 / 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 : 0.425 Fit side-chains 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: 0.6365 time to fit residues: 78.7842 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 : 0.472 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.096519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.080823 restraints weight = 52721.623| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.70 r_work: 0.3604 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14287 Z= 0.172 Angle : 0.693 9.630 19567 Z= 0.370 Chirality : 0.046 0.411 2143 Planarity : 0.004 0.045 2279 Dihedral : 18.854 179.977 2515 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.10 % Allowed : 9.93 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1546 helix: 0.06 (0.19), residues: 718 sheet: -1.00 (0.37), residues: 198 loop : -0.78 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 799 TYR 0.021 0.001 TYR A 698 PHE 0.020 0.001 PHE A1107 TRP 0.010 0.001 TRP A 560 HIS 0.007 0.001 HIS A1192 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (14287) covalent geometry : angle 0.69277 / 0.37 (19567) hydrogen bonds : bond 0.05475 / 3.73 ( 601) hydrogen bonds : angle 5.24727 / 3.62 ( 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 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.419 Fit side-chains REVERT: A 608 ASN cc_start: 0.8912 (t0) cc_final: 0.8648 (t0) REVERT: A 924 ASP cc_start: 0.8633 (m-30) cc_final: 0.8352 (t0) REVERT: A 1172 GLU cc_start: 0.8398 (pm20) cc_final: 0.8193 (pm20) REVERT: B 601 LYS cc_start: 0.9385 (mmpt) cc_final: 0.9149 (pptt) REVERT: B 966 TYR cc_start: 0.8841 (m-80) cc_final: 0.8502 (m-10) REVERT: B 1048 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7653 (mpp) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 0.5452 time to fit residues: 53.2600 Evaluate side-chains 73 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 542 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: 5.9990 chunk 44 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN A1114 ASN B1014 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.094102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.077994 restraints weight = 53555.522| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.72 r_work: 0.3538 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14287 Z= 0.224 Angle : 0.708 9.751 19567 Z= 0.370 Chirality : 0.048 0.465 2143 Planarity : 0.005 0.074 2279 Dihedral : 18.487 173.915 2515 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.57 % Allowed : 13.24 % 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 are not related in a simple way. whole: -0.63 (0.22), residues: 1546 helix: 0.19 (0.19), residues: 726 sheet: -0.97 (0.36), residues: 208 loop : -0.79 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 863 TYR 0.023 0.002 TYR A 698 PHE 0.028 0.002 PHE B1107 TRP 0.008 0.001 TRP A 820 HIS 0.008 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (14287) covalent geometry : angle 0.70819 / 0.37 (19567) hydrogen bonds : bond 0.04898 / 3.33 ( 601) hydrogen bonds : angle 4.93628 / 3.40 ( 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: 35 poor density : 70 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 608 ASN cc_start: 0.8946 (t0) cc_final: 0.8688 (t0) REVERT: A 799 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7205 (mtm-85) REVERT: A 924 ASP cc_start: 0.8695 (m-30) cc_final: 0.8347 (t0) REVERT: A 1041 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 1173 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: B 593 GLU cc_start: 0.8422 (pm20) cc_final: 0.8217 (OUTLIER) REVERT: B 601 LYS cc_start: 0.9378 (mmpt) cc_final: 0.9167 (pptt) REVERT: B 846 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8178 (mpt) REVERT: B 966 TYR cc_start: 0.8896 (m-80) cc_final: 0.8540 (m-10) REVERT: B 1173 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8017 (mt-10) outliers start: 35 outliers final: 14 residues processed: 93 average time/residue: 0.5356 time to fit residues: 55.1664 Evaluate side-chains 80 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1041 GLU 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 845 ILE 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: 8.9990 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: 0.0060 chunk 119 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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 = 0.094548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.078488 restraints weight = 52543.367| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.70 r_work: 0.3549 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14287 Z= 0.167 Angle : 0.647 9.611 19567 Z= 0.341 Chirality : 0.046 0.432 2143 Planarity : 0.004 0.044 2279 Dihedral : 18.341 175.648 2515 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.43 % Allowed : 15.44 % Favored : 82.13 % 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: 0.34 (0.20), residues: 726 sheet: -0.87 (0.36), residues: 208 loop : -0.76 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 799 TYR 0.022 0.001 TYR A 698 PHE 0.021 0.001 PHE B1107 TRP 0.008 0.001 TRP A 820 HIS 0.004 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (14287) covalent geometry : angle 0.64746 / 0.34 (19567) hydrogen bonds : bond 0.04338 / 2.96 ( 601) hydrogen bonds : angle 4.82853 / 3.32 ( 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 103 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8565 (t60) cc_final: 0.8331 (t60) REVERT: A 608 ASN cc_start: 0.8936 (t0) cc_final: 0.8668 (t0) REVERT: A 924 ASP cc_start: 0.8720 (m-30) cc_final: 0.8350 (t0) REVERT: A 993 THR cc_start: 0.9691 (OUTLIER) cc_final: 0.9475 (p) REVERT: A 1048 MET cc_start: 0.7864 (pmm) cc_final: 0.7662 (pmm) REVERT: A 1173 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: B 593 GLU cc_start: 0.8446 (pm20) cc_final: 0.8221 (pp20) REVERT: B 601 LYS cc_start: 0.9385 (mmpt) cc_final: 0.9175 (pptt) REVERT: B 739 PHE cc_start: 0.8884 (t80) cc_final: 0.8611 (m-80) REVERT: B 966 TYR cc_start: 0.8865 (m-80) cc_final: 0.8489 (m-10) REVERT: B 1173 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7950 (mt-10) outliers start: 33 outliers final: 14 residues processed: 97 average time/residue: 0.5016 time to fit residues: 54.5698 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 : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 993 THR 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 542 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 845 ILE 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: 1.9990 chunk 122 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.094892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078916 restraints weight = 52623.618| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.72 r_work: 0.3561 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2027 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= 0.143 Angle : 0.646 10.242 19567 Z= 0.335 Chirality : 0.044 0.410 2143 Planarity : 0.004 0.044 2279 Dihedral : 18.162 176.122 2513 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.35 % Allowed : 16.84 % Favored : 80.81 % 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: -0.35 (0.22), residues: 1546 helix: 0.42 (0.20), residues: 726 sheet: -0.80 (0.36), residues: 208 loop : -0.67 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1039 TYR 0.021 0.001 TYR A 698 PHE 0.019 0.001 PHE B1107 TRP 0.009 0.001 TRP A 861 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14287) covalent geometry : angle 0.64599 / 0.33 (19567) hydrogen bonds : bond 0.04123 / 2.82 ( 601) hydrogen bonds : angle 4.73593 / 3.25 ( 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: 32 poor density : 69 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8700 (m-80) cc_final: 0.8213 (m-80) REVERT: A 599 TRP cc_start: 0.8580 (t60) cc_final: 0.8337 (t60) REVERT: A 608 ASN cc_start: 0.8954 (t0) cc_final: 0.8679 (t0) REVERT: A 924 ASP cc_start: 0.8740 (m-30) cc_final: 0.8345 (t0) REVERT: A 1041 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: A 1173 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: B 593 GLU cc_start: 0.8436 (pm20) cc_final: 0.8223 (pp20) REVERT: B 601 LYS cc_start: 0.9386 (mmpt) cc_final: 0.9176 (pptt) REVERT: B 635 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6917 (ppp) REVERT: B 739 PHE cc_start: 0.8912 (t80) cc_final: 0.8619 (m-80) REVERT: B 848 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6126 (p90) REVERT: B 966 TYR cc_start: 0.8868 (m-80) cc_final: 0.8464 (m-10) REVERT: B 1173 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8024 (mt-10) outliers start: 32 outliers final: 13 residues processed: 93 average time/residue: 0.5283 time to fit residues: 54.8404 Evaluate side-chains 81 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1041 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 10 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 0.0010 chunk 126 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 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 = 0.094230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.078209 restraints weight = 52347.213| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.70 r_work: 0.3550 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14287 Z= 0.168 Angle : 0.651 10.743 19567 Z= 0.340 Chirality : 0.045 0.419 2143 Planarity : 0.004 0.057 2279 Dihedral : 18.124 178.598 2513 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.79 % Allowed : 17.79 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1546 helix: 0.55 (0.20), residues: 714 sheet: -0.79 (0.37), residues: 208 loop : -0.58 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 736 TYR 0.021 0.001 TYR A 698 PHE 0.022 0.001 PHE B1107 TRP 0.008 0.001 TRP A 820 HIS 0.005 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (14287) covalent geometry : angle 0.65137 / 0.34 (19567) hydrogen bonds : bond 0.04138 / 2.82 ( 601) hydrogen bonds : angle 4.72655 / 3.26 ( 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 102 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8702 (m-80) cc_final: 0.8244 (m-80) REVERT: A 599 TRP cc_start: 0.8637 (t60) cc_final: 0.8405 (t60) REVERT: A 608 ASN cc_start: 0.8955 (t0) cc_final: 0.8673 (t0) REVERT: A 924 ASP cc_start: 0.8756 (m-30) cc_final: 0.8357 (t0) REVERT: A 993 THR cc_start: 0.9683 (OUTLIER) cc_final: 0.9465 (p) REVERT: A 1048 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7781 (pmm) REVERT: A 1173 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: B 593 GLU cc_start: 0.8457 (pm20) cc_final: 0.8257 (pp20) REVERT: B 601 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9175 (pptt) REVERT: B 635 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.6933 (ppp) REVERT: B 739 PHE cc_start: 0.8907 (t80) cc_final: 0.8656 (m-80) REVERT: B 848 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6118 (p90) REVERT: B 966 TYR cc_start: 0.8849 (m-80) cc_final: 0.8435 (m-10) REVERT: B 1173 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7729 (mp0) outliers start: 38 outliers final: 19 residues processed: 94 average time/residue: 0.4677 time to fit residues: 49.1674 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 : 0.480 ------------------------------------------------------------------------------- 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 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 966 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 433 MET 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 635 MET Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 845 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 0.0170 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.094959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.079331 restraints weight = 52577.509| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.62 r_work: 0.3578 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14287 Z= 0.132 Angle : 0.643 11.185 19567 Z= 0.332 Chirality : 0.044 0.390 2143 Planarity : 0.004 0.038 2279 Dihedral : 18.017 178.615 2513 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.50 % Allowed : 18.24 % 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: -0.09 (0.22), residues: 1546 helix: 0.53 (0.20), residues: 728 sheet: -0.49 (0.37), residues: 200 loop : -0.46 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 571 TYR 0.021 0.001 TYR A 698 PHE 0.017 0.001 PHE B1107 TRP 0.008 0.001 TRP B 820 HIS 0.002 0.001 HIS B 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14287) covalent geometry : angle 0.64282 / 0.33 (19567) hydrogen bonds : bond 0.03918 / 2.68 ( 601) hydrogen bonds : angle 4.67651 / 3.22 ( 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: 34 poor density : 66 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8655 (m-80) cc_final: 0.8222 (m-80) REVERT: A 599 TRP cc_start: 0.8637 (t60) cc_final: 0.8395 (t60) REVERT: A 608 ASN cc_start: 0.8941 (t0) cc_final: 0.8641 (t0) REVERT: A 924 ASP cc_start: 0.8768 (m-30) cc_final: 0.8378 (t0) REVERT: A 993 THR cc_start: 0.9661 (OUTLIER) cc_final: 0.9448 (p) REVERT: A 1048 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7794 (pmm) REVERT: A 1173 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 593 GLU cc_start: 0.8446 (pm20) cc_final: 0.8240 (pp20) REVERT: B 599 TRP cc_start: 0.8597 (t60) cc_final: 0.8333 (t60) REVERT: B 635 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7015 (ppp) REVERT: B 739 PHE cc_start: 0.8889 (t80) cc_final: 0.8653 (m-80) REVERT: B 966 TYR cc_start: 0.8828 (m-80) cc_final: 0.8423 (m-10) REVERT: B 1061 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7075 (tp30) REVERT: B 1173 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7821 (mp0) outliers start: 34 outliers final: 14 residues processed: 93 average time/residue: 0.4345 time to fit residues: 45.0916 Evaluate side-chains 80 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 433 MET 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 635 MET Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1064 ILE 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: 0.5980 chunk 146 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.4063 r_free = 0.4063 target = 0.094950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079174 restraints weight = 51918.949| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.69 r_work: 0.3567 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14287 Z= 0.138 Angle : 0.656 11.602 19567 Z= 0.340 Chirality : 0.044 0.388 2143 Planarity : 0.004 0.039 2279 Dihedral : 17.958 179.664 2513 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 2.21 % Allowed : 18.82 % Favored : 78.97 % 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: -0.09 (0.22), residues: 1546 helix: 0.52 (0.20), residues: 730 sheet: -0.42 (0.38), residues: 200 loop : -0.48 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 929 TYR 0.020 0.001 TYR A 698 PHE 0.018 0.001 PHE B1107 TRP 0.011 0.001 TRP A1170 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (14287) covalent geometry : angle 0.65589 / 0.34 (19567) hydrogen bonds : bond 0.03898 / 2.66 ( 601) hydrogen bonds : angle 4.66474 / 3.21 ( 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 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8693 (m-80) cc_final: 0.8220 (m-80) REVERT: A 599 TRP cc_start: 0.8613 (t60) cc_final: 0.8355 (t60) REVERT: A 608 ASN cc_start: 0.8936 (t0) cc_final: 0.8635 (t0) REVERT: A 924 ASP cc_start: 0.8807 (m-30) cc_final: 0.8380 (t0) REVERT: A 993 THR cc_start: 0.9676 (OUTLIER) cc_final: 0.9441 (p) REVERT: A 1031 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 1048 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7721 (pmm) REVERT: A 1173 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: B 635 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6995 (ppp) REVERT: B 739 PHE cc_start: 0.8917 (t80) cc_final: 0.8643 (m-80) REVERT: B 848 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6039 (p90) REVERT: B 966 TYR cc_start: 0.8833 (m-80) cc_final: 0.8410 (m-10) REVERT: B 1061 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7077 (tp30) REVERT: B 1173 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8253 (mt-10) outliers start: 30 outliers final: 15 residues processed: 90 average time/residue: 0.4504 time to fit residues: 45.3807 Evaluate side-chains 85 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 433 MET 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 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 1064 ILE 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: 0.0370 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.094712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.079050 restraints weight = 52948.880| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.54 r_work: 0.3574 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2458 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= 0.152 Angle : 0.675 12.133 19567 Z= 0.350 Chirality : 0.045 0.389 2143 Planarity : 0.004 0.039 2279 Dihedral : 17.926 178.177 2513 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.06 % Allowed : 19.78 % Favored : 78.16 % 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: -0.07 (0.22), residues: 1546 helix: 0.51 (0.20), residues: 728 sheet: -0.40 (0.38), residues: 200 loop : -0.44 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 956 TYR 0.021 0.001 TYR A 698 PHE 0.020 0.001 PHE B1107 TRP 0.026 0.001 TRP B 599 HIS 0.003 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14287) covalent geometry : angle 0.67490 / 0.35 (19567) hydrogen bonds : bond 0.04018 / 2.73 ( 601) hydrogen bonds : angle 4.71600 / 3.24 ( 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 92 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8627 (m-80) cc_final: 0.8197 (m-80) REVERT: A 599 TRP cc_start: 0.8608 (t60) cc_final: 0.8364 (t60) REVERT: A 608 ASN cc_start: 0.8923 (t0) cc_final: 0.8613 (t0) REVERT: A 848 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.6216 (p90) REVERT: A 924 ASP cc_start: 0.8790 (m-30) cc_final: 0.8425 (t0) REVERT: A 993 THR cc_start: 0.9648 (OUTLIER) cc_final: 0.9429 (p) REVERT: A 1031 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8527 (mm) REVERT: A 1048 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7764 (pmm) REVERT: A 1173 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: B 635 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7110 (ppp) REVERT: B 739 PHE cc_start: 0.8892 (t80) cc_final: 0.8630 (m-80) REVERT: B 848 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.6160 (p90) REVERT: B 966 TYR cc_start: 0.8778 (m-80) cc_final: 0.8374 (m-10) REVERT: B 1061 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7100 (tp30) REVERT: B 1173 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7860 (mp0) outliers start: 28 outliers final: 15 residues processed: 87 average time/residue: 0.4566 time to fit residues: 44.5722 Evaluate side-chains 86 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 110 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 0.0000 chunk 96 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.4057 r_free = 0.4057 target = 0.093812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.078161 restraints weight = 52565.581| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.56 r_work: 0.3552 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2605 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= 0.174 Angle : 0.701 13.740 19567 Z= 0.362 Chirality : 0.046 0.398 2143 Planarity : 0.004 0.040 2279 Dihedral : 17.945 175.934 2513 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 1.91 % Allowed : 19.85 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.22), residues: 1546 helix: 0.46 (0.20), residues: 728 sheet: -0.60 (0.38), residues: 196 loop : -0.43 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.021 0.001 TYR A 698 PHE 0.023 0.001 PHE B1107 TRP 0.032 0.001 TRP B 599 HIS 0.005 0.001 HIS B1099 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14287) covalent geometry : angle 0.70075 / 0.36 (19567) hydrogen bonds : bond 0.04066 / 2.78 ( 601) hydrogen bonds : angle 4.72761 / 3.26 ( 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 88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8685 (m-80) cc_final: 0.8209 (m-80) REVERT: A 599 TRP cc_start: 0.8592 (t60) cc_final: 0.8326 (t60) REVERT: A 608 ASN cc_start: 0.8928 (t0) cc_final: 0.8623 (t0) REVERT: A 848 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.6172 (p90) REVERT: A 966 TYR cc_start: 0.8675 (m-10) cc_final: 0.8450 (m-10) REVERT: A 993 THR cc_start: 0.9657 (OUTLIER) cc_final: 0.9420 (p) REVERT: A 1031 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8575 (mm) REVERT: A 1048 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7743 (pmm) REVERT: A 1173 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: B 593 GLU cc_start: 0.8424 (pm20) cc_final: 0.8117 (OUTLIER) REVERT: B 635 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.6982 (ppp) REVERT: B 714 MET cc_start: 0.8492 (ptt) cc_final: 0.8279 (ptt) REVERT: B 739 PHE cc_start: 0.8963 (t80) cc_final: 0.8651 (m-80) REVERT: B 848 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.6212 (p90) REVERT: B 966 TYR cc_start: 0.8807 (m-80) cc_final: 0.8386 (m-10) REVERT: B 1061 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7070 (tp30) REVERT: B 1173 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7804 (mp0) outliers start: 26 outliers final: 15 residues processed: 84 average time/residue: 0.4442 time to fit residues: 41.6944 Evaluate side-chains 82 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 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 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 1 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.4076 r_free = 0.4076 target = 0.094892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079323 restraints weight = 52899.305| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.54 r_work: 0.3583 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14287 Z= 0.136 Angle : 0.685 12.514 19567 Z= 0.352 Chirality : 0.044 0.369 2143 Planarity : 0.004 0.041 2279 Dihedral : 17.840 176.610 2513 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 1.76 % Allowed : 20.15 % 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 are not related in a simple way. whole: -0.08 (0.22), residues: 1546 helix: 0.49 (0.20), residues: 728 sheet: -0.57 (0.38), residues: 196 loop : -0.37 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.020 0.001 TYR A 698 PHE 0.017 0.001 PHE B1107 TRP 0.033 0.001 TRP B 599 HIS 0.002 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (14287) covalent geometry : angle 0.68511 / 0.35 (19567) hydrogen bonds : bond 0.03934 / 2.69 ( 601) hydrogen bonds : angle 4.72647 / 3.25 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.07 seconds wall clock time: 65 minutes 55.76 seconds (3955.76 seconds total)