Starting phenix.real_space_refine on Tue Nov 19 03:29:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smx_40605/11_2024/8smx_40605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smx_40605/11_2024/8smx_40605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smx_40605/11_2024/8smx_40605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smx_40605/11_2024/8smx_40605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smx_40605/11_2024/8smx_40605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smx_40605/11_2024/8smx_40605.cif" } resolution = 3.2 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= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 Zn 2 6.06 5 P 294 5.49 5 S 32 5.16 5 C 7891 2.51 5 N 2608 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13998 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 32.756 69.086 46.490 1.00 27.36 S ATOM 12446 SG CYS K 51 31.674 65.517 46.031 1.00 24.79 S ATOM 12470 SG CYS K 54 32.868 67.529 43.025 1.00 27.29 S ATOM 12187 SG CYS K 16 23.703 62.014 53.077 1.00 58.61 S ATOM 12205 SG CYS K 19 21.687 59.882 55.391 1.00 62.50 S ATOM 12335 SG CYS K 36 23.658 62.811 56.830 1.00 42.90 S ATOM 12357 SG CYS K 39 25.492 59.705 55.463 1.00 39.01 S Time building chain proxies: 9.39, per 1000 atoms: 0.67 Number of scatterers: 13998 At special positions: 0 Unit cell: (108.896, 130.144, 126.16, 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) Zn 2 29.99 S 32 16.00 P 294 15.00 O 3171 8.00 N 2608 7.00 C 7891 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: 3.81 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " Number of angles added : 9 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 64.1% alpha, 4.5% beta 136 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 7.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.611A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.565A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.844A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.593A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.740A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.508A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.640A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.764A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.538A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.761A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.579A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.588A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.585A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.819A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.684A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.559A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.641A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.574A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 37 through 46 Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.858A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 84 removed outlier: 4.158A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR K 84 " --> pdb=" O ILE K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.917A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.538A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.860A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 Processing helix chain 'L' and resid 130 through 143 removed outlier: 3.639A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.155A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.444A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.800A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.010A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.606A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 462 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2974 1.33 - 1.45: 4495 1.45 - 1.57: 6762 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CG PRO L 61 " pdb=" CD PRO L 61 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.57e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB ARG A 129 " pdb=" CG ARG A 129 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CB THR K 66 " pdb=" CG2 THR K 66 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.17e-01 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 20929 1.77 - 3.54: 395 3.54 - 5.31: 22 5.31 - 7.08: 5 7.08 - 8.85: 2 Bond angle restraints: 21353 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 121.55 -8.85 3.00e+00 1.11e-01 8.71e+00 angle pdb=" C3' DG J -70 " pdb=" C2' DG J -70 " pdb=" C1' DG J -70 " ideal model delta sigma weight residual 101.60 105.56 -3.96 1.50e+00 4.44e-01 6.98e+00 angle pdb=" C LEU L 89 " pdb=" N ARG L 90 " pdb=" CA ARG L 90 " ideal model delta sigma weight residual 122.58 117.16 5.42 2.07e+00 2.33e-01 6.85e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 113.18 118.96 -5.78 2.37e+00 1.78e-01 5.94e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 118.62 -5.44 2.37e+00 1.78e-01 5.26e+00 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 6792 35.13 - 70.26: 1410 70.26 - 105.39: 20 105.39 - 140.51: 0 140.51 - 175.64: 2 Dihedral angle restraints: 8224 sinusoidal: 5302 harmonic: 2922 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 44.36 175.64 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.14 153.86 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1636 0.030 - 0.061: 556 0.061 - 0.091: 160 0.091 - 0.121: 60 0.121 - 0.151: 7 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CG LEU L 103 " pdb=" CB LEU L 103 " pdb=" CD1 LEU L 103 " pdb=" CD2 LEU L 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2416 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.026 2.00e-02 2.50e+03 1.14e-02 3.60e+00 pdb=" N9 DA I -35 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.03e-02 3.20e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " 0.024 2.00e-02 2.50e+03 1.06e-02 3.07e+00 pdb=" N9 DA I 17 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " -0.002 2.00e-02 2.50e+03 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1781 2.76 - 3.47: 17175 3.47 - 4.19: 37807 4.19 - 4.90: 59329 Nonbonded interactions: 116094 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.236 2.496 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.246 3.120 nonbonded pdb=" N SER G 11 " pdb=" O SER H 123 " model vdw 2.253 3.120 ... (remaining 116089 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 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.17 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.330 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.003 0.038 14864 Z= 0.170 Angle : 0.566 8.854 21353 Z= 0.333 Chirality : 0.036 0.151 2419 Planarity : 0.004 0.041 1688 Dihedral : 26.376 175.642 6336 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.43 (0.27), residues: 983 helix: 1.97 (0.21), residues: 628 sheet: -0.51 (0.92), residues: 24 loop : -0.96 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 77 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE F 61 TYR 0.010 0.001 TYR D 121 ARG 0.004 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.156 Fit side-chains REVERT: C 118 LYS cc_start: 0.7865 (pttm) cc_final: 0.7286 (ptpp) REVERT: D 35 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8128 (mt-10) REVERT: D 116 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7592 (mtmm) REVERT: E 53 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8015 (ttm170) REVERT: H 54 ILE cc_start: 0.9102 (tt) cc_final: 0.8879 (tt) REVERT: H 112 SER cc_start: 0.9103 (t) cc_final: 0.8481 (m) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4003 time to fit residues: 52.9380 Evaluate side-chains 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 110 optimal weight: 40.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.251 Angle : 0.577 6.985 21353 Z= 0.338 Chirality : 0.037 0.147 2419 Planarity : 0.005 0.040 1688 Dihedral : 29.349 176.280 4332 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.43 (0.26), residues: 983 helix: 1.98 (0.21), residues: 634 sheet: -0.83 (0.88), residues: 24 loop : -1.04 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.005 0.001 HIS A 113 PHE 0.011 0.002 PHE F 61 TYR 0.019 0.002 TYR G 50 ARG 0.005 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.182 Fit side-chains REVERT: C 118 LYS cc_start: 0.7846 (pttm) cc_final: 0.7257 (ptpp) REVERT: D 35 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7900 (mt-10) REVERT: H 54 ILE cc_start: 0.9138 (tt) cc_final: 0.8890 (tt) REVERT: H 112 SER cc_start: 0.9122 (t) cc_final: 0.8500 (m) REVERT: H 122 THR cc_start: 0.9154 (t) cc_final: 0.8829 (m) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.3827 time to fit residues: 51.2832 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 50.0000 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14864 Z= 0.377 Angle : 0.634 7.771 21353 Z= 0.367 Chirality : 0.041 0.159 2419 Planarity : 0.005 0.048 1688 Dihedral : 29.612 176.267 4332 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.58 % Allowed : 6.43 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.01 (0.26), residues: 983 helix: 1.68 (0.20), residues: 636 sheet: -0.66 (0.87), residues: 24 loop : -1.31 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.008 0.002 HIS A 113 PHE 0.015 0.002 PHE D 65 TYR 0.016 0.002 TYR D 121 ARG 0.007 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.205 Fit side-chains REVERT: C 118 LYS cc_start: 0.7887 (pttm) cc_final: 0.7287 (ptpp) REVERT: D 35 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7840 (mt-10) REVERT: H 54 ILE cc_start: 0.9099 (tt) cc_final: 0.8843 (tt) REVERT: H 112 SER cc_start: 0.9117 (t) cc_final: 0.8499 (m) outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 0.3720 time to fit residues: 49.1042 Evaluate side-chains 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14864 Z= 0.175 Angle : 0.541 6.907 21353 Z= 0.321 Chirality : 0.035 0.134 2419 Planarity : 0.004 0.040 1688 Dihedral : 29.313 176.023 4332 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.58 % Allowed : 7.71 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.57 (0.27), residues: 983 helix: 2.13 (0.21), residues: 637 sheet: -0.55 (0.92), residues: 24 loop : -1.13 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 77 HIS 0.004 0.001 HIS L 75 PHE 0.008 0.001 PHE F 61 TYR 0.008 0.001 TYR G 57 ARG 0.006 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.125 Fit side-chains REVERT: C 118 LYS cc_start: 0.7822 (pttm) cc_final: 0.7245 (ptpp) REVERT: H 54 ILE cc_start: 0.9061 (tt) cc_final: 0.8792 (tt) REVERT: H 112 SER cc_start: 0.9113 (t) cc_final: 0.8468 (m) REVERT: H 122 THR cc_start: 0.9000 (t) cc_final: 0.8716 (m) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.3677 time to fit residues: 50.6128 Evaluate side-chains 98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.254 Angle : 0.566 7.128 21353 Z= 0.333 Chirality : 0.037 0.145 2419 Planarity : 0.004 0.040 1688 Dihedral : 29.378 176.124 4332 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.70 % Allowed : 9.58 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.47 (0.26), residues: 983 helix: 2.06 (0.21), residues: 637 sheet: -0.68 (0.92), residues: 24 loop : -1.16 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.005 0.001 HIS A 113 PHE 0.011 0.002 PHE F 61 TYR 0.012 0.001 TYR D 121 ARG 0.004 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.119 Fit side-chains REVERT: C 118 LYS cc_start: 0.7843 (pttm) cc_final: 0.7261 (ptpp) REVERT: H 54 ILE cc_start: 0.9066 (tt) cc_final: 0.8808 (tt) REVERT: H 112 SER cc_start: 0.9116 (t) cc_final: 0.8488 (m) REVERT: H 122 THR cc_start: 0.9079 (t) cc_final: 0.8747 (m) outliers start: 6 outliers final: 5 residues processed: 99 average time/residue: 0.3775 time to fit residues: 49.9931 Evaluate side-chains 100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14864 Z= 0.194 Angle : 0.554 7.026 21353 Z= 0.327 Chirality : 0.035 0.140 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.371 176.031 4332 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.93 % Allowed : 9.93 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.54 (0.26), residues: 983 helix: 2.11 (0.21), residues: 637 sheet: -0.69 (0.91), residues: 24 loop : -1.14 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 PHE 0.010 0.002 PHE F 61 TYR 0.011 0.001 TYR D 121 ARG 0.003 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.143 Fit side-chains REVERT: C 118 LYS cc_start: 0.7835 (pttm) cc_final: 0.7258 (ptpp) REVERT: H 54 ILE cc_start: 0.9059 (tt) cc_final: 0.8801 (tt) REVERT: H 112 SER cc_start: 0.9102 (t) cc_final: 0.8482 (m) REVERT: H 122 THR cc_start: 0.9010 (t) cc_final: 0.8678 (m) outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 0.3838 time to fit residues: 51.6113 Evaluate side-chains 101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14864 Z= 0.224 Angle : 0.555 7.199 21353 Z= 0.328 Chirality : 0.036 0.139 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.365 176.169 4332 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.93 % Allowed : 9.93 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.56 (0.26), residues: 983 helix: 2.14 (0.21), residues: 635 sheet: -0.71 (0.91), residues: 24 loop : -1.12 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.002 PHE F 61 TYR 0.011 0.001 TYR D 121 ARG 0.004 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.074 Fit side-chains REVERT: C 118 LYS cc_start: 0.7835 (pttm) cc_final: 0.7257 (ptpp) REVERT: H 54 ILE cc_start: 0.9059 (tt) cc_final: 0.8801 (tt) REVERT: H 112 SER cc_start: 0.9112 (t) cc_final: 0.8472 (m) REVERT: H 122 THR cc_start: 0.9013 (t) cc_final: 0.8680 (m) outliers start: 8 outliers final: 7 residues processed: 102 average time/residue: 0.3842 time to fit residues: 52.1597 Evaluate side-chains 103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14864 Z= 0.180 Angle : 0.548 7.061 21353 Z= 0.325 Chirality : 0.035 0.136 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.359 176.143 4332 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.82 % Allowed : 10.28 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.60 (0.26), residues: 983 helix: 2.17 (0.21), residues: 635 sheet: -0.71 (0.92), residues: 24 loop : -1.10 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 PHE 0.010 0.001 PHE F 61 TYR 0.010 0.001 TYR D 121 ARG 0.002 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.224 Fit side-chains REVERT: C 118 LYS cc_start: 0.7831 (pttm) cc_final: 0.7254 (ptpp) REVERT: H 54 ILE cc_start: 0.9055 (tt) cc_final: 0.8788 (tt) REVERT: H 112 SER cc_start: 0.9105 (t) cc_final: 0.8471 (m) REVERT: H 122 THR cc_start: 0.9011 (t) cc_final: 0.8679 (m) outliers start: 7 outliers final: 7 residues processed: 101 average time/residue: 0.3759 time to fit residues: 51.2473 Evaluate side-chains 103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.222 Angle : 0.553 7.255 21353 Z= 0.327 Chirality : 0.036 0.138 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.354 176.337 4332 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.93 % Allowed : 10.16 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.59 (0.26), residues: 983 helix: 2.16 (0.21), residues: 635 sheet: -0.71 (0.92), residues: 24 loop : -1.10 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.002 PHE F 61 TYR 0.010 0.001 TYR D 121 ARG 0.002 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.180 Fit side-chains REVERT: C 118 LYS cc_start: 0.7834 (pttm) cc_final: 0.7256 (ptpp) REVERT: H 54 ILE cc_start: 0.9056 (tt) cc_final: 0.8792 (tt) REVERT: H 112 SER cc_start: 0.9117 (t) cc_final: 0.8473 (m) REVERT: H 122 THR cc_start: 0.9012 (t) cc_final: 0.8680 (m) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.4032 time to fit residues: 54.4324 Evaluate side-chains 103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14864 Z= 0.267 Angle : 0.571 7.477 21353 Z= 0.335 Chirality : 0.037 0.146 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.397 176.458 4332 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.93 % Allowed : 10.28 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.43 (0.26), residues: 983 helix: 2.03 (0.20), residues: 638 sheet: -0.54 (0.93), residues: 24 loop : -1.20 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.005 0.001 HIS A 113 PHE 0.011 0.002 PHE A 78 TYR 0.012 0.001 TYR D 121 ARG 0.004 0.000 ARG C 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.215 Fit side-chains REVERT: A 129 ARG cc_start: 0.8337 (tmt170) cc_final: 0.8134 (tmt170) REVERT: C 118 LYS cc_start: 0.7853 (pttm) cc_final: 0.7261 (ptpp) REVERT: G 95 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8411 (ttpt) REVERT: H 54 ILE cc_start: 0.9072 (tt) cc_final: 0.8822 (tt) REVERT: H 112 SER cc_start: 0.9112 (t) cc_final: 0.8479 (m) REVERT: H 122 THR cc_start: 0.9075 (t) cc_final: 0.8726 (m) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.3792 time to fit residues: 51.2757 Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.155463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.119955 restraints weight = 23026.468| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.86 r_work: 0.2720 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14864 Z= 0.218 Angle : 0.575 13.683 21353 Z= 0.334 Chirality : 0.036 0.143 2419 Planarity : 0.004 0.038 1688 Dihedral : 29.393 176.407 4332 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.93 % Allowed : 10.40 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.49 (0.26), residues: 983 helix: 2.07 (0.20), residues: 638 sheet: -0.57 (0.93), residues: 24 loop : -1.17 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS A 113 PHE 0.011 0.002 PHE A 78 TYR 0.011 0.001 TYR D 121 ARG 0.002 0.000 ARG K 68 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: