Starting phenix.real_space_refine on Sat Jul 4 04:28:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.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/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.cif" model { file = "/net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smy_40606/07_2026/8smy_40606.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.115 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 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 32.961 68.212 47.437 1.00 46.50 S ATOM 12446 SG CYS K 51 31.741 64.804 46.427 1.00 38.48 S ATOM 12470 SG CYS K 54 31.689 67.804 43.930 1.00 45.98 S ATOM 12187 SG CYS K 16 23.164 61.088 52.931 1.00 62.13 S ATOM 12205 SG CYS K 19 21.277 58.686 55.106 1.00 60.25 S ATOM 12335 SG CYS K 36 24.123 60.787 56.601 1.00 49.24 S ATOM 12357 SG CYS K 39 25.001 57.974 54.445 1.00 47.55 S Time building chain proxies: 2.77, per 1000 atoms: 0.20 Number of scatterers: 13998 At special positions: 0 Unit cell: (108.896, 130.144, 127.488, 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 399.5 milliseconds 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 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " 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 11 sheets defined 63.4% alpha, 4.3% beta 137 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.697A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.706A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.642A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.836A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.608A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.724A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.737A 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: 3.541A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.564A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 4.180A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.618A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (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 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.881A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.595A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.757A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.620A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 67 removed outlier: 4.044A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.656A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.887A 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: 3.703A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 Processing helix chain 'L' and resid 131 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.687A 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 removed outlier: 3.535A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.696A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.458A 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 101 through 102 removed outlier: 6.826A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.097A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.767A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 29 removed outlier: 3.788A pdb=" N HIS K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25 452 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 698 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.20 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: 3240 1.34 - 1.46: 4293 1.46 - 1.58: 6698 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT I 62 " pdb=" C2' DT I 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.10e+00 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 20463 1.75 - 3.50: 866 3.50 - 5.25: 20 5.25 - 6.99: 2 6.99 - 8.74: 2 Bond angle restraints: 21353 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 6813 35.30 - 70.59: 1393 70.59 - 105.89: 22 105.89 - 141.19: 0 141.19 - 176.49: 2 Dihedral angle restraints: 8230 sinusoidal: 5306 harmonic: 2924 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 43.51 176.49 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 66.28 153.72 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CB GLU G 41 " pdb=" CG GLU G 41 " pdb=" CD GLU G 41 " pdb=" OE1 GLU G 41 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1367 0.031 - 0.063: 705 0.063 - 0.094: 259 0.094 - 0.125: 85 0.125 - 0.157: 3 Chirality restraints: 2419 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" C3' DC J 49 " pdb=" C4' DC J 49 " pdb=" O3' DC J 49 " pdb=" C2' DC J 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2416 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO L 61 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 42 " -0.182 9.50e-02 1.11e+02 8.19e-02 4.21e+00 pdb=" NE ARG A 42 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 42 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 42 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 42 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 75 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO L 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 76 " -0.028 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 610 2.71 - 3.26: 12002 3.26 - 3.80: 24351 3.80 - 4.35: 31976 4.35 - 4.90: 46643 Nonbonded interactions: 115582 Sorted by model distance: nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.162 3.120 nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER K 60 " model vdw 2.189 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.244 2.496 nonbonded pdb=" O LEU E 61 " pdb=" NH1 ARG F 36 " model vdw 2.256 3.120 nonbonded pdb=" N4 DC I 21 " pdb=" O6 DG J -21 " model vdw 2.271 3.120 ... (remaining 115577 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14874 Z= 0.476 Angle : 0.697 8.742 21368 Z= 0.606 Chirality : 0.043 0.157 2419 Planarity : 0.005 0.082 1688 Dihedral : 26.398 176.486 6336 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.27), residues: 983 helix: 1.87 (0.22), residues: 613 sheet: 0.67 (1.00), residues: 24 loop : -0.77 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 68 TYR 0.012 0.001 TYR L 134 PHE 0.009 0.001 PHE F 61 TRP 0.006 0.001 TRP K 77 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.48 (14864) covalent geometry : angle 0.69328 / 0.61 (21353) hydrogen bonds : bond 0.11106 / 7.24 ( 803) hydrogen bonds : angle 3.48440 / 2.48 ( 2033) metal coordination : bond 0.01386 / 0.70 ( 8) metal coordination : angle 3.50716 / 1.84 ( 9) link_TRANS : bond 0.00192 / 0.10 ( 2) link_TRANS : angle 0.58269 / 0.25 ( 6) *********************** 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 117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.276 Fit side-chains REVERT: A 58 THR cc_start: 0.9392 (p) cc_final: 0.9020 (p) REVERT: B 63 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7675 (mt-10) REVERT: G 74 LYS cc_start: 0.8650 (mttp) cc_final: 0.8190 (mmtm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1420 time to fit residues: 22.4303 Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124444 restraints weight = 28745.427| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.75 r_work: 0.3042 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (18 function evaluations) r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14874 Z= 0.139 Angle : 0.583 7.585 21368 Z= 0.342 Chirality : 0.044 0.255 2419 Planarity : 0.005 0.053 1688 Dihedral : 29.487 178.074 4332 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.58 % Allowed : 6.07 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 983 helix: 1.85 (0.21), residues: 632 sheet: 0.62 (0.99), residues: 24 loop : -0.80 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 139 TYR 0.008 0.001 TYR D 40 PHE 0.008 0.001 PHE F 61 TRP 0.006 0.001 TRP K 77 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (14864) covalent geometry : angle 0.57615 / 0.34 (21353) hydrogen bonds : bond 0.05689 / 3.65 ( 803) hydrogen bonds : angle 3.07692 / 2.19 ( 2033) metal coordination : bond 0.01572 / 0.81 ( 8) metal coordination : angle 4.43747 / 2.30 ( 9) link_TRANS : bond 0.00059 / 0.03 ( 2) link_TRANS : angle 0.54406 / 0.22 ( 6) *********************** 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 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9398 (p) cc_final: 0.9086 (p) REVERT: B 63 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8122 (mt-10) REVERT: E 59 GLU cc_start: 0.8545 (pt0) cc_final: 0.8299 (pt0) REVERT: G 74 LYS cc_start: 0.8684 (mttp) cc_final: 0.8186 (mmtm) outliers start: 5 outliers final: 5 residues processed: 109 average time/residue: 0.1593 time to fit residues: 23.8003 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.151751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.105446 restraints weight = 25038.093| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.66 r_work: 0.2942 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14874 Z= 0.177 Angle : 0.603 7.507 21368 Z= 0.346 Chirality : 0.045 0.285 2419 Planarity : 0.005 0.050 1688 Dihedral : 29.658 177.235 4332 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.17 % Allowed : 8.41 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.27), residues: 983 helix: 1.77 (0.21), residues: 631 sheet: 0.56 (0.98), residues: 24 loop : -0.95 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 55 TYR 0.012 0.002 TYR C 50 PHE 0.010 0.002 PHE K 53 TRP 0.006 0.001 TRP K 61 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (14864) covalent geometry : angle 0.59653 / 0.35 (21353) hydrogen bonds : bond 0.06051 / 3.94 ( 803) hydrogen bonds : angle 3.02021 / 2.16 ( 2033) metal coordination : bond 0.01470 / 0.76 ( 8) metal coordination : angle 4.30533 / 2.25 ( 9) link_TRANS : bond 0.00046 / 0.02 ( 2) link_TRANS : angle 0.35763 / 0.16 ( 6) *********************** 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 115 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8105 (mt-10) REVERT: E 59 GLU cc_start: 0.8572 (pt0) cc_final: 0.8311 (pt0) REVERT: G 74 LYS cc_start: 0.8808 (mttp) cc_final: 0.8321 (mmtm) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.1389 time to fit residues: 20.9202 Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.162076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110071 restraints weight = 19923.844| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.44 r_work: 0.2763 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14874 Z= 0.234 Angle : 0.672 7.901 21368 Z= 0.372 Chirality : 0.049 0.307 2419 Planarity : 0.005 0.053 1688 Dihedral : 29.924 177.521 4332 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.40 % Allowed : 10.98 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.27), residues: 983 helix: 1.50 (0.21), residues: 632 sheet: 0.41 (0.96), residues: 24 loop : -1.16 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 55 TYR 0.014 0.002 TYR C 50 PHE 0.015 0.002 PHE L 56 TRP 0.007 0.001 TRP K 61 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (14864) covalent geometry : angle 0.66588 / 0.37 (21353) hydrogen bonds : bond 0.06903 / 4.54 ( 803) hydrogen bonds : angle 3.11427 / 2.23 ( 2033) metal coordination : bond 0.01567 / 0.81 ( 8) metal coordination : angle 4.59640 / 2.39 ( 9) link_TRANS : bond 0.00038 / 0.02 ( 2) link_TRANS : angle 0.67566 / 0.29 ( 6) *********************** 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 108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8856 (tpt90) cc_final: 0.8572 (tpt90) REVERT: C 73 ASN cc_start: 0.7623 (m-40) cc_final: 0.7027 (t0) REVERT: G 74 LYS cc_start: 0.8859 (mttp) cc_final: 0.8407 (mmtm) REVERT: H 86 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.7875 (mmt180) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.1373 time to fit residues: 19.5439 Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114378 restraints weight = 27777.792| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.71 r_work: 0.2780 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14874 Z= 0.134 Angle : 0.619 7.375 21368 Z= 0.350 Chirality : 0.046 0.262 2419 Planarity : 0.005 0.052 1688 Dihedral : 29.835 176.357 4332 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.52 % Allowed : 11.80 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 983 helix: 1.76 (0.21), residues: 631 sheet: 0.56 (0.98), residues: 24 loop : -1.07 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 68 TYR 0.011 0.001 TYR D 40 PHE 0.010 0.001 PHE F 61 TRP 0.005 0.001 TRP K 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (14864) covalent geometry : angle 0.61298 / 0.35 (21353) hydrogen bonds : bond 0.05823 / 3.79 ( 803) hydrogen bonds : angle 3.06557 / 2.20 ( 2033) metal coordination : bond 0.01418 / 0.72 ( 8) metal coordination : angle 4.26458 / 2.24 ( 9) link_TRANS : bond 0.00121 / 0.06 ( 2) link_TRANS : angle 0.63398 / 0.28 ( 6) *********************** 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 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8309 (mt-10) REVERT: G 74 LYS cc_start: 0.8757 (mttp) cc_final: 0.7874 (mmtt) REVERT: H 86 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.7790 (mmt180) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.1277 time to fit residues: 18.2468 Evaluate side-chains 107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121958 restraints weight = 20067.424| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.18 r_work: 0.2752 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.158 Angle : 0.610 8.002 21368 Z= 0.344 Chirality : 0.045 0.282 2419 Planarity : 0.005 0.052 1688 Dihedral : 29.843 177.376 4332 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 12.62 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.27), residues: 983 helix: 1.80 (0.21), residues: 631 sheet: 0.57 (0.98), residues: 24 loop : -1.08 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 139 TYR 0.010 0.001 TYR D 40 PHE 0.010 0.001 PHE F 61 TRP 0.006 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14864) covalent geometry : angle 0.60422 / 0.34 (21353) hydrogen bonds : bond 0.05847 / 3.79 ( 803) hydrogen bonds : angle 3.00655 / 2.15 ( 2033) metal coordination : bond 0.01299 / 0.67 ( 8) metal coordination : angle 4.16871 / 2.20 ( 9) link_TRANS : bond 0.00034 / 0.02 ( 2) link_TRANS : angle 0.42755 / 0.18 ( 6) *********************** 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 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8389 (mt-10) REVERT: G 74 LYS cc_start: 0.8747 (mttp) cc_final: 0.8241 (mmtm) REVERT: H 86 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.7754 (mmt180) outliers start: 10 outliers final: 9 residues processed: 102 average time/residue: 0.1431 time to fit residues: 20.1257 Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.168303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117361 restraints weight = 19862.420| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.26 r_work: 0.2882 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14874 Z= 0.153 Angle : 0.603 8.283 21368 Z= 0.341 Chirality : 0.045 0.274 2419 Planarity : 0.005 0.083 1688 Dihedral : 29.825 177.453 4332 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.75 % Allowed : 11.92 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.27), residues: 983 helix: 1.81 (0.21), residues: 631 sheet: 0.62 (0.98), residues: 24 loop : -1.07 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 55 TYR 0.009 0.001 TYR D 40 PHE 0.010 0.001 PHE F 61 TRP 0.006 0.001 TRP K 61 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (14864) covalent geometry : angle 0.59761 / 0.34 (21353) hydrogen bonds : bond 0.05740 / 3.72 ( 803) hydrogen bonds : angle 2.98759 / 2.14 ( 2033) metal coordination : bond 0.01299 / 0.67 ( 8) metal coordination : angle 4.10481 / 2.17 ( 9) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.47076 / 0.20 ( 6) *********************** 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 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8388 (mt-10) REVERT: G 74 LYS cc_start: 0.8809 (mttp) cc_final: 0.8311 (mmtm) REVERT: H 86 ARG cc_start: 0.8397 (mmt-90) cc_final: 0.7830 (mmt180) outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 0.1465 time to fit residues: 20.4178 Evaluate side-chains 110 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.0010 chunk 95 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.165926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113080 restraints weight = 25192.012| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.58 r_work: 0.2850 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14874 Z= 0.146 Angle : 0.597 7.337 21368 Z= 0.339 Chirality : 0.045 0.274 2419 Planarity : 0.005 0.104 1688 Dihedral : 29.817 177.367 4332 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.64 % Allowed : 12.27 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.27), residues: 983 helix: 1.84 (0.21), residues: 631 sheet: 0.64 (0.98), residues: 24 loop : -1.05 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 55 TYR 0.009 0.001 TYR D 40 PHE 0.009 0.001 PHE F 61 TRP 0.006 0.001 TRP K 61 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (14864) covalent geometry : angle 0.59173 / 0.34 (21353) hydrogen bonds : bond 0.05654 / 3.66 ( 803) hydrogen bonds : angle 2.98067 / 2.14 ( 2033) metal coordination : bond 0.01256 / 0.65 ( 8) metal coordination : angle 4.07391 / 2.15 ( 9) link_TRANS : bond 0.00014 / 0.01 ( 2) link_TRANS : angle 0.48429 / 0.21 ( 6) *********************** 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 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8358 (mt-10) REVERT: G 74 LYS cc_start: 0.8785 (mttp) cc_final: 0.8275 (mmtm) REVERT: H 86 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7783 (mmt180) outliers start: 14 outliers final: 13 residues processed: 100 average time/residue: 0.1539 time to fit residues: 21.0676 Evaluate side-chains 108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123811 restraints weight = 27633.341| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.48 r_work: 0.2999 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14874 Z= 0.176 Angle : 0.613 7.616 21368 Z= 0.345 Chirality : 0.046 0.288 2419 Planarity : 0.005 0.052 1688 Dihedral : 29.848 177.169 4332 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.64 % Allowed : 12.15 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.27), residues: 983 helix: 1.74 (0.21), residues: 632 sheet: 0.67 (0.98), residues: 24 loop : -1.11 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 139 TYR 0.009 0.001 TYR D 40 PHE 0.011 0.002 PHE L 56 TRP 0.007 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (14864) covalent geometry : angle 0.60729 / 0.34 (21353) hydrogen bonds : bond 0.05933 / 3.86 ( 803) hydrogen bonds : angle 2.98536 / 2.14 ( 2033) metal coordination : bond 0.01353 / 0.70 ( 8) metal coordination : angle 4.14444 / 2.18 ( 9) link_TRANS : bond 0.00015 / 0.01 ( 2) link_TRANS : angle 0.43637 / 0.19 ( 6) *********************** 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 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8324 (mt-10) REVERT: G 74 LYS cc_start: 0.8792 (mttp) cc_final: 0.8276 (mmtm) REVERT: H 86 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.7957 (mmt180) outliers start: 14 outliers final: 13 residues processed: 103 average time/residue: 0.1463 time to fit residues: 20.5240 Evaluate side-chains 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114770 restraints weight = 25606.179| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.59 r_work: 0.2826 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14874 Z= 0.133 Angle : 0.597 8.690 21368 Z= 0.339 Chirality : 0.044 0.279 2419 Planarity : 0.005 0.050 1688 Dihedral : 29.822 176.650 4332 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.64 % Allowed : 12.38 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.27), residues: 983 helix: 1.86 (0.21), residues: 631 sheet: 0.67 (0.98), residues: 24 loop : -1.07 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 55 TYR 0.010 0.001 TYR D 40 PHE 0.010 0.002 PHE L 56 TRP 0.005 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (14864) covalent geometry : angle 0.59098 / 0.34 (21353) hydrogen bonds : bond 0.05540 / 3.59 ( 803) hydrogen bonds : angle 2.98573 / 2.15 ( 2033) metal coordination : bond 0.01356 / 0.69 ( 8) metal coordination : angle 4.08083 / 2.15 ( 9) link_TRANS : bond 0.00065 / 0.03 ( 2) link_TRANS : angle 0.50424 / 0.22 ( 6) ********************** 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 114 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8819 (tt0) cc_final: 0.8564 (tt0) REVERT: A 94 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8362 (mt-10) REVERT: G 74 LYS cc_start: 0.8783 (mttp) cc_final: 0.8280 (mmtm) REVERT: H 86 ARG cc_start: 0.8371 (mmt-90) cc_final: 0.7916 (mmt180) REVERT: L 139 ARG cc_start: 0.6728 (mpt180) cc_final: 0.6024 (mmt-90) outliers start: 14 outliers final: 13 residues processed: 107 average time/residue: 0.1493 time to fit residues: 22.0732 Evaluate side-chains 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 25 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123080 restraints weight = 19582.212| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.17 r_work: 0.2914 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14874 Z= 0.133 Angle : 0.595 8.463 21368 Z= 0.338 Chirality : 0.045 0.269 2419 Planarity : 0.004 0.051 1688 Dihedral : 29.815 177.026 4332 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.75 % Allowed : 12.38 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.27), residues: 983 helix: 1.87 (0.21), residues: 631 sheet: 0.68 (0.98), residues: 24 loop : -1.06 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 55 TYR 0.009 0.001 TYR D 40 PHE 0.009 0.001 PHE F 61 TRP 0.006 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (14864) covalent geometry : angle 0.58898 / 0.34 (21353) hydrogen bonds : bond 0.05499 / 3.56 ( 803) hydrogen bonds : angle 2.96043 / 2.13 ( 2033) metal coordination : bond 0.01340 / 0.69 ( 8) metal coordination : angle 4.03398 / 2.13 ( 9) link_TRANS : bond 0.00145 / 0.08 ( 2) link_TRANS : angle 1.05326 / 0.39 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.55 seconds wall clock time: 54 minutes 31.48 seconds (3271.48 seconds total)