Starting phenix.real_space_refine on Fri Aug 1 00:07:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9w_36117/07_2025/8j9w_36117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9w_36117/07_2025/8j9w_36117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2025/8j9w_36117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2025/8j9w_36117.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2025/8j9w_36117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9w_36117/07_2025/8j9w_36117_neut.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.20, per 1000 atoms: 0.74 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: 3.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.89 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: 5.63 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2121 1.31 - 1.44: 4227 1.44 - 1.56: 7739 1.56 - 1.68: 112 1.68 - 1.81: 88 Bond restraints: 14287 Sorted by residual: bond pdb=" N VAL B 941 " pdb=" CA VAL B 941 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.94e+01 bond pdb=" CA TRP A1189 " pdb=" C TRP A1189 " ideal model delta sigma weight residual 1.525 1.457 0.068 1.63e-02 3.76e+03 1.72e+01 bond pdb=" C CYS B 545 " pdb=" O CYS B 545 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" CA LEU B 542 " pdb=" C LEU B 542 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" C LEU B 542 " pdb=" O LEU B 542 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.18e-02 7.18e+03 1.28e+01 ... (remaining 14282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 19079 2.31 - 4.62: 395 4.62 - 6.93: 63 6.93 - 9.24: 23 9.24 - 11.55: 7 Bond angle restraints: 19567 Sorted by residual: angle pdb=" N ARG B 940 " pdb=" CA ARG B 940 " pdb=" C ARG B 940 " ideal model delta sigma weight residual 111.52 120.84 -9.32 1.40e+00 5.10e-01 4.43e+01 angle pdb=" C LEU A1047 " pdb=" N MET A1048 " pdb=" CA MET A1048 " ideal model delta sigma weight residual 121.14 109.59 11.55 1.75e+00 3.27e-01 4.36e+01 angle pdb=" N CYS B 545 " pdb=" CA CYS B 545 " pdb=" C CYS B 545 " ideal model delta sigma weight residual 109.46 99.17 10.29 1.66e+00 3.63e-01 3.84e+01 angle pdb=" N GLU B1041 " pdb=" CA GLU B1041 " pdb=" CB GLU B1041 " ideal model delta sigma weight residual 110.39 119.34 -8.95 1.66e+00 3.63e-01 2.91e+01 angle pdb=" N GLU A1041 " pdb=" CA GLU A1041 " pdb=" CB GLU A1041 " ideal model delta sigma weight residual 110.39 119.32 -8.93 1.66e+00 3.63e-01 2.89e+01 ... (remaining 19562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 8170 35.78 - 71.56: 330 71.56 - 107.34: 17 107.34 - 143.12: 6 143.12 - 178.90: 2 Dihedral angle restraints: 8525 sinusoidal: 3981 harmonic: 4544 Sorted by residual: dihedral pdb=" CA PRO A 938 " pdb=" C PRO A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta harmonic sigma weight residual -180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" N HIS A1192 " pdb=" C HIS A1192 " pdb=" CA HIS A1192 " pdb=" CB HIS A1192 " ideal model delta harmonic sigma weight residual 122.80 133.62 -10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA VAL A 941 " pdb=" C VAL A 941 " pdb=" N PRO A 942 " pdb=" CA PRO A 942 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1873 0.074 - 0.148: 239 0.148 - 0.222: 25 0.222 - 0.296: 3 0.296 - 0.370: 3 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA HIS A1192 " pdb=" N HIS A1192 " pdb=" C HIS A1192 " pdb=" CB HIS A1192 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C9 EVP D 101 " pdb=" C10 EVP D 101 " pdb=" C6 EVP D 101 " pdb=" C8 EVP D 101 " both_signs ideal model delta sigma weight residual False 2.49 2.83 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ARG B 940 " pdb=" N ARG B 940 " pdb=" C ARG B 940 " pdb=" CB ARG B 940 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2140 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1190 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS A1190 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS A1190 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A1191 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1044 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" CD GLN A1044 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A1044 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN A1044 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1169 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C VAL B1169 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B1169 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B1170 " -0.014 2.00e-02 2.50e+03 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 622 2.72 - 3.26: 13561 3.26 - 3.81: 24019 3.81 - 4.35: 29180 4.35 - 4.90: 47198 Nonbonded interactions: 114580 Sorted by model distance: nonbonded pdb=" OD2 ASP B 541 " pdb="MG MG B1201 " model vdw 2.175 2.170 nonbonded pdb=" OD2 ASP A 541 " pdb="MG MG A1201 " model vdw 2.202 2.170 nonbonded pdb=" O PRO A1095 " pdb=" OH TYR A1124 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 580 " pdb=" OE1 GLU B 624 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 751 " pdb=" OP2 DA E 12 " model vdw 2.286 3.040 ... (remaining 114575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 12 or (resid 13 and (name P or name OP1 or name \ OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' or n \ ame C2' or name C1')))) selection = chain 'E' } ncs_group { reference = (chain 'D' and resid 1 through 17) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.420 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.680 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14287 Z= 0.241 Angle : 0.839 11.552 19567 Z= 0.454 Chirality : 0.052 0.370 2143 Planarity : 0.006 0.084 2279 Dihedral : 18.058 178.896 5613 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 560 HIS 0.004 0.001 HIS B 680 PHE 0.015 0.002 PHE A1107 TYR 0.031 0.002 TYR B1067 ARG 0.011 0.001 ARG A 863 Details of bonding type rmsd hydrogen bonds : bond 0.16105 ( 601) hydrogen bonds : angle 6.77115 ( 1693) covalent geometry : bond 0.00456 (14287) covalent geometry : angle 0.83888 (19567) *********************** 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 : 1.525 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: 1.4852 time to fit residues: 184.6521 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 : 1.504 ------------------------------------------------------------------------------- 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 133 optimal weight: 0.2980 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS A1014 ASN B 752 HIS B 804 GLN B1186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.096837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.081439 restraints weight = 53264.222| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.67 r_work: 0.3620 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14287 Z= 0.148 Angle : 0.652 8.928 19567 Z= 0.340 Chirality : 0.043 0.271 2143 Planarity : 0.004 0.047 2279 Dihedral : 18.341 179.771 2515 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.25 % Allowed : 9.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1546 helix: 0.17 (0.19), residues: 720 sheet: -1.04 (0.36), residues: 198 loop : -0.68 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.004 0.001 HIS A1192 PHE 0.018 0.001 PHE B1107 TYR 0.020 0.001 TYR A 698 ARG 0.006 0.000 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 601) hydrogen bonds : angle 4.96513 ( 1693) covalent geometry : bond 0.00327 (14287) covalent geometry : angle 0.65218 (19567) *********************** 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 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: A 924 ASP cc_start: 0.8646 (m-30) cc_final: 0.8360 (t0) REVERT: B 593 GLU cc_start: 0.8389 (pm20) cc_final: 0.8101 (pp20) REVERT: B 601 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9155 (pptt) REVERT: B 966 TYR cc_start: 0.8791 (m-80) cc_final: 0.8447 (m-10) REVERT: B 1048 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7626 (mpp) outliers start: 17 outliers final: 4 residues processed: 89 average time/residue: 1.5035 time to fit residues: 148.8146 Evaluate side-chains 72 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1048 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN A1114 ASN B 928 GLN B1114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.093840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.077813 restraints weight = 52424.216| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.66 r_work: 0.3538 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2006 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= 0.219 Angle : 0.683 9.796 19567 Z= 0.356 Chirality : 0.045 0.273 2143 Planarity : 0.004 0.043 2279 Dihedral : 18.244 172.729 2515 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.50 % Allowed : 13.38 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.22), residues: 1546 helix: 0.26 (0.20), residues: 726 sheet: -1.01 (0.36), residues: 208 loop : -0.70 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 861 HIS 0.006 0.001 HIS B1099 PHE 0.028 0.002 PHE B1107 TYR 0.024 0.002 TYR A1028 ARG 0.006 0.001 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 601) hydrogen bonds : angle 4.81788 ( 1693) covalent geometry : bond 0.00494 (14287) covalent geometry : angle 0.68324 (19567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 1.699 Fit side-chains REVERT: A 599 TRP cc_start: 0.8606 (t60) cc_final: 0.8344 (t60) REVERT: A 799 ARG cc_start: 0.8505 (mpp-170) cc_final: 0.8153 (mpt180) REVERT: A 924 ASP cc_start: 0.8725 (m-30) cc_final: 0.8398 (t0) REVERT: A 1097 LEU cc_start: 0.6846 (pt) cc_final: 0.5881 (tt) REVERT: A 1173 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 593 GLU cc_start: 0.8437 (pm20) cc_final: 0.8177 (pp20) REVERT: B 966 TYR cc_start: 0.8850 (m-80) cc_final: 0.8499 (m-10) REVERT: B 1048 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: B 1173 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7766 (mp0) outliers start: 34 outliers final: 11 residues processed: 93 average time/residue: 1.7313 time to fit residues: 180.4231 Evaluate side-chains 72 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 2.496 ------------------------------------------------------------------------------- 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 622 THR Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 941 VAL 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 1048 MET 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 100 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 0.0040 chunk 150 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.095579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079795 restraints weight = 52797.883| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.63 r_work: 0.3595 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14287 Z= 0.135 Angle : 0.619 10.571 19567 Z= 0.319 Chirality : 0.042 0.237 2143 Planarity : 0.004 0.056 2279 Dihedral : 17.956 176.149 2513 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.99 % Allowed : 16.25 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1546 helix: 0.47 (0.20), residues: 730 sheet: -1.01 (0.36), residues: 204 loop : -0.62 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.002 0.001 HIS B 887 PHE 0.016 0.001 PHE A 596 TYR 0.020 0.001 TYR A 698 ARG 0.008 0.000 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 601) hydrogen bonds : angle 4.68924 ( 1693) covalent geometry : bond 0.00300 (14287) covalent geometry : angle 0.61900 (19567) *********************** 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 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8662 (t60) cc_final: 0.8387 (t60) REVERT: A 608 ASN cc_start: 0.8963 (t0) cc_final: 0.8655 (t0) REVERT: A 924 ASP cc_start: 0.8757 (m-30) cc_final: 0.8437 (t0) REVERT: A 1048 MET cc_start: 0.8112 (ptp) cc_final: 0.7896 (pmm) REVERT: A 1173 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 599 TRP cc_start: 0.8566 (t60) cc_final: 0.8323 (t60) REVERT: B 739 PHE cc_start: 0.8804 (t80) cc_final: 0.8548 (m-80) REVERT: B 848 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6076 (p90) REVERT: B 966 TYR cc_start: 0.8792 (m-80) cc_final: 0.8429 (m-10) REVERT: B 1048 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7663 (mpp) REVERT: B 1173 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7813 (mp0) outliers start: 27 outliers final: 7 residues processed: 91 average time/residue: 1.8702 time to fit residues: 191.6404 Evaluate side-chains 73 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 800 TYR Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 75 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.095533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.079963 restraints weight = 53046.559| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.55 r_work: 0.3597 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14287 Z= 0.132 Angle : 0.617 10.793 19567 Z= 0.313 Chirality : 0.042 0.230 2143 Planarity : 0.004 0.039 2279 Dihedral : 17.657 175.860 2513 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.69 % Allowed : 17.87 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1546 helix: 0.70 (0.20), residues: 718 sheet: -0.93 (0.37), residues: 204 loop : -0.46 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1170 HIS 0.002 0.001 HIS B1099 PHE 0.017 0.001 PHE B1107 TYR 0.020 0.001 TYR A 698 ARG 0.005 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 601) hydrogen bonds : angle 4.52978 ( 1693) covalent geometry : bond 0.00293 (14287) covalent geometry : angle 0.61682 (19567) *********************** 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 89 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8637 (m-80) cc_final: 0.8199 (m-80) REVERT: A 599 TRP cc_start: 0.8678 (t60) cc_final: 0.8430 (t60) REVERT: A 608 ASN cc_start: 0.8967 (t0) cc_final: 0.8651 (t0) REVERT: A 924 ASP cc_start: 0.8777 (m-30) cc_final: 0.8447 (t0) REVERT: A 1173 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 599 TRP cc_start: 0.8578 (t60) cc_final: 0.8351 (t60) REVERT: B 739 PHE cc_start: 0.8822 (t80) cc_final: 0.8602 (m-80) REVERT: B 848 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6046 (p90) REVERT: B 966 TYR cc_start: 0.8769 (m-80) cc_final: 0.8398 (m-10) REVERT: B 1121 CYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6221 (p) REVERT: B 1173 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8052 (mt-10) outliers start: 23 outliers final: 4 residues processed: 86 average time/residue: 1.1814 time to fit residues: 114.5206 Evaluate side-chains 72 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 542 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.094650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.079062 restraints weight = 52919.372| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.56 r_work: 0.3576 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14287 Z= 0.148 Angle : 0.624 11.483 19567 Z= 0.319 Chirality : 0.042 0.232 2143 Planarity : 0.004 0.040 2279 Dihedral : 17.375 175.757 2513 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.06 % Allowed : 17.79 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1546 helix: 0.68 (0.20), residues: 730 sheet: -0.70 (0.38), residues: 196 loop : -0.38 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1170 HIS 0.003 0.001 HIS B1099 PHE 0.020 0.001 PHE B1107 TYR 0.021 0.001 TYR A 698 ARG 0.010 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 601) hydrogen bonds : angle 4.49505 ( 1693) covalent geometry : bond 0.00333 (14287) covalent geometry : angle 0.62405 (19567) *********************** 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 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8634 (m-80) cc_final: 0.8212 (m-80) REVERT: A 599 TRP cc_start: 0.8674 (t60) cc_final: 0.8390 (t60) REVERT: A 608 ASN cc_start: 0.8952 (t0) cc_final: 0.8633 (t0) REVERT: A 799 ARG cc_start: 0.9018 (mmt90) cc_final: 0.8739 (mmp80) REVERT: A 846 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: A 848 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.6063 (p90) REVERT: A 924 ASP cc_start: 0.8782 (m-30) cc_final: 0.8443 (t0) REVERT: A 993 THR cc_start: 0.9634 (OUTLIER) cc_final: 0.9410 (p) REVERT: A 1048 MET cc_start: 0.7955 (ptp) cc_final: 0.7721 (pmm) REVERT: A 1173 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: B 593 GLU cc_start: 0.8397 (pm20) cc_final: 0.8136 (OUTLIER) REVERT: B 599 TRP cc_start: 0.8592 (t60) cc_final: 0.8346 (t60) REVERT: B 635 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: B 739 PHE cc_start: 0.8912 (t80) cc_final: 0.8656 (m-80) REVERT: B 966 TYR cc_start: 0.8798 (m-80) cc_final: 0.8447 (m-10) REVERT: B 1121 CYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6564 (p) REVERT: B 1173 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8142 (mt-10) outliers start: 28 outliers final: 11 residues processed: 90 average time/residue: 1.1542 time to fit residues: 116.2652 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 : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 635 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.094881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079280 restraints weight = 53033.894| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.63 r_work: 0.3576 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14287 Z= 0.136 Angle : 0.625 11.822 19567 Z= 0.316 Chirality : 0.041 0.215 2143 Planarity : 0.004 0.039 2279 Dihedral : 17.254 176.272 2513 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.91 % Allowed : 18.90 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1546 helix: 0.70 (0.20), residues: 730 sheet: -0.59 (0.38), residues: 196 loop : -0.30 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 PHE 0.018 0.001 PHE B1107 TYR 0.020 0.001 TYR A 698 ARG 0.007 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 601) hydrogen bonds : angle 4.47920 ( 1693) covalent geometry : bond 0.00306 (14287) covalent geometry : angle 0.62511 (19567) *********************** 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 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8634 (m-80) cc_final: 0.8176 (m-80) REVERT: A 599 TRP cc_start: 0.8610 (t60) cc_final: 0.8362 (t60) REVERT: A 608 ASN cc_start: 0.8954 (t0) cc_final: 0.8631 (t0) REVERT: A 799 ARG cc_start: 0.9024 (mmt90) cc_final: 0.8815 (mmp80) REVERT: A 846 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: A 848 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.6027 (p90) REVERT: A 924 ASP cc_start: 0.8797 (m-30) cc_final: 0.8446 (t0) REVERT: A 993 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9410 (p) REVERT: A 1173 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 593 GLU cc_start: 0.8411 (pm20) cc_final: 0.8157 (OUTLIER) REVERT: B 599 TRP cc_start: 0.8589 (t60) cc_final: 0.8326 (t60) REVERT: B 635 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7020 (ppp) REVERT: B 739 PHE cc_start: 0.8973 (t80) cc_final: 0.8692 (m-80) REVERT: B 848 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.5984 (p90) REVERT: B 966 TYR cc_start: 0.8831 (m-80) cc_final: 0.8465 (m-10) REVERT: B 1121 CYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6123 (p) REVERT: B 1173 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7826 (mp0) outliers start: 26 outliers final: 10 residues processed: 90 average time/residue: 1.1679 time to fit residues: 117.4385 Evaluate side-chains 82 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 635 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 1173 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 112 optimal weight: 0.0270 chunk 61 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.095320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.079381 restraints weight = 52073.816| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.71 r_work: 0.3571 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2775 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= 0.133 Angle : 0.631 12.094 19567 Z= 0.322 Chirality : 0.041 0.225 2143 Planarity : 0.004 0.037 2279 Dihedral : 17.116 176.409 2513 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 1.99 % Allowed : 19.49 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1546 helix: 0.72 (0.20), residues: 730 sheet: -0.55 (0.38), residues: 196 loop : -0.23 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.002 0.001 HIS B1099 PHE 0.016 0.001 PHE B1107 TYR 0.019 0.001 TYR A 698 ARG 0.007 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 601) hydrogen bonds : angle 4.49008 ( 1693) covalent geometry : bond 0.00299 (14287) covalent geometry : angle 0.63146 (19567) *********************** 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 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8726 (m-80) cc_final: 0.8200 (m-80) REVERT: A 599 TRP cc_start: 0.8567 (t60) cc_final: 0.8307 (t60) REVERT: A 608 ASN cc_start: 0.8979 (t0) cc_final: 0.8650 (t0) REVERT: A 715 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 799 ARG cc_start: 0.9024 (mmt90) cc_final: 0.8761 (mmp80) REVERT: A 846 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: A 848 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.5886 (p90) REVERT: A 924 ASP cc_start: 0.8853 (m-30) cc_final: 0.8472 (t0) REVERT: A 966 TYR cc_start: 0.8624 (m-10) cc_final: 0.8324 (m-10) REVERT: A 993 THR cc_start: 0.9647 (OUTLIER) cc_final: 0.9391 (p) REVERT: A 1048 MET cc_start: 0.7927 (ptp) cc_final: 0.7557 (pmm) REVERT: A 1173 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: B 593 GLU cc_start: 0.8435 (pm20) cc_final: 0.8182 (OUTLIER) REVERT: B 599 TRP cc_start: 0.8525 (t60) cc_final: 0.8263 (t60) REVERT: B 635 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6902 (ppp) REVERT: B 739 PHE cc_start: 0.9016 (t80) cc_final: 0.8770 (t80) REVERT: B 848 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.5781 (p90) REVERT: B 966 TYR cc_start: 0.8890 (m-80) cc_final: 0.8462 (m-10) REVERT: B 1121 CYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6193 (p) REVERT: B 1173 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7916 (mt-10) outliers start: 27 outliers final: 12 residues processed: 89 average time/residue: 1.1796 time to fit residues: 117.1695 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 : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 635 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 1173 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.093604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.077331 restraints weight = 52252.358| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.72 r_work: 0.3521 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14287 Z= 0.180 Angle : 0.681 12.610 19567 Z= 0.346 Chirality : 0.043 0.226 2143 Planarity : 0.004 0.040 2279 Dihedral : 17.234 173.564 2513 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 1.99 % Allowed : 19.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1546 helix: 0.57 (0.19), residues: 740 sheet: -0.48 (0.37), residues: 200 loop : -0.32 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 861 HIS 0.004 0.001 HIS B1099 PHE 0.025 0.002 PHE B1107 TYR 0.021 0.001 TYR A 698 ARG 0.007 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 601) hydrogen bonds : angle 4.58251 ( 1693) covalent geometry : bond 0.00409 (14287) covalent geometry : angle 0.68052 (19567) *********************** 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 91 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8549 (t60) cc_final: 0.8284 (t60) REVERT: A 608 ASN cc_start: 0.8973 (t0) cc_final: 0.8644 (t0) REVERT: A 715 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 799 ARG cc_start: 0.8996 (mmt90) cc_final: 0.8746 (mmp80) REVERT: A 848 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.5945 (p90) REVERT: A 993 THR cc_start: 0.9643 (OUTLIER) cc_final: 0.9385 (p) REVERT: A 1048 MET cc_start: 0.7988 (ptp) cc_final: 0.7652 (pmm) REVERT: A 1173 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: B 593 GLU cc_start: 0.8481 (pm20) cc_final: 0.8222 (pp20) REVERT: B 599 TRP cc_start: 0.8554 (t60) cc_final: 0.8272 (t60) REVERT: B 635 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6872 (ppp) REVERT: B 739 PHE cc_start: 0.9048 (t80) cc_final: 0.8790 (t80) REVERT: B 848 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.5913 (p90) REVERT: B 966 TYR cc_start: 0.8865 (m-80) cc_final: 0.8437 (m-10) REVERT: B 1173 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7669 (mp0) outliers start: 27 outliers final: 10 residues processed: 86 average time/residue: 1.2534 time to fit residues: 119.8942 Evaluate side-chains 79 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 635 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.093756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.077861 restraints weight = 51728.123| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.64 r_work: 0.3536 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14287 Z= 0.169 Angle : 0.671 12.660 19567 Z= 0.342 Chirality : 0.043 0.222 2143 Planarity : 0.004 0.044 2279 Dihedral : 17.186 173.788 2513 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 1.84 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1546 helix: 0.54 (0.19), residues: 740 sheet: -0.42 (0.37), residues: 200 loop : -0.32 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 820 HIS 0.004 0.001 HIS B1099 PHE 0.021 0.001 PHE B1107 TYR 0.021 0.001 TYR A 698 ARG 0.008 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 601) hydrogen bonds : angle 4.59151 ( 1693) covalent geometry : bond 0.00384 (14287) covalent geometry : angle 0.67096 (19567) ********************** 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 90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8572 (t60) cc_final: 0.8298 (t60) REVERT: A 608 ASN cc_start: 0.8957 (t0) cc_final: 0.8618 (t0) REVERT: A 715 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 799 ARG cc_start: 0.8977 (mmt90) cc_final: 0.8708 (mmp80) REVERT: A 848 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.5982 (p90) REVERT: A 993 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9342 (p) REVERT: A 1048 MET cc_start: 0.8025 (ptp) cc_final: 0.7637 (pmm) REVERT: A 1173 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: B 593 GLU cc_start: 0.8448 (pm20) cc_final: 0.8189 (pp20) REVERT: B 599 TRP cc_start: 0.8568 (t60) cc_final: 0.8282 (t60) REVERT: B 714 MET cc_start: 0.8577 (ptt) cc_final: 0.8373 (ptt) REVERT: B 739 PHE cc_start: 0.9061 (t80) cc_final: 0.8781 (t80) REVERT: B 848 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.5892 (p90) REVERT: B 966 TYR cc_start: 0.8850 (m-80) cc_final: 0.8382 (m-10) REVERT: B 1173 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7670 (mp0) outliers start: 25 outliers final: 12 residues processed: 87 average time/residue: 1.3585 time to fit residues: 131.5663 Evaluate side-chains 77 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1041 GLU 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 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 114 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 13 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 103 optimal weight: 0.0570 chunk 106 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 903 ASN B 789 HIS B 903 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.095610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.080045 restraints weight = 52711.546| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.73 r_work: 0.3586 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3107 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= 0.123 Angle : 0.652 13.708 19567 Z= 0.329 Chirality : 0.041 0.247 2143 Planarity : 0.004 0.043 2279 Dihedral : 16.880 177.770 2513 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 1.40 % Allowed : 20.59 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1546 helix: 0.75 (0.20), residues: 732 sheet: -0.60 (0.37), residues: 204 loop : -0.27 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 820 HIS 0.002 0.000 HIS B 623 PHE 0.010 0.001 PHE A1107 TYR 0.018 0.001 TYR A 698 ARG 0.007 0.000 ARG A 799 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 601) hydrogen bonds : angle 4.46999 ( 1693) covalent geometry : bond 0.00273 (14287) covalent geometry : angle 0.65219 (19567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9826.17 seconds wall clock time: 177 minutes 15.11 seconds (10635.11 seconds total)