Starting phenix.real_space_refine on Tue Dec 31 04:26:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v99_31811/12_2024/7v99_31811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v99_31811/12_2024/7v99_31811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v99_31811/12_2024/7v99_31811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v99_31811/12_2024/7v99_31811.map" model { file = "/net/cci-nas-00/data/ceres_data/7v99_31811/12_2024/7v99_31811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v99_31811/12_2024/7v99_31811.cif" } resolution = 3.54 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= 0.008 sd= 0.242 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: 5 Type Number sf(0) Gaussians P 249 5.49 5 S 39 5.16 5 C 8291 2.51 5 N 2662 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14582 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7898 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 62, 'TRANS': 928} Chain breaks: 1 Chain: "K" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 668 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "L" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "R" Number of atoms: 5156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 5156 Classifications: {'RNA': 243} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 105, 'rna3p_pyr': 123} Link IDs: {'rna2p': 15, 'rna3p': 227} Chain breaks: 2 Chain: "S" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 9.60, per 1000 atoms: 0.66 Number of scatterers: 14582 At special positions: 0 Unit cell: (148.5, 125.4, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 249 15.00 O 3341 8.00 N 2662 7.00 C 8291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 845 " - pdb=" SG CYS A 896 " distance=2.05 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1043 " distance=2.05 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: 3.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 57.2% alpha, 9.1% beta 53 base pairs and 118 stacking pairs defined. Time for finding SS restraints: 5.85 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.783A pdb=" N LEU A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 31 through 42 removed outlier: 3.587A pdb=" N ARG A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.649A pdb=" N ALA A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 132 through 140 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.653A pdb=" N MET A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.624A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 397 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.607A pdb=" N LEU A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Proline residue: A 421 - end of helix removed outlier: 3.875A pdb=" N LYS A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 4.258A pdb=" N ASP A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 3.503A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.837A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.781A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.624A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.537A pdb=" N HIS A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.960A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.843A pdb=" N VAL A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 672 removed outlier: 3.535A pdb=" N ARG A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 699 removed outlier: 3.858A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 737 removed outlier: 4.192A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 733 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.924A pdb=" N THR A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 removed outlier: 4.650A pdb=" N ASP A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.704A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 887 " --> pdb=" O PHE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.848A pdb=" N SER A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 removed outlier: 4.014A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1018 removed outlier: 3.511A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 4.418A pdb=" N ALA A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 4.046A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1107 removed outlier: 4.052A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.655A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 22 Processing helix chain 'K' and resid 27 through 37 Processing helix chain 'K' and resid 46 through 72 removed outlier: 3.730A pdb=" N TYR K 50 " --> pdb=" O GLY K 46 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.649A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 Processing helix chain 'L' and resid 37 through 49 removed outlier: 3.776A pdb=" N VAL L 44 " --> pdb=" O TYR L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 83 removed outlier: 3.725A pdb=" N ILE L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.844A pdb=" N LEU L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 124 removed outlier: 3.815A pdb=" N HIS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 3.542A pdb=" N VAL A 119 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.981A pdb=" N ARG A 108 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A 113 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 removed outlier: 3.638A pdb=" N THR A 564 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 598 through 600 removed outlier: 4.313A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 618 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 862 through 865 removed outlier: 3.542A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 874 " --> pdb=" O TYR A 707 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 707 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 712 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 904 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 765 removed outlier: 3.999A pdb=" N ARG A 756 " --> pdb=" O LYS A 749 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 749 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 758 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS A 740 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 799 " --> pdb=" O CYS A 740 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 744 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 795 " --> pdb=" O TYR A 744 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 746 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU A 793 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN A 748 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 791 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA A 750 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA A 789 " --> pdb=" O ALA A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 928 through 929 Processing sheet with id=AB1, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.581A pdb=" N ARG K 42 " --> pdb=" O ILE L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 77 through 78 468 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 118 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3841 1.34 - 1.46: 4715 1.46 - 1.58: 6300 1.58 - 1.70: 494 1.70 - 1.82: 52 Bond restraints: 15402 Sorted by residual: bond pdb=" C PRO A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.12e-02 7.97e+03 8.17e+00 bond pdb=" C ASN A1120 " pdb=" N PRO A1121 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.12e-02 7.97e+03 3.34e+00 bond pdb=" C ALA K 47 " pdb=" N PRO K 48 " ideal model delta sigma weight residual 1.336 1.356 -0.021 1.23e-02 6.61e+03 2.78e+00 bond pdb=" C LYS A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.30e-02 5.92e+03 2.42e+00 bond pdb=" CA ASN A 799 " pdb=" CB ASN A 799 " ideal model delta sigma weight residual 1.527 1.562 -0.035 2.48e-02 1.63e+03 2.00e+00 ... (remaining 15397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21458 1.41 - 2.82: 499 2.82 - 4.23: 66 4.23 - 5.64: 26 5.64 - 7.05: 4 Bond angle restraints: 22053 Sorted by residual: angle pdb=" N GLN A 569 " pdb=" CA GLN A 569 " pdb=" C GLN A 569 " ideal model delta sigma weight residual 110.44 106.41 4.03 1.20e+00 6.94e-01 1.13e+01 angle pdb=" N ALA A 918 " pdb=" CA ALA A 918 " pdb=" C ALA A 918 " ideal model delta sigma weight residual 114.56 110.75 3.81 1.27e+00 6.20e-01 9.00e+00 angle pdb=" C VAL A 162 " pdb=" N ALA A 163 " pdb=" CA ALA A 163 " ideal model delta sigma weight residual 122.85 119.74 3.11 1.10e+00 8.26e-01 7.97e+00 angle pdb=" C LEU A1042 " pdb=" N CYS A1043 " pdb=" CA CYS A1043 " ideal model delta sigma weight residual 121.58 116.08 5.50 1.95e+00 2.63e-01 7.95e+00 angle pdb=" N VAL A1087 " pdb=" CA VAL A1087 " pdb=" C VAL A1087 " ideal model delta sigma weight residual 112.12 109.77 2.35 8.40e-01 1.42e+00 7.84e+00 ... (remaining 22048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8983 35.43 - 70.86: 639 70.86 - 106.29: 100 106.29 - 141.72: 1 141.72 - 177.14: 4 Dihedral angle restraints: 9727 sinusoidal: 6325 harmonic: 3402 Sorted by residual: dihedral pdb=" CB CYS A 982 " pdb=" SG CYS A 982 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 45.52 47.48 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA GLN A 569 " pdb=" C GLN A 569 " pdb=" N LYS A 570 " pdb=" CA LYS A 570 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C4' G R 76 " pdb=" C3' G R 76 " pdb=" O3' G R 76 " pdb=" P U R 77 " ideal model delta sinusoidal sigma weight residual -140.00 37.14 -177.14 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 9724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2105 0.028 - 0.057: 414 0.057 - 0.085: 106 0.085 - 0.113: 51 0.113 - 0.142: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" C3' C R 72 " pdb=" C4' C R 72 " pdb=" O3' C R 72 " pdb=" C2' C R 72 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" C1' A R 174 " pdb=" O4' A R 174 " pdb=" C2' A R 174 " pdb=" N9 A R 174 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CB THR A 375 " pdb=" CA THR A 375 " pdb=" OG1 THR A 375 " pdb=" CG2 THR A 375 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2685 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 68 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO A 69 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 79 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO K 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1043 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C CYS A1043 " -0.025 2.00e-02 2.50e+03 pdb=" O CYS A1043 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A1044 " 0.008 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3114 2.79 - 3.31: 12557 3.31 - 3.84: 24599 3.84 - 4.37: 27023 4.37 - 4.90: 42288 Nonbonded interactions: 109581 Sorted by model distance: nonbonded pdb=" O2' G R 76 " pdb=" OP1 U R 77 " model vdw 2.258 3.040 nonbonded pdb=" O2' C R 72 " pdb=" O5' G R 73 " model vdw 2.273 3.040 nonbonded pdb=" NH2 ARG A 390 " pdb=" OP2 C R 290 " model vdw 2.292 3.120 nonbonded pdb=" O ARG A 696 " pdb=" NE2 GLN A 700 " model vdw 2.314 3.120 nonbonded pdb=" OG SER A 619 " pdb=" O ALA A 817 " model vdw 2.324 3.040 ... (remaining 109576 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 4.410 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.430 Find NCS groups from input model: 0.160 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 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 : 0.002 0.035 15402 Z= 0.138 Angle : 0.530 7.050 22053 Z= 0.320 Chirality : 0.028 0.142 2688 Planarity : 0.004 0.061 1895 Dihedral : 20.831 177.144 7521 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.21), residues: 1162 helix: -1.05 (0.19), residues: 615 sheet: -1.52 (0.50), residues: 77 loop : -3.76 (0.22), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 581 HIS 0.003 0.000 HIS A 815 PHE 0.013 0.001 PHE A 776 TYR 0.007 0.001 TYR A 18 ARG 0.005 0.000 ARG A 979 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8189 (mt) cc_final: 0.7831 (mt) REVERT: A 378 ARG cc_start: 0.5594 (ttt180) cc_final: 0.3153 (mtt180) REVERT: A 452 LEU cc_start: 0.9325 (mt) cc_final: 0.8793 (pp) REVERT: K 73 ASN cc_start: 0.7407 (m110) cc_final: 0.7099 (p0) REVERT: K 82 HIS cc_start: 0.8773 (m-70) cc_final: 0.8517 (m90) REVERT: L 62 MET cc_start: 0.7049 (mmp) cc_final: 0.6450 (mtt) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.4339 time to fit residues: 100.4627 Evaluate side-chains 98 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 95 ASN A 490 ASN A 506 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS A 906 ASN A 921 GLN A1022 HIS A1023 GLN K 31 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15402 Z= 0.175 Angle : 0.565 8.903 22053 Z= 0.278 Chirality : 0.033 0.166 2688 Planarity : 0.004 0.054 1895 Dihedral : 22.008 171.552 5262 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.01 % Allowed : 11.33 % Favored : 86.66 % 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: -1.69 (0.23), residues: 1162 helix: 0.34 (0.21), residues: 613 sheet: -0.94 (0.51), residues: 77 loop : -3.24 (0.23), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 690 HIS 0.006 0.001 HIS A 779 PHE 0.019 0.002 PHE A 776 TYR 0.013 0.002 TYR A1002 ARG 0.006 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6414 (pm20) REVERT: A 332 LEU cc_start: 0.8242 (mt) cc_final: 0.7966 (mt) REVERT: A 378 ARG cc_start: 0.5658 (ttt180) cc_final: 0.3159 (mtt180) REVERT: A 452 LEU cc_start: 0.9265 (mt) cc_final: 0.8807 (pp) REVERT: A 872 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 979 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7865 (ttm110) REVERT: K 82 HIS cc_start: 0.8785 (m-70) cc_final: 0.8580 (m-70) outliers start: 20 outliers final: 9 residues processed: 116 average time/residue: 0.3622 time to fit residues: 57.6638 Evaluate side-chains 95 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 490 ASN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15402 Z= 0.193 Angle : 0.559 10.083 22053 Z= 0.276 Chirality : 0.033 0.183 2688 Planarity : 0.005 0.058 1895 Dihedral : 21.966 169.493 5262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.63 % Rotamer: Outliers : 2.11 % Allowed : 14.64 % Favored : 83.25 % 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: -1.12 (0.24), residues: 1162 helix: 0.85 (0.21), residues: 623 sheet: -0.69 (0.49), residues: 92 loop : -3.21 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 510 HIS 0.035 0.002 HIS K 31 PHE 0.015 0.002 PHE A 776 TYR 0.021 0.001 TYR A 638 ARG 0.005 0.000 ARG L 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8380 (mt) cc_final: 0.7975 (mt) REVERT: A 378 ARG cc_start: 0.5674 (ttt180) cc_final: 0.3297 (mtt180) REVERT: A 452 LEU cc_start: 0.9292 (mt) cc_final: 0.8804 (pp) REVERT: A 979 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7983 (ttm-80) REVERT: K 82 HIS cc_start: 0.8787 (m-70) cc_final: 0.8574 (m90) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.3555 time to fit residues: 49.8583 Evaluate side-chains 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 112 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS A 969 ASN A1023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15402 Z= 0.168 Angle : 0.539 12.740 22053 Z= 0.267 Chirality : 0.034 0.211 2688 Planarity : 0.004 0.054 1895 Dihedral : 21.876 170.969 5262 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 2.61 % Allowed : 16.45 % Favored : 80.94 % 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: -0.72 (0.25), residues: 1162 helix: 1.13 (0.22), residues: 629 sheet: -0.36 (0.51), residues: 92 loop : -3.05 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 137 HIS 0.011 0.001 HIS K 31 PHE 0.018 0.002 PHE A 159 TYR 0.019 0.002 TYR A 717 ARG 0.007 0.001 ARG A1034 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.6946 (OUTLIER) cc_final: 0.6674 (m) REVERT: A 332 LEU cc_start: 0.8353 (mt) cc_final: 0.8047 (mt) REVERT: A 378 ARG cc_start: 0.5687 (ttt180) cc_final: 0.3601 (mtt180) REVERT: A 389 MET cc_start: 0.7888 (mtm) cc_final: 0.7643 (mtm) REVERT: A 452 LEU cc_start: 0.9292 (mt) cc_final: 0.8831 (pp) REVERT: A 683 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6243 (pp) REVERT: A 922 MET cc_start: 0.7194 (pmm) cc_final: 0.6687 (ptt) REVERT: K 79 ILE cc_start: 0.4932 (tp) cc_final: 0.4660 (tp) REVERT: K 82 HIS cc_start: 0.8826 (m-70) cc_final: 0.8599 (m170) outliers start: 26 outliers final: 11 residues processed: 106 average time/residue: 0.3134 time to fit residues: 48.3700 Evaluate side-chains 95 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.0270 chunk 115 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15402 Z= 0.143 Angle : 0.524 11.930 22053 Z= 0.253 Chirality : 0.032 0.153 2688 Planarity : 0.004 0.053 1895 Dihedral : 21.804 170.323 5262 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 2.01 % Allowed : 18.66 % Favored : 79.34 % 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: -0.48 (0.25), residues: 1162 helix: 1.32 (0.22), residues: 630 sheet: -0.14 (0.52), residues: 92 loop : -2.97 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 510 HIS 0.003 0.001 HIS A 534 PHE 0.015 0.001 PHE A 776 TYR 0.016 0.001 TYR A 638 ARG 0.004 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.6978 (t) cc_final: 0.6704 (m) REVERT: A 332 LEU cc_start: 0.8354 (mt) cc_final: 0.8015 (mt) REVERT: A 378 ARG cc_start: 0.5663 (ttt180) cc_final: 0.3500 (mtt180) REVERT: A 452 LEU cc_start: 0.9311 (mt) cc_final: 0.8756 (pp) REVERT: A 922 MET cc_start: 0.7209 (pmm) cc_final: 0.6791 (ptt) REVERT: K 79 ILE cc_start: 0.5291 (tp) cc_final: 0.5024 (tp) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.3073 time to fit residues: 42.5051 Evaluate side-chains 95 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 135 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15402 Z= 0.162 Angle : 0.539 13.218 22053 Z= 0.260 Chirality : 0.032 0.164 2688 Planarity : 0.004 0.049 1895 Dihedral : 21.758 170.930 5262 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.51 % Allowed : 19.96 % Favored : 77.53 % 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: -0.44 (0.26), residues: 1162 helix: 1.40 (0.22), residues: 633 sheet: -0.39 (0.52), residues: 102 loop : -3.02 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 547 HIS 0.005 0.001 HIS A 815 PHE 0.022 0.001 PHE A 776 TYR 0.016 0.001 TYR A 638 ARG 0.004 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 VAL cc_start: 0.6980 (t) cc_final: 0.6621 (m) REVERT: A 332 LEU cc_start: 0.8311 (mt) cc_final: 0.7966 (mt) REVERT: A 378 ARG cc_start: 0.5773 (ttt180) cc_final: 0.3715 (mtt180) REVERT: A 922 MET cc_start: 0.7309 (pmm) cc_final: 0.6974 (ptt) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.2602 time to fit residues: 36.7583 Evaluate side-chains 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 15402 Z= 0.208 Angle : 0.576 13.602 22053 Z= 0.281 Chirality : 0.035 0.379 2688 Planarity : 0.004 0.037 1895 Dihedral : 21.829 170.472 5262 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 2.41 % Allowed : 20.36 % Favored : 77.23 % 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 (0.25), residues: 1162 helix: 1.27 (0.21), residues: 636 sheet: -0.63 (0.52), residues: 96 loop : -2.88 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 371 HIS 0.008 0.001 HIS K 82 PHE 0.013 0.001 PHE A 393 TYR 0.017 0.001 TYR A 638 ARG 0.006 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8338 (mt) cc_final: 0.7999 (mt) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.2727 time to fit residues: 37.3616 Evaluate side-chains 91 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15402 Z= 0.210 Angle : 0.588 14.229 22053 Z= 0.287 Chirality : 0.034 0.190 2688 Planarity : 0.004 0.044 1895 Dihedral : 21.868 170.546 5262 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 2.11 % Allowed : 21.46 % Favored : 76.43 % 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: -0.41 (0.26), residues: 1162 helix: 1.29 (0.21), residues: 641 sheet: -0.56 (0.51), residues: 101 loop : -2.79 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 547 HIS 0.008 0.001 HIS K 82 PHE 0.017 0.002 PHE A 812 TYR 0.014 0.001 TYR A 638 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8353 (mt) cc_final: 0.8060 (mt) REVERT: A 378 ARG cc_start: 0.5739 (ttt180) cc_final: 0.3566 (mtt180) REVERT: A 690 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.8158 (t60) REVERT: A 774 ARG cc_start: 0.8526 (ttt180) cc_final: 0.8186 (tmm-80) REVERT: A 905 VAL cc_start: 0.8542 (t) cc_final: 0.8066 (p) outliers start: 21 outliers final: 17 residues processed: 84 average time/residue: 0.2612 time to fit residues: 33.7157 Evaluate side-chains 88 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 690 TRP Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 82 optimal weight: 0.0470 chunk 132 optimal weight: 6.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15402 Z= 0.162 Angle : 0.553 13.754 22053 Z= 0.266 Chirality : 0.033 0.203 2688 Planarity : 0.004 0.045 1895 Dihedral : 21.818 170.550 5262 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 1.81 % Allowed : 21.97 % Favored : 76.23 % 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: -0.29 (0.26), residues: 1162 helix: 1.40 (0.22), residues: 641 sheet: -0.45 (0.53), residues: 94 loop : -2.75 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 371 HIS 0.004 0.001 HIS K 82 PHE 0.015 0.001 PHE A 776 TYR 0.012 0.001 TYR A 638 ARG 0.007 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8346 (mt) cc_final: 0.8014 (mt) REVERT: A 905 VAL cc_start: 0.8510 (t) cc_final: 0.8011 (p) outliers start: 18 outliers final: 17 residues processed: 83 average time/residue: 0.2678 time to fit residues: 34.0503 Evaluate side-chains 86 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 HIS ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15402 Z= 0.169 Angle : 0.568 13.825 22053 Z= 0.272 Chirality : 0.033 0.203 2688 Planarity : 0.004 0.049 1895 Dihedral : 21.766 172.157 5262 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.11 % Allowed : 21.36 % Favored : 76.53 % 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: -0.27 (0.26), residues: 1162 helix: 1.37 (0.22), residues: 640 sheet: -0.31 (0.54), residues: 99 loop : -2.72 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 371 HIS 0.004 0.001 HIS K 82 PHE 0.017 0.001 PHE A 776 TYR 0.013 0.001 TYR A 552 ARG 0.005 0.000 ARG A 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.5682 (ttt180) cc_final: 0.3515 (mtt180) REVERT: A 389 MET cc_start: 0.7952 (mtm) cc_final: 0.7608 (ttm) REVERT: A 905 VAL cc_start: 0.8419 (t) cc_final: 0.7876 (p) outliers start: 21 outliers final: 18 residues processed: 83 average time/residue: 0.2600 time to fit residues: 34.1843 Evaluate side-chains 88 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 500 HIS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 779 HIS Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 121 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 0.0470 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 HIS ** 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 = 0.4401 r_free = 0.4401 target = 0.103013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.073318 restraints weight = 82183.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.075198 restraints weight = 44635.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.076131 restraints weight = 32870.653| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15402 Z= 0.154 Angle : 0.561 13.636 22053 Z= 0.265 Chirality : 0.032 0.204 2688 Planarity : 0.004 0.050 1895 Dihedral : 21.721 173.120 5262 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 2.01 % Allowed : 21.56 % Favored : 76.43 % 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: -0.23 (0.26), residues: 1162 helix: 1.41 (0.22), residues: 640 sheet: -0.23 (0.54), residues: 99 loop : -2.74 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 371 HIS 0.005 0.001 HIS K 82 PHE 0.017 0.001 PHE K 25 TYR 0.011 0.001 TYR A 638 ARG 0.005 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2749.67 seconds wall clock time: 51 minutes 51.98 seconds (3111.98 seconds total)