Starting phenix.real_space_refine on Fri May 16 03:41:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9w_36117/05_2025/8j9w_36117_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9w_36117/05_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_36117/05_2025/8j9w_36117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9w_36117/05_2025/8j9w_36117.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9w_36117/05_2025/8j9w_36117_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9w_36117/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.87, per 1000 atoms: 0.64 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: 3.58 Conformation dependent library (CDL) restraints added in 1.6 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: 4.62 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: 5.17 Time building geometry restraints manager: 4.12 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 36.670 Find NCS groups from input model: 0.450 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: 0.000 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- 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 : 1.645 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: 1.4146 time to fit residues: 175.8960 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 : 1.512 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.081441 restraints weight = 53264.284| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.68 r_work: 0.3621 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 8.927 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 4.96514 ( 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 : 1.549 Fit side-chains revert: symmetry clash REVERT: A 924 ASP cc_start: 0.8649 (m-30) cc_final: 0.8360 (t0) REVERT: B 593 GLU cc_start: 0.8391 (pm20) cc_final: 0.8103 (pp20) REVERT: B 601 LYS cc_start: 0.9390 (mmpt) cc_final: 0.9155 (pptt) REVERT: B 966 TYR cc_start: 0.8799 (m-80) cc_final: 0.8455 (m-10) REVERT: B 1048 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7630 (mpp) outliers start: 17 outliers final: 4 residues processed: 89 average time/residue: 1.2903 time to fit residues: 127.5409 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 : 1.567 ------------------------------------------------------------------------------- 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: 0.2980 chunk 116 optimal weight: 0.6980 chunk 51 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 87 optimal weight: 0.0070 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.082605 restraints weight = 52992.691| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.52 r_work: 0.3646 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1707 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= 0.122 Angle : 0.614 10.300 19567 Z= 0.315 Chirality : 0.042 0.232 2143 Planarity : 0.004 0.043 2279 Dihedral : 17.793 177.479 2515 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.69 % Allowed : 12.72 % Favored : 85.59 % 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: -0.28 (0.22), residues: 1546 helix: 0.51 (0.20), residues: 720 sheet: -0.84 (0.36), residues: 202 loop : -0.63 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.002 0.000 HIS A1051 PHE 0.022 0.001 PHE A 596 TYR 0.019 0.001 TYR A 698 ARG 0.005 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 601) hydrogen bonds : angle 4.61612 ( 1693) covalent geometry : bond 0.00266 (14287) covalent geometry : angle 0.61407 (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 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 597 ASP cc_start: 0.9368 (m-30) cc_final: 0.9133 (m-30) REVERT: A 599 TRP cc_start: 0.8625 (t60) cc_final: 0.8397 (t60) REVERT: A 800 TYR cc_start: 0.9081 (m-80) cc_final: 0.8847 (m-80) REVERT: A 924 ASP cc_start: 0.8694 (m-30) cc_final: 0.8360 (t0) REVERT: A 1173 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: B 593 GLU cc_start: 0.8355 (pm20) cc_final: 0.8111 (pp20) REVERT: B 846 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8242 (mpt) REVERT: B 966 TYR cc_start: 0.8716 (m-80) cc_final: 0.8395 (m-10) REVERT: B 1048 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7666 (mpp) REVERT: B 1173 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7875 (mp0) outliers start: 23 outliers final: 8 residues processed: 87 average time/residue: 1.3403 time to fit residues: 128.6771 Evaluate side-chains 78 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 433 MET 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 848 TYR Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 100 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A1014 ASN A1114 ASN B 804 GLN B 928 GLN B1114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.094458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078674 restraints weight = 52858.280| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.57 r_work: 0.3572 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14287 Z= 0.179 Angle : 0.652 11.211 19567 Z= 0.336 Chirality : 0.044 0.254 2143 Planarity : 0.004 0.045 2279 Dihedral : 17.843 174.606 2515 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.57 % Allowed : 15.37 % Favored : 82.06 % 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: -0.32 (0.22), residues: 1546 helix: 0.50 (0.20), residues: 730 sheet: -1.04 (0.36), residues: 212 loop : -0.62 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 861 HIS 0.005 0.001 HIS B1099 PHE 0.025 0.002 PHE B1107 TYR 0.023 0.002 TYR A1028 ARG 0.005 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 601) hydrogen bonds : angle 4.62338 ( 1693) covalent geometry : bond 0.00407 (14287) covalent geometry : angle 0.65168 (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 105 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8690 (t60) cc_final: 0.8449 (t60) REVERT: A 799 ARG cc_start: 0.9095 (mtt180) cc_final: 0.8456 (mpt180) REVERT: A 800 TYR cc_start: 0.9063 (m-80) cc_final: 0.8838 (m-80) REVERT: A 924 ASP cc_start: 0.8753 (m-30) cc_final: 0.8420 (t0) REVERT: A 1173 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: B 593 GLU cc_start: 0.8445 (pm20) cc_final: 0.8222 (pp20) REVERT: B 599 TRP cc_start: 0.8596 (t60) cc_final: 0.8362 (t60) REVERT: B 966 TYR cc_start: 0.8755 (m-80) cc_final: 0.8418 (m-10) REVERT: B 1048 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7630 (mpp) REVERT: B 1173 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7773 (mp0) outliers start: 35 outliers final: 12 residues processed: 98 average time/residue: 1.2327 time to fit residues: 133.7385 Evaluate side-chains 75 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 800 TYR 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 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: 0.9990 chunk 94 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.095094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.079407 restraints weight = 53046.773| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.64 r_work: 0.3585 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2359 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= 0.147 Angle : 0.629 11.025 19567 Z= 0.322 Chirality : 0.042 0.241 2143 Planarity : 0.004 0.064 2279 Dihedral : 17.615 177.122 2515 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.91 % Allowed : 16.84 % Favored : 81.25 % 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: 0.71 (0.20), residues: 716 sheet: -0.95 (0.37), residues: 204 loop : -0.45 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.003 0.001 HIS B1099 PHE 0.017 0.001 PHE B1107 TYR 0.022 0.001 TYR A1028 ARG 0.008 0.000 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 601) hydrogen bonds : angle 4.59709 ( 1693) covalent geometry : bond 0.00333 (14287) covalent geometry : angle 0.62853 (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 90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8660 (m-80) cc_final: 0.8076 (m-80) REVERT: A 599 TRP cc_start: 0.8682 (t60) cc_final: 0.8422 (t60) REVERT: A 608 ASN cc_start: 0.8965 (t0) cc_final: 0.8652 (t0) REVERT: A 799 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8358 (mpt180) REVERT: A 800 TYR cc_start: 0.9062 (m-80) cc_final: 0.8768 (m-80) REVERT: A 846 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8199 (mmm) REVERT: A 924 ASP cc_start: 0.8761 (m-30) cc_final: 0.8411 (t0) REVERT: A 993 THR cc_start: 0.9641 (OUTLIER) cc_final: 0.9402 (p) REVERT: A 1173 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 599 TRP cc_start: 0.8601 (t60) cc_final: 0.8349 (t60) REVERT: B 739 PHE cc_start: 0.8861 (t80) cc_final: 0.8609 (m-80) REVERT: B 846 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8235 (mpp) REVERT: B 966 TYR cc_start: 0.8809 (m-80) cc_final: 0.8472 (m-10) REVERT: B 1121 CYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6523 (p) REVERT: B 1173 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7827 (mp0) outliers start: 26 outliers final: 7 residues processed: 84 average time/residue: 1.2683 time to fit residues: 119.5022 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 868 ILE Chi-restraints excluded: chain A residue 993 THR 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 846 MET Chi-restraints excluded: chain B residue 868 ILE 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: 0.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.094636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.078890 restraints weight = 52582.165| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.56 r_work: 0.3573 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2546 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= 0.151 Angle : 0.634 11.553 19567 Z= 0.324 Chirality : 0.042 0.234 2143 Planarity : 0.004 0.038 2279 Dihedral : 17.421 176.202 2515 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.91 % Allowed : 17.94 % 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: -0.01 (0.22), residues: 1546 helix: 0.65 (0.20), residues: 730 sheet: -0.67 (0.37), residues: 204 loop : -0.41 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 861 HIS 0.003 0.001 HIS B1099 PHE 0.019 0.001 PHE B1107 TYR 0.020 0.001 TYR A 698 ARG 0.003 0.000 ARG B 799 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 601) hydrogen bonds : angle 4.53519 ( 1693) covalent geometry : bond 0.00340 (14287) covalent geometry : angle 0.63411 (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 92 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8622 (m-80) cc_final: 0.8007 (m-80) REVERT: A 599 TRP cc_start: 0.8689 (t60) cc_final: 0.8437 (t60) REVERT: A 608 ASN cc_start: 0.8943 (t0) cc_final: 0.8622 (t0) REVERT: A 800 TYR cc_start: 0.9086 (m-80) cc_final: 0.8801 (m-80) REVERT: A 846 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: A 924 ASP cc_start: 0.8785 (m-30) cc_final: 0.8440 (t0) REVERT: A 993 THR cc_start: 0.9637 (OUTLIER) cc_final: 0.9403 (p) REVERT: A 1173 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: B 599 TRP cc_start: 0.8619 (t60) cc_final: 0.8384 (t60) REVERT: B 739 PHE cc_start: 0.8901 (t80) cc_final: 0.8627 (m-80) REVERT: B 848 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6108 (p90) REVERT: B 966 TYR cc_start: 0.8789 (m-80) cc_final: 0.8476 (m-10) REVERT: B 1173 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8151 (mt-10) outliers start: 26 outliers final: 7 residues processed: 89 average time/residue: 1.1757 time to fit residues: 117.1001 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 593 GLU 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 94 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 42 optimal weight: 0.0970 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.095561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.079991 restraints weight = 53296.442| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.58 r_work: 0.3596 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2613 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= 0.128 Angle : 0.626 12.008 19567 Z= 0.320 Chirality : 0.041 0.225 2143 Planarity : 0.003 0.037 2279 Dihedral : 17.218 177.344 2513 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.06 % Allowed : 18.16 % Favored : 79.78 % 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: 0.08 (0.22), residues: 1546 helix: 0.67 (0.20), residues: 732 sheet: -0.57 (0.38), residues: 196 loop : -0.33 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.002 0.001 HIS B 887 PHE 0.015 0.001 PHE B1107 TYR 0.019 0.001 TYR A 698 ARG 0.002 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 601) hydrogen bonds : angle 4.50619 ( 1693) covalent geometry : bond 0.00283 (14287) covalent geometry : angle 0.62650 (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 99 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8641 (m-80) cc_final: 0.8021 (m-80) REVERT: A 593 GLU cc_start: 0.8783 (mp0) cc_final: 0.8574 (pp20) REVERT: A 599 TRP cc_start: 0.8601 (t60) cc_final: 0.8359 (t60) REVERT: A 608 ASN cc_start: 0.8957 (t0) cc_final: 0.8631 (t0) REVERT: A 800 TYR cc_start: 0.9076 (m-80) cc_final: 0.8791 (m-80) REVERT: A 846 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8107 (mmm) REVERT: A 848 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.5960 (p90) REVERT: A 924 ASP cc_start: 0.8797 (m-30) cc_final: 0.8450 (t0) REVERT: A 993 THR cc_start: 0.9637 (OUTLIER) cc_final: 0.9409 (p) REVERT: B 599 TRP cc_start: 0.8585 (t60) cc_final: 0.8352 (t60) REVERT: B 739 PHE cc_start: 0.8892 (t80) cc_final: 0.8646 (m-80) REVERT: B 846 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8281 (mpp) REVERT: B 848 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6029 (p90) REVERT: B 966 TYR cc_start: 0.8761 (m-80) cc_final: 0.8400 (m-10) REVERT: B 1121 CYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6215 (p) REVERT: B 1173 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8025 (mt-10) outliers start: 28 outliers final: 10 residues processed: 92 average time/residue: 1.1807 time to fit residues: 121.1068 Evaluate side-chains 81 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 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: 0.0170 chunk 61 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 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: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.094884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.079176 restraints weight = 52489.111| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.65 r_work: 0.3564 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14287 Z= 0.140 Angle : 0.642 12.247 19567 Z= 0.326 Chirality : 0.042 0.220 2143 Planarity : 0.004 0.039 2279 Dihedral : 17.129 176.311 2513 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.35 % Allowed : 18.46 % 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: 0.10 (0.22), residues: 1546 helix: 0.68 (0.20), residues: 732 sheet: -0.59 (0.38), residues: 196 loop : -0.28 (0.26), residues: 618 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 0.003 0.000 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 601) hydrogen bonds : angle 4.48512 ( 1693) covalent geometry : bond 0.00317 (14287) covalent geometry : angle 0.64210 (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 99 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 2.053 Fit side-chains revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8705 (m-80) cc_final: 0.8002 (m-80) REVERT: A 593 GLU cc_start: 0.8800 (mp0) cc_final: 0.8554 (pp20) REVERT: A 599 TRP cc_start: 0.8567 (t60) cc_final: 0.8311 (t60) REVERT: A 608 ASN cc_start: 0.8954 (t0) cc_final: 0.8632 (t0) REVERT: A 715 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 800 TYR cc_start: 0.9049 (m-80) cc_final: 0.8720 (m-80) REVERT: A 846 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: A 848 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.5791 (p90) REVERT: A 993 THR cc_start: 0.9635 (OUTLIER) cc_final: 0.9379 (p) REVERT: A 1173 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: B 599 TRP cc_start: 0.8579 (t60) cc_final: 0.8346 (t60) REVERT: B 739 PHE cc_start: 0.8976 (t80) cc_final: 0.8655 (m-80) REVERT: B 846 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8266 (mpp) REVERT: B 848 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.5901 (p90) REVERT: B 966 TYR cc_start: 0.8847 (m-80) cc_final: 0.8496 (m-10) REVERT: B 1121 CYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6133 (p) REVERT: B 1173 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7926 (mt-10) outliers start: 32 outliers final: 12 residues processed: 92 average time/residue: 1.1049 time to fit residues: 114.2825 Evaluate side-chains 84 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 993 THR 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 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 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: 2.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.092567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.076575 restraints weight = 51778.444| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.65 r_work: 0.3507 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14287 Z= 0.214 Angle : 0.706 12.798 19567 Z= 0.362 Chirality : 0.045 0.236 2143 Planarity : 0.004 0.043 2279 Dihedral : 17.451 171.601 2513 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 2.13 % Allowed : 18.97 % Favored : 78.90 % 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: 0.48 (0.20), residues: 728 sheet: -0.57 (0.38), residues: 200 loop : -0.40 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1170 HIS 0.005 0.001 HIS B1099 PHE 0.029 0.002 PHE A1107 TYR 0.022 0.002 TYR A 698 ARG 0.003 0.000 ARG B 571 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 601) hydrogen bonds : angle 4.70932 ( 1693) covalent geometry : bond 0.00488 (14287) covalent geometry : angle 0.70552 (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 93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 GLU cc_start: 0.8827 (mp0) cc_final: 0.8614 (pp20) REVERT: A 599 TRP cc_start: 0.8540 (t60) cc_final: 0.8248 (t60) REVERT: A 608 ASN cc_start: 0.8947 (t0) cc_final: 0.8630 (t0) REVERT: A 715 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 848 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.6035 (p90) REVERT: A 993 THR cc_start: 0.9635 (OUTLIER) cc_final: 0.9361 (p) REVERT: A 1097 LEU cc_start: 0.6945 (pt) cc_final: 0.5959 (tt) REVERT: A 1173 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: B 599 TRP cc_start: 0.8603 (t60) cc_final: 0.8307 (t60) REVERT: B 739 PHE cc_start: 0.9076 (t80) cc_final: 0.8803 (t80) REVERT: B 848 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6113 (p90) REVERT: B 966 TYR cc_start: 0.8831 (m-80) cc_final: 0.8430 (m-10) REVERT: B 1173 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7794 (mt-10) outliers start: 29 outliers final: 14 residues processed: 87 average time/residue: 1.1664 time to fit residues: 114.0113 Evaluate side-chains 78 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 514 LEU 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 715 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1121 CYS Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 131 optimal weight: 0.0670 chunk 133 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.094148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.078301 restraints weight = 51829.704| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.67 r_work: 0.3548 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14287 Z= 0.145 Angle : 0.674 13.184 19567 Z= 0.344 Chirality : 0.042 0.250 2143 Planarity : 0.004 0.041 2279 Dihedral : 17.267 173.764 2513 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 1.62 % Allowed : 19.85 % 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: 0.01 (0.22), residues: 1546 helix: 0.55 (0.20), residues: 728 sheet: -0.45 (0.38), residues: 200 loop : -0.31 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 820 HIS 0.002 0.001 HIS B1099 PHE 0.017 0.001 PHE A1107 TYR 0.020 0.001 TYR A 698 ARG 0.004 0.000 ARG A1039 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 601) hydrogen bonds : angle 4.66844 ( 1693) covalent geometry : bond 0.00326 (14287) covalent geometry : angle 0.67415 (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 83 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8557 (t60) cc_final: 0.8256 (t60) REVERT: A 608 ASN cc_start: 0.8966 (t0) cc_final: 0.8628 (t0) REVERT: A 715 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 800 TYR cc_start: 0.8942 (m-80) cc_final: 0.8642 (m-80) REVERT: A 848 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.5970 (p90) REVERT: A 993 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9339 (p) REVERT: A 1048 MET cc_start: 0.7853 (pmm) cc_final: 0.7646 (pmm) REVERT: A 1173 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: B 573 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8568 (tt) REVERT: B 599 TRP cc_start: 0.8587 (t60) cc_final: 0.8279 (t60) REVERT: B 739 PHE cc_start: 0.9062 (t80) cc_final: 0.8801 (t80) REVERT: B 846 MET cc_start: 0.9112 (mpp) cc_final: 0.8147 (mpp) REVERT: B 848 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6015 (p90) REVERT: B 966 TYR cc_start: 0.8808 (m-80) cc_final: 0.8446 (m-10) REVERT: B 1173 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7883 (mt-10) outliers start: 22 outliers final: 10 residues processed: 81 average time/residue: 1.1424 time to fit residues: 103.3929 Evaluate side-chains 76 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 909 HIS 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 573 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 114 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 103 optimal weight: 0.0070 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.094454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.078741 restraints weight = 52162.356| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.67 r_work: 0.3559 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3082 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= 0.140 Angle : 0.666 13.209 19567 Z= 0.339 Chirality : 0.042 0.223 2143 Planarity : 0.004 0.047 2279 Dihedral : 17.093 174.867 2513 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.21 % Rotamer: Outliers : 1.54 % Allowed : 20.07 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.22), residues: 1546 helix: 0.69 (0.20), residues: 716 sheet: -0.68 (0.37), residues: 212 loop : -0.24 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.002 0.001 HIS B1099 PHE 0.017 0.001 PHE A1107 TYR 0.020 0.001 TYR A 698 ARG 0.014 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 601) hydrogen bonds : angle 4.63416 ( 1693) covalent geometry : bond 0.00315 (14287) covalent geometry : angle 0.66634 (19567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8867.63 seconds wall clock time: 154 minutes 0.51 seconds (9240.51 seconds total)