Starting phenix.real_space_refine on Sun Nov 17 14:58:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/11_2024/8j9w_36117_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/11_2024/8j9w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/11_2024/8j9w_36117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/11_2024/8j9w_36117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/11_2024/8j9w_36117_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9w_36117/11_2024/8j9w_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-5513/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: 9.27, per 1000 atoms: 0.67 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: 3.56 Conformation dependent library (CDL) restraints added in 1.2 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: 5.12 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: 5.33 Time building geometry restraints manager: 4.13 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: 3.730 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.560 Find NCS groups from input model: 0.400 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.450 ------------------------------------------------------------------------------- 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= 0.284 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 *********************** 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 : 1.665 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: 1.5095 time to fit residues: 187.6681 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 : 1.609 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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= 0.208 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 *********************** 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 : 1.671 Fit side-chains revert: symmetry clash REVERT: A 924 ASP cc_start: 0.8620 (m-30) cc_final: 0.8357 (t0) REVERT: B 593 GLU cc_start: 0.8316 (pm20) cc_final: 0.8043 (pp20) REVERT: B 601 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9151 (pptt) REVERT: B 966 TYR cc_start: 0.8620 (m-80) cc_final: 0.8287 (m-10) REVERT: B 1048 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7663 (mpp) outliers start: 17 outliers final: 4 residues processed: 89 average time/residue: 1.3654 time to fit residues: 134.0840 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 : 1.650 ------------------------------------------------------------------------------- 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 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14287 Z= 0.287 Angle : 0.677 10.137 19567 Z= 0.351 Chirality : 0.045 0.267 2143 Planarity : 0.005 0.044 2279 Dihedral : 18.163 172.758 2515 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.87 % Allowed : 13.31 % Favored : 83.82 % 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: -0.51 (0.22), residues: 1546 helix: 0.30 (0.20), residues: 726 sheet: -1.12 (0.36), residues: 212 loop : -0.66 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 861 HIS 0.005 0.001 HIS B1099 PHE 0.027 0.002 PHE B1107 TYR 0.024 0.002 TYR A1028 ARG 0.008 0.001 ARG B 929 *********************** 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 108 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 69 time to evaluate : 1.577 Fit side-chains REVERT: A 597 ASP cc_start: 0.9387 (m-30) cc_final: 0.9136 (t70) REVERT: A 599 TRP cc_start: 0.8582 (t60) cc_final: 0.8334 (t60) REVERT: A 800 TYR cc_start: 0.8877 (m-80) cc_final: 0.8605 (m-80) REVERT: A 924 ASP cc_start: 0.8698 (m-30) cc_final: 0.8393 (t0) REVERT: A 1041 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: A 1173 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: B 593 GLU cc_start: 0.8366 (pm20) cc_final: 0.8152 (pp20) REVERT: B 601 LYS cc_start: 0.9377 (mmpt) cc_final: 0.9174 (pptt) REVERT: B 966 TYR cc_start: 0.8655 (m-80) cc_final: 0.8318 (m-10) REVERT: B 1048 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7589 (mpp) REVERT: B 1173 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7707 (mp0) outliers start: 39 outliers final: 9 residues processed: 97 average time/residue: 1.3556 time to fit residues: 144.8978 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 : 1.602 ------------------------------------------------------------------------------- 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 1041 GLU 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 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 142 optimal weight: 4.9990 chunk 108 optimal weight: 0.0170 chunk 74 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN B 804 GLN B 864 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2182 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= 0.179 Angle : 0.617 10.436 19567 Z= 0.317 Chirality : 0.042 0.221 2143 Planarity : 0.004 0.057 2279 Dihedral : 17.863 176.928 2513 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.91 % Allowed : 16.47 % Favored : 81.62 % 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: -0.19 (0.22), residues: 1546 helix: 0.59 (0.20), residues: 718 sheet: -0.96 (0.37), residues: 204 loop : -0.53 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 820 HIS 0.002 0.001 HIS B 887 PHE 0.014 0.001 PHE B1107 TYR 0.019 0.001 TYR A 698 ARG 0.009 0.000 ARG B 799 *********************** 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 99 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8630 (t60) cc_final: 0.8372 (t60) REVERT: A 601 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9104 (pptt) REVERT: A 608 ASN cc_start: 0.9000 (t0) cc_final: 0.8686 (t0) REVERT: A 800 TYR cc_start: 0.8833 (m-80) cc_final: 0.8488 (m-80) REVERT: A 848 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.5856 (p90) REVERT: A 924 ASP cc_start: 0.8741 (m-30) cc_final: 0.8428 (t0) REVERT: A 1173 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: B 601 LYS cc_start: 0.9385 (mmpt) cc_final: 0.9167 (pptt) REVERT: B 846 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: B 848 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.5835 (p90) REVERT: B 966 TYR cc_start: 0.8626 (m-80) cc_final: 0.8263 (m-10) REVERT: B 1048 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7639 (mpp) REVERT: B 1173 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7754 (mp0) outliers start: 26 outliers final: 5 residues processed: 91 average time/residue: 1.2255 time to fit residues: 124.6870 Evaluate side-chains 75 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 848 TYR 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 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN B 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14287 Z= 0.364 Angle : 0.704 10.967 19567 Z= 0.363 Chirality : 0.046 0.290 2143 Planarity : 0.005 0.059 2279 Dihedral : 18.184 170.887 2513 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.57 % Allowed : 17.94 % Favored : 79.49 % 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: -0.36 (0.22), residues: 1546 helix: 0.35 (0.19), residues: 726 sheet: -0.85 (0.38), residues: 196 loop : -0.57 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 861 HIS 0.006 0.001 HIS A1099 PHE 0.033 0.002 PHE B1107 TYR 0.030 0.002 TYR A1028 ARG 0.007 0.001 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8746 (m-80) cc_final: 0.8235 (m-80) REVERT: A 599 TRP cc_start: 0.8630 (t60) cc_final: 0.8280 (t60) REVERT: A 608 ASN cc_start: 0.9006 (t0) cc_final: 0.8705 (t0) REVERT: A 800 TYR cc_start: 0.8870 (m-80) cc_final: 0.8580 (m-80) REVERT: A 848 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6172 (p90) REVERT: A 924 ASP cc_start: 0.8751 (m-30) cc_final: 0.8443 (t0) REVERT: A 1048 MET cc_start: 0.7921 (ptp) cc_final: 0.7536 (pmm) REVERT: A 1097 LEU cc_start: 0.6919 (pt) cc_final: 0.6014 (tt) REVERT: A 1173 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: B 467 MET cc_start: 0.7671 (tpp) cc_final: 0.7210 (mtm) REVERT: B 635 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6830 (ppp) REVERT: B 966 TYR cc_start: 0.8660 (m-80) cc_final: 0.8241 (m-10) REVERT: B 1048 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7507 (mpp) REVERT: B 1173 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7865 (mt-10) outliers start: 35 outliers final: 15 residues processed: 94 average time/residue: 1.3183 time to fit residues: 137.8701 Evaluate side-chains 81 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU 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 846 MET Chi-restraints excluded: chain B residue 848 TYR Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 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 51 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3141 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= 0.327 Angle : 0.680 11.763 19567 Z= 0.352 Chirality : 0.045 0.283 2143 Planarity : 0.004 0.044 2279 Dihedral : 18.201 170.749 2513 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.43 % Allowed : 19.12 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.22), residues: 1546 helix: 0.30 (0.19), residues: 726 sheet: -0.85 (0.37), residues: 204 loop : -0.53 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.006 0.001 HIS B1099 PHE 0.029 0.002 PHE A1107 TYR 0.021 0.002 TYR A 698 ARG 0.007 0.000 ARG A 799 *********************** 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 100 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 TRP cc_start: 0.8591 (t60) cc_final: 0.8328 (t60) REVERT: A 608 ASN cc_start: 0.8991 (t0) cc_final: 0.8681 (t0) REVERT: A 800 TYR cc_start: 0.8832 (m-80) cc_final: 0.8524 (m-80) REVERT: A 846 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.7969 (mmm) REVERT: A 848 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6171 (p90) REVERT: A 924 ASP cc_start: 0.8785 (m-30) cc_final: 0.8482 (t0) REVERT: A 993 THR cc_start: 0.9619 (OUTLIER) cc_final: 0.9392 (p) REVERT: A 1097 LEU cc_start: 0.7011 (pt) cc_final: 0.6103 (tt) REVERT: A 1173 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: B 599 TRP cc_start: 0.8569 (t60) cc_final: 0.8306 (t60) REVERT: B 848 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.6170 (p90) REVERT: B 966 TYR cc_start: 0.8671 (m-80) cc_final: 0.8202 (m-10) REVERT: B 1173 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7666 (mp0) outliers start: 33 outliers final: 13 residues processed: 94 average time/residue: 1.2168 time to fit residues: 128.2437 Evaluate side-chains 80 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 846 MET Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1121 CYS Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 593 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 85 optimal weight: 0.0060 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3032 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= 0.179 Angle : 0.645 12.146 19567 Z= 0.326 Chirality : 0.042 0.195 2143 Planarity : 0.004 0.045 2279 Dihedral : 17.766 173.925 2513 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.21 % Allowed : 20.07 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.22), residues: 1546 helix: 0.64 (0.20), residues: 716 sheet: -0.85 (0.37), residues: 204 loop : -0.37 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 820 HIS 0.002 0.001 HIS B 623 PHE 0.015 0.001 PHE A1107 TYR 0.020 0.001 TYR A 698 ARG 0.009 0.000 ARG A 799 *********************** 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 101 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8724 (m-80) cc_final: 0.8011 (m-80) REVERT: A 599 TRP cc_start: 0.8614 (t60) cc_final: 0.8328 (t60) REVERT: A 608 ASN cc_start: 0.8991 (t0) cc_final: 0.8654 (t0) REVERT: A 800 TYR cc_start: 0.8804 (m-80) cc_final: 0.8439 (m-80) REVERT: A 848 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.6087 (p90) REVERT: A 924 ASP cc_start: 0.8814 (m-30) cc_final: 0.8503 (t0) REVERT: A 993 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9399 (p) REVERT: A 1173 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 599 TRP cc_start: 0.8552 (t60) cc_final: 0.8333 (t60) REVERT: B 739 PHE cc_start: 0.8694 (t80) cc_final: 0.8344 (m-80) REVERT: B 846 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8228 (mpp) REVERT: B 848 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.5889 (p90) REVERT: B 966 TYR cc_start: 0.8704 (m-80) cc_final: 0.8227 (m-10) REVERT: B 1121 CYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6446 (p) REVERT: B 1173 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7793 (mt-10) outliers start: 30 outliers final: 10 residues processed: 95 average time/residue: 1.2166 time to fit residues: 129.1644 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 : 1.616 ------------------------------------------------------------------------------- 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 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 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 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 94 optimal weight: 0.9980 chunk 60 optimal weight: 0.0020 chunk 90 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3099 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= 0.188 Angle : 0.643 12.385 19567 Z= 0.326 Chirality : 0.042 0.211 2143 Planarity : 0.004 0.044 2279 Dihedral : 17.559 171.532 2513 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 2.43 % Allowed : 19.85 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.22), residues: 1546 helix: 0.69 (0.20), residues: 718 sheet: -0.80 (0.37), residues: 204 loop : -0.28 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.002 0.001 HIS B1099 PHE 0.018 0.001 PHE B1107 TYR 0.020 0.001 TYR A 698 ARG 0.009 0.000 ARG A 799 *********************** 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 106 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8734 (m-80) cc_final: 0.8062 (m-80) REVERT: A 586 MET cc_start: 0.8718 (mmp) cc_final: 0.8494 (tpp) REVERT: A 599 TRP cc_start: 0.8595 (t60) cc_final: 0.8322 (t60) REVERT: A 608 ASN cc_start: 0.8980 (t0) cc_final: 0.8652 (t0) REVERT: A 799 ARG cc_start: 0.8883 (mmt90) cc_final: 0.8517 (mmp80) REVERT: A 800 TYR cc_start: 0.8711 (m-80) cc_final: 0.8363 (m-80) REVERT: A 848 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6078 (p90) REVERT: A 993 THR cc_start: 0.9610 (OUTLIER) cc_final: 0.9390 (p) REVERT: A 1173 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: B 573 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 599 TRP cc_start: 0.8548 (t60) cc_final: 0.8300 (t60) REVERT: B 714 MET cc_start: 0.8404 (ptt) cc_final: 0.8177 (ptt) REVERT: B 739 PHE cc_start: 0.8694 (t80) cc_final: 0.8332 (m-80) REVERT: B 846 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8297 (mpp) REVERT: B 966 TYR cc_start: 0.8673 (m-80) cc_final: 0.8202 (m-10) REVERT: B 1061 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7097 (tp30) REVERT: B 1121 CYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6458 (p) REVERT: B 1173 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8050 (mt-10) outliers start: 33 outliers final: 11 residues processed: 102 average time/residue: 1.2049 time to fit residues: 137.3029 Evaluate side-chains 80 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR 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 573 LEU Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 909 HIS 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 145 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14287 Z= 0.276 Angle : 0.706 12.825 19567 Z= 0.357 Chirality : 0.044 0.228 2143 Planarity : 0.004 0.045 2279 Dihedral : 17.706 170.042 2513 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 2.06 % Allowed : 20.59 % Favored : 77.35 % 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: -0.03 (0.22), residues: 1546 helix: 0.65 (0.20), residues: 716 sheet: -0.68 (0.37), residues: 208 loop : -0.42 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 861 HIS 0.005 0.001 HIS A1099 PHE 0.028 0.002 PHE A1107 TYR 0.022 0.001 TYR A 698 ARG 0.008 0.000 ARG A 799 *********************** 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 90 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8769 (m-80) cc_final: 0.8045 (m-80) REVERT: A 599 TRP cc_start: 0.8608 (t60) cc_final: 0.8323 (t60) REVERT: A 608 ASN cc_start: 0.8980 (t0) cc_final: 0.8661 (t0) REVERT: A 799 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8561 (mmp80) REVERT: A 848 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.6150 (p90) REVERT: A 993 THR cc_start: 0.9627 (OUTLIER) cc_final: 0.9389 (p) REVERT: A 1048 MET cc_start: 0.7870 (ptp) cc_final: 0.7577 (pmm) REVERT: A 1173 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: B 599 TRP cc_start: 0.8569 (t60) cc_final: 0.8317 (t60) REVERT: B 846 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: B 966 TYR cc_start: 0.8658 (m-80) cc_final: 0.8209 (m-10) REVERT: B 1061 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7139 (tp30) outliers start: 28 outliers final: 14 residues processed: 86 average time/residue: 1.2767 time to fit residues: 122.7542 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 : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 909 HIS 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 91 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14287 Z= 0.210 Angle : 0.680 13.261 19567 Z= 0.345 Chirality : 0.042 0.199 2143 Planarity : 0.004 0.043 2279 Dihedral : 17.570 171.504 2513 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 1.62 % Allowed : 21.10 % Favored : 77.28 % 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: 718 sheet: -0.70 (0.37), residues: 204 loop : -0.33 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 820 HIS 0.003 0.001 HIS B1099 PHE 0.019 0.001 PHE A1107 TYR 0.020 0.001 TYR A 698 ARG 0.008 0.000 ARG A 799 ********************** 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 85 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8780 (m-80) cc_final: 0.8050 (m-80) REVERT: A 586 MET cc_start: 0.8723 (mmp) cc_final: 0.8504 (tpp) REVERT: A 599 TRP cc_start: 0.8604 (t60) cc_final: 0.8313 (t60) REVERT: A 608 ASN cc_start: 0.9002 (t0) cc_final: 0.8659 (t0) REVERT: A 799 ARG cc_start: 0.8869 (mmt90) cc_final: 0.8564 (mmp80) REVERT: A 848 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.6133 (p90) REVERT: A 868 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 993 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9370 (p) REVERT: A 1048 MET cc_start: 0.7843 (ptp) cc_final: 0.7556 (pmm) REVERT: A 1173 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: B 573 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8612 (tt) REVERT: B 599 TRP cc_start: 0.8565 (t60) cc_final: 0.8314 (t60) REVERT: B 714 MET cc_start: 0.8442 (ptt) cc_final: 0.8240 (ptt) REVERT: B 846 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8753 (mtp) REVERT: B 966 TYR cc_start: 0.8663 (m-80) cc_final: 0.8220 (m-10) outliers start: 22 outliers final: 11 residues processed: 81 average time/residue: 1.3109 time to fit residues: 117.9688 Evaluate side-chains 78 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 848 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 846 MET Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.093318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.077535 restraints weight = 52354.606| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.69 r_work: 0.3527 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3322 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= 0.214 Angle : 0.686 13.260 19567 Z= 0.346 Chirality : 0.042 0.204 2143 Planarity : 0.004 0.057 2279 Dihedral : 17.513 171.051 2513 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 1.76 % Allowed : 21.03 % Favored : 77.21 % 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: 0.74 (0.20), residues: 718 sheet: -0.68 (0.37), residues: 204 loop : -0.32 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 820 HIS 0.003 0.001 HIS B1099 PHE 0.021 0.001 PHE A1107 TYR 0.020 0.001 TYR A 698 ARG 0.012 0.000 ARG B 929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3711.66 seconds wall clock time: 79 minutes 22.75 seconds (4762.75 seconds total)