Starting phenix.real_space_refine on Wed Aug 5 23:31:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gck_51231/08_2026/9gck_51231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gck_51231/08_2026/9gck_51231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gck_51231/08_2026/9gck_51231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gck_51231/08_2026/9gck_51231.map" model { file = "/net/cci-nas-00/data/ceres_data/9gck_51231/08_2026/9gck_51231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gck_51231/08_2026/9gck_51231.cif" } resolution = 3.7 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 41 5.16 5 C 7590 2.51 5 N 2092 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12298 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3491 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 13, 'TRANS': 415} Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2443 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "C" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1823 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 20, 'TRANS': 210} Chain: "D" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2696 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 900 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 945 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Time building chain proxies: 2.00, per 1000 atoms: 0.16 Number of scatterers: 12298 At special positions: 0 Unit cell: (89.598, 116.724, 160.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 90 15.00 O 2485 8.00 N 2092 7.00 C 7590 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: 0.85 Conformation dependent library (CDL) restraints added in 453.0 milliseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 50.4% alpha, 7.7% beta 33 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 739 through 758 removed outlier: 4.211A pdb=" N GLN A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 766 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 773 through 809 removed outlier: 6.192A pdb=" N HIS A 790 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 794 " --> pdb=" O HIS A 790 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 removed outlier: 3.598A pdb=" N VAL A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 838 Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 897 through 916 removed outlier: 4.039A pdb=" N SER A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 906 " --> pdb=" O GLN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 927 removed outlier: 4.146A pdb=" N GLU A 927 " --> pdb=" O ARG A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 927' Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 961 through 971 Processing helix chain 'A' and resid 972 through 991 removed outlier: 3.882A pdb=" N PHE A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS A 984 " --> pdb=" O PHE A 980 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU A 989 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 4.557A pdb=" N ASP A1012 " --> pdb=" O TRP A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.660A pdb=" N LEU A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1105 removed outlier: 4.265A pdb=" N PHE A1104 " --> pdb=" O ASN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1117 removed outlier: 3.668A pdb=" N LEU A1113 " --> pdb=" O THR A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1136 removed outlier: 4.536A pdb=" N GLU A1128 " --> pdb=" O HIS A1124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A1132 " --> pdb=" O GLU A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'B' and resid 733 through 747 Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.502A pdb=" N VAL B 758 " --> pdb=" O ASP B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 Processing helix chain 'B' and resid 771 through 787 removed outlier: 3.533A pdb=" N LEU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 804 removed outlier: 3.714A pdb=" N ASN B 804 " --> pdb=" O ARG B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 832 removed outlier: 3.785A pdb=" N LEU B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 852 removed outlier: 3.774A pdb=" N PHE B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 887 removed outlier: 4.131A pdb=" N ILE B 880 " --> pdb=" O TYR B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 removed outlier: 3.851A pdb=" N TYR B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 924 removed outlier: 3.774A pdb=" N ASN B 912 " --> pdb=" O ASP B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 953 removed outlier: 3.507A pdb=" N HIS B 937 " --> pdb=" O PHE B 933 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY B 938 " --> pdb=" O GLN B 934 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 957 Processing helix chain 'B' and resid 958 through 972 Processing helix chain 'B' and resid 974 through 988 removed outlier: 3.749A pdb=" N TYR B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1009 removed outlier: 3.915A pdb=" N HIS B 997 " --> pdb=" O LYS B 993 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B1005 " --> pdb=" O ASN B1001 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B1008 " --> pdb=" O ILE B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1023 Processing helix chain 'C' and resid 48 through 59 removed outlier: 4.066A pdb=" N LYS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 4.176A pdb=" N LYS C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 187 through 196 removed outlier: 5.185A pdb=" N SER C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.562A pdb=" N LEU D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 removed outlier: 3.597A pdb=" N LEU D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) Proline residue: D 75 - end of helix removed outlier: 3.813A pdb=" N LYS D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 107 through 115 removed outlier: 4.435A pdb=" N LYS D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 158 Proline residue: D 148 - end of helix removed outlier: 3.520A pdb=" N LYS D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 182 removed outlier: 3.603A pdb=" N LEU D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 Processing sheet with id=AA1, first strand: chain 'A' and resid 858 through 860 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 858 through 860 current: chain 'C' and resid 103 through 107 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 103 through 107 current: chain 'C' and resid 147 through 162 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 147 through 162 current: chain 'D' and resid 328 through 331 removed outlier: 4.396A pdb=" N LEU D 335 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 337 " --> pdb=" O SER D 430 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS D 424 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N GLY D 345 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N ARG D 422 " --> pdb=" O GLY D 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 920 through 922 Processing sheet with id=AA3, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA5, first strand: chain 'D' and resid 119 through 120 removed outlier: 6.326A pdb=" N VAL D 84 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA D 61 " --> pdb=" O TYR D 85 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS D 206 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN D 241 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU D 208 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR D 239 " --> pdb=" O GLU D 208 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1985 1.32 - 1.46: 3902 1.46 - 1.61: 6685 1.61 - 1.75: 105 1.75 - 1.89: 72 Bond restraints: 12749 Sorted by residual: bond pdb=" CA SER A1076 " pdb=" CB SER A1076 " ideal model delta sigma weight residual 1.530 1.443 0.086 1.69e-02 3.50e+03 2.61e+01 bond pdb=" C VAL A1080 " pdb=" O VAL A1080 " ideal model delta sigma weight residual 1.238 1.182 0.056 1.10e-02 8.26e+03 2.59e+01 bond pdb=" C TYR B1000 " pdb=" O TYR B1000 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.15e-02 7.56e+03 2.55e+01 bond pdb=" N VAL D 104 " pdb=" CA VAL D 104 " ideal model delta sigma weight residual 1.454 1.493 -0.039 7.70e-03 1.69e+04 2.54e+01 bond pdb=" C ASN B 964 " pdb=" O ASN B 964 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.16e-02 7.43e+03 2.40e+01 ... (remaining 12744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 13962 2.31 - 4.62: 3269 4.62 - 6.93: 373 6.93 - 9.24: 22 9.24 - 11.55: 6 Bond angle restraints: 17632 Sorted by residual: angle pdb=" CA PHE B 933 " pdb=" CB PHE B 933 " pdb=" CG PHE B 933 " ideal model delta sigma weight residual 113.80 124.03 -10.23 1.00e+00 1.00e+00 1.05e+02 angle pdb=" C3' DA F 11 " pdb=" C2' DA F 11 " pdb=" C1' DA F 11 " ideal model delta sigma weight residual 102.50 94.34 8.16 1.20e+00 6.94e-01 4.63e+01 angle pdb=" CA ASN B 964 " pdb=" CB ASN B 964 " pdb=" CG ASN B 964 " ideal model delta sigma weight residual 112.60 105.87 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" C LEU C 140 " pdb=" N LYS C 141 " pdb=" CA LYS C 141 " ideal model delta sigma weight residual 120.38 129.13 -8.75 1.37e+00 5.33e-01 4.08e+01 angle pdb=" C ASN C 44 " pdb=" CA ASN C 44 " pdb=" CB ASN C 44 " ideal model delta sigma weight residual 112.07 121.26 -9.19 1.48e+00 4.57e-01 3.85e+01 ... (remaining 17627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6066 17.93 - 35.86: 963 35.86 - 53.79: 355 53.79 - 71.72: 198 71.72 - 89.65: 10 Dihedral angle restraints: 7592 sinusoidal: 3794 harmonic: 3798 Sorted by residual: dihedral pdb=" CA LEU D 343 " pdb=" C LEU D 343 " pdb=" N VAL D 344 " pdb=" CA VAL D 344 " ideal model delta harmonic sigma weight residual 180.00 147.73 32.27 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA ARG C 35 " pdb=" C ARG C 35 " pdb=" N ILE C 36 " pdb=" CA ILE C 36 " ideal model delta harmonic sigma weight residual -180.00 -148.21 -31.79 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA TYR C 242 " pdb=" C TYR C 242 " pdb=" N LYS C 243 " pdb=" CA LYS C 243 " ideal model delta harmonic sigma weight residual 180.00 148.55 31.45 0 5.00e+00 4.00e-02 3.96e+01 ... (remaining 7589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1627 0.130 - 0.259: 235 0.259 - 0.389: 38 0.389 - 0.518: 55 0.518 - 0.648: 2 Chirality restraints: 1957 Sorted by residual: chirality pdb=" P DA F 1 " pdb=" OP1 DA F 1 " pdb=" OP2 DA F 1 " pdb=" O5' DA F 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DT E 1 " pdb=" OP1 DT E 1 " pdb=" OP2 DT E 1 " pdb=" O5' DT E 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" P DT E 28 " pdb=" OP1 DT E 28 " pdb=" OP2 DT E 28 " pdb=" O5' DT E 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.55e+00 ... (remaining 1954 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 943 " 0.126 2.00e-02 2.50e+03 7.04e-02 9.91e+01 pdb=" CG TYR B 943 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 943 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 943 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR B 943 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR B 943 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 943 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR B 943 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 886 " 0.095 2.00e-02 2.50e+03 4.88e-02 4.76e+01 pdb=" CG TYR B 886 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 886 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 886 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 886 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 886 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 886 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 963 " -0.094 2.00e-02 2.50e+03 4.85e-02 4.70e+01 pdb=" CG TYR B 963 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 963 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 963 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 963 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 963 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 963 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR B 963 " -0.046 2.00e-02 2.50e+03 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 33 2.54 - 3.13: 9360 3.13 - 3.72: 20085 3.72 - 4.31: 30106 4.31 - 4.90: 45890 Nonbonded interactions: 105474 Sorted by model distance: nonbonded pdb=" NZ LYS B 811 " pdb=" O SER C 197 " model vdw 1.954 3.120 nonbonded pdb=" OG SER C 38 " pdb=" OE2 GLU D 347 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 879 " pdb=" O PRO C 228 " model vdw 2.276 3.040 nonbonded pdb=" NE2 GLN B 814 " pdb=" O GLN C 226 " model vdw 2.280 3.120 nonbonded pdb=" OD1 ASN A1054 " pdb=" NZ LYS B 947 " model vdw 2.286 3.120 ... (remaining 105469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.050 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 : 0.015 0.091 12749 Z= 1.083 Angle : 1.889 11.545 17632 Z= 1.298 Chirality : 0.122 0.648 1957 Planarity : 0.010 0.153 1931 Dihedral : 21.024 89.645 5132 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.03 % Favored : 94.74 % Rotamer: Outliers : 0.77 % Allowed : 3.33 % Favored : 95.90 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.69 (0.21), residues: 1273 helix: -2.43 (0.16), residues: 547 sheet: -0.46 (0.56), residues: 64 loop : -1.23 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG A 923 TYR 0.126 0.014 TYR B 943 PHE 0.055 0.009 PHE D 350 TRP 0.062 0.012 TRP A1153 HIS 0.027 0.005 HIS A1151 Details of bonding type rmsd/Z covalent geometry : bond 0.01485 / 1.08 (12749) covalent geometry : angle 1.88923 / 1.30 (17632) hydrogen bonds : bond 0.19361 / 12.54 ( 497) hydrogen bonds : angle 8.39377 / 5.92 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6572 (mtm) cc_final: 0.5435 (ttp) REVERT: A 872 MET cc_start: 0.5620 (mtm) cc_final: 0.4170 (mtm) REVERT: A 1033 LEU cc_start: 0.8015 (mp) cc_final: 0.7517 (tp) REVERT: A 1040 PHE cc_start: 0.6134 (t80) cc_final: 0.5764 (t80) REVERT: A 1045 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6536 (tt) REVERT: A 1068 LYS cc_start: 0.9081 (mptt) cc_final: 0.8727 (tmtt) REVERT: A 1069 VAL cc_start: 0.7888 (t) cc_final: 0.7630 (t) REVERT: A 1097 MET cc_start: 0.9627 (ttp) cc_final: 0.9303 (tmm) REVERT: B 740 MET cc_start: 0.6936 (mmp) cc_final: 0.6432 (mmt) REVERT: B 777 MET cc_start: 0.5755 (ttm) cc_final: 0.5470 (ttt) REVERT: B 793 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8652 (tm-30) REVERT: B 870 ASN cc_start: 0.9605 (m-40) cc_final: 0.9337 (t0) REVERT: B 871 LYS cc_start: 0.8782 (mttt) cc_final: 0.8354 (ptmm) REVERT: B 910 MET cc_start: 0.7625 (mmm) cc_final: 0.7205 (mmm) REVERT: C 79 HIS cc_start: 0.8358 (m-70) cc_final: 0.7978 (m90) REVERT: C 116 ILE cc_start: 0.8724 (mt) cc_final: 0.8512 (mm) REVERT: C 204 GLN cc_start: 0.9396 (mt0) cc_final: 0.9108 (mm-40) REVERT: C 233 LEU cc_start: 0.8461 (mt) cc_final: 0.8168 (mt) REVERT: D 55 ASP cc_start: 0.8666 (m-30) cc_final: 0.8384 (m-30) REVERT: D 141 MET cc_start: 0.8862 (mmm) cc_final: 0.8579 (mtt) REVERT: D 204 LEU cc_start: 0.6800 (tp) cc_final: 0.6393 (tp) REVERT: D 239 THR cc_start: 0.2250 (p) cc_final: 0.1807 (p) REVERT: D 311 ILE cc_start: 0.8154 (mt) cc_final: 0.7935 (mm) REVERT: D 323 GLU cc_start: 0.8586 (pm20) cc_final: 0.8254 (mp0) outliers start: 9 outliers final: 1 residues processed: 211 average time/residue: 0.1437 time to fit residues: 41.1211 Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain B residue 836 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 HIS D 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.125684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.103439 restraints weight = 57384.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.105986 restraints weight = 33017.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.107202 restraints weight = 18817.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.107310 restraints weight = 14854.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.107470 restraints weight = 13200.691| |-----------------------------------------------------------------------------| r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12749 Z= 0.216 Angle : 0.919 10.304 17632 Z= 0.491 Chirality : 0.058 0.254 1957 Planarity : 0.006 0.070 1931 Dihedral : 23.777 84.442 2487 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 2.47 % Allowed : 9.22 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.22), residues: 1273 helix: -1.02 (0.20), residues: 568 sheet: -0.71 (0.51), residues: 79 loop : -0.86 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 748 TYR 0.032 0.003 TYR B1000 PHE 0.030 0.003 PHE B 839 TRP 0.027 0.002 TRP A 800 HIS 0.015 0.002 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (12749) covalent geometry : angle 0.91913 / 0.49 (17632) hydrogen bonds : bond 0.06879 / 4.62 ( 497) hydrogen bonds : angle 5.87061 / 4.12 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7924 (ptp-170) REVERT: A 803 MET cc_start: 0.6296 (mtm) cc_final: 0.5461 (ttp) REVERT: A 826 LEU cc_start: 0.8634 (mm) cc_final: 0.8241 (pp) REVERT: A 830 TRP cc_start: 0.7346 (t60) cc_final: 0.7071 (t60) REVERT: A 833 PHE cc_start: 0.8539 (m-80) cc_final: 0.7896 (m-80) REVERT: A 1033 LEU cc_start: 0.7098 (mp) cc_final: 0.6716 (mp) REVERT: B 774 ARG cc_start: 0.7960 (mmp-170) cc_final: 0.7632 (mmp-170) REVERT: B 871 LYS cc_start: 0.8088 (mttt) cc_final: 0.7822 (ptmm) REVERT: C 204 GLN cc_start: 0.8459 (mt0) cc_final: 0.8089 (mp10) REVERT: D 141 MET cc_start: 0.8211 (mmm) cc_final: 0.7925 (mtt) REVERT: D 158 TYR cc_start: 0.5628 (m-80) cc_final: 0.4773 (m-80) REVERT: D 233 ASP cc_start: 0.4503 (t0) cc_final: 0.4217 (t0) outliers start: 29 outliers final: 10 residues processed: 153 average time/residue: 0.1264 time to fit residues: 27.3111 Evaluate side-chains 120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 258 ASP Chi-restraints excluded: chain D residue 355 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1151 HIS ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.121978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.097138 restraints weight = 57798.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.099740 restraints weight = 31820.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.101506 restraints weight = 20879.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.102440 restraints weight = 15881.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.103466 restraints weight = 13457.877| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12749 Z= 0.176 Angle : 0.808 11.492 17632 Z= 0.433 Chirality : 0.050 0.237 1957 Planarity : 0.005 0.044 1931 Dihedral : 23.350 76.859 2485 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 2.47 % Allowed : 11.18 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.02 (0.23), residues: 1273 helix: -0.53 (0.20), residues: 560 sheet: -0.41 (0.53), residues: 81 loop : -0.72 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 940 TYR 0.043 0.002 TYR B 818 PHE 0.028 0.002 PHE B 839 TRP 0.019 0.002 TRP A 800 HIS 0.011 0.001 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (12749) covalent geometry : angle 0.80843 / 0.43 (17632) hydrogen bonds : bond 0.05917 / 4.03 ( 497) hydrogen bonds : angle 5.39559 / 3.77 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 ARG cc_start: 0.7958 (ptp-110) cc_final: 0.7729 (ptp-170) REVERT: A 803 MET cc_start: 0.6209 (mtm) cc_final: 0.5315 (ttp) REVERT: A 826 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8122 (pp) REVERT: A 830 TRP cc_start: 0.7637 (t60) cc_final: 0.7328 (t60) REVERT: A 833 PHE cc_start: 0.8725 (m-80) cc_final: 0.8048 (m-80) REVERT: A 1104 PHE cc_start: 0.7020 (m-80) cc_final: 0.6481 (m-80) REVERT: B 871 LYS cc_start: 0.8375 (mttt) cc_final: 0.7921 (pttp) REVERT: C 58 MET cc_start: 0.6966 (mtp) cc_final: 0.6683 (ttm) REVERT: C 204 GLN cc_start: 0.8493 (mt0) cc_final: 0.8002 (mp10) REVERT: D 139 MET cc_start: -0.0969 (ppp) cc_final: -0.1308 (ppp) REVERT: D 141 MET cc_start: 0.8243 (mmm) cc_final: 0.7988 (mtt) REVERT: D 158 TYR cc_start: 0.6460 (m-80) cc_final: 0.6062 (m-80) REVERT: D 188 MET cc_start: 0.0142 (mmm) cc_final: -0.1610 (tpt) REVERT: D 253 MET cc_start: 0.8540 (tpt) cc_final: 0.8144 (tpt) outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 0.1112 time to fit residues: 22.6356 Evaluate side-chains 122 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.0670 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 836 GLN ** C 86 ASN ** 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 = 0.4729 r_free = 0.4729 target = 0.122582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.098141 restraints weight = 57609.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.100731 restraints weight = 32094.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.102479 restraints weight = 21026.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.103679 restraints weight = 15888.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.104058 restraints weight = 13181.089| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12749 Z= 0.162 Angle : 0.734 10.137 17632 Z= 0.397 Chirality : 0.047 0.222 1957 Planarity : 0.004 0.053 1931 Dihedral : 23.234 72.403 2485 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 2.47 % Allowed : 12.71 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.72 (0.23), residues: 1273 helix: -0.21 (0.21), residues: 560 sheet: -0.25 (0.55), residues: 84 loop : -0.64 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 878 TYR 0.029 0.002 TYR B1000 PHE 0.028 0.002 PHE B 739 TRP 0.016 0.002 TRP A 800 HIS 0.009 0.002 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (12749) covalent geometry : angle 0.73400 / 0.40 (17632) hydrogen bonds : bond 0.05294 / 3.58 ( 497) hydrogen bonds : angle 5.22922 / 3.64 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6164 (mtm) cc_final: 0.5333 (ttt) REVERT: A 826 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8183 (pp) REVERT: A 830 TRP cc_start: 0.7718 (t60) cc_final: 0.7465 (t60) REVERT: A 833 PHE cc_start: 0.8761 (m-80) cc_final: 0.7891 (m-80) REVERT: A 1104 PHE cc_start: 0.6976 (m-80) cc_final: 0.6454 (m-80) REVERT: B 871 LYS cc_start: 0.8467 (mttt) cc_final: 0.7987 (pttp) REVERT: C 204 GLN cc_start: 0.8486 (mt0) cc_final: 0.7992 (mp10) REVERT: D 158 TYR cc_start: 0.6516 (m-80) cc_final: 0.6049 (m-80) REVERT: D 188 MET cc_start: 0.0004 (mmm) cc_final: -0.1509 (tpt) outliers start: 29 outliers final: 16 residues processed: 134 average time/residue: 0.1154 time to fit residues: 22.6065 Evaluate side-chains 118 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 959 GLN ** C 86 ASN ** 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 = 0.4692 r_free = 0.4692 target = 0.120705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.095876 restraints weight = 56836.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.098422 restraints weight = 32046.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.100128 restraints weight = 21343.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.101208 restraints weight = 16387.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.101716 restraints weight = 13876.292| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12749 Z= 0.187 Angle : 0.734 8.590 17632 Z= 0.394 Chirality : 0.047 0.255 1957 Planarity : 0.005 0.059 1931 Dihedral : 23.275 67.384 2485 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 2.30 % Allowed : 14.85 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.80 (0.23), residues: 1273 helix: -0.30 (0.21), residues: 566 sheet: -0.26 (0.59), residues: 81 loop : -0.66 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 784 TYR 0.054 0.002 TYR B 818 PHE 0.032 0.002 PHE B 739 TRP 0.016 0.002 TRP A 800 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (12749) covalent geometry : angle 0.73429 / 0.39 (17632) hydrogen bonds : bond 0.05261 / 3.58 ( 497) hydrogen bonds : angle 5.19309 / 3.62 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6154 (mtm) cc_final: 0.5361 (ttt) REVERT: A 826 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8163 (pp) REVERT: A 830 TRP cc_start: 0.7694 (t60) cc_final: 0.7442 (t60) REVERT: A 833 PHE cc_start: 0.8809 (m-10) cc_final: 0.7947 (m-80) REVERT: A 1104 PHE cc_start: 0.6884 (m-80) cc_final: 0.6409 (m-80) REVERT: B 871 LYS cc_start: 0.8452 (mttt) cc_final: 0.7981 (pttp) REVERT: C 204 GLN cc_start: 0.8611 (mt0) cc_final: 0.8079 (mp10) REVERT: D 141 MET cc_start: 0.8267 (mtt) cc_final: 0.7963 (mpp) REVERT: D 158 TYR cc_start: 0.6606 (m-80) cc_final: 0.6052 (m-80) REVERT: D 188 MET cc_start: 0.0008 (mmm) cc_final: -0.0629 (mmm) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.1178 time to fit residues: 21.7895 Evaluate side-chains 119 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1069 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 0.0970 chunk 119 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 50.0000 chunk 64 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.120441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.095419 restraints weight = 56994.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.098099 restraints weight = 31192.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.099897 restraints weight = 20913.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.100997 restraints weight = 15882.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.101370 restraints weight = 13233.208| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12749 Z= 0.186 Angle : 0.732 8.913 17632 Z= 0.392 Chirality : 0.046 0.241 1957 Planarity : 0.005 0.068 1931 Dihedral : 23.230 68.306 2482 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 2.22 % Allowed : 15.53 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.84 (0.23), residues: 1273 helix: -0.35 (0.21), residues: 565 sheet: -0.28 (0.59), residues: 81 loop : -0.66 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 142 TYR 0.042 0.002 TYR B 818 PHE 0.028 0.002 PHE B 736 TRP 0.033 0.002 TRP D 93 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (12749) covalent geometry : angle 0.73215 / 0.39 (17632) hydrogen bonds : bond 0.05096 / 3.45 ( 497) hydrogen bonds : angle 5.15613 / 3.60 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6160 (mtm) cc_final: 0.5385 (ttt) REVERT: A 826 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8178 (pp) REVERT: A 830 TRP cc_start: 0.7717 (t60) cc_final: 0.7444 (t60) REVERT: A 833 PHE cc_start: 0.8829 (m-10) cc_final: 0.7994 (m-80) REVERT: A 1104 PHE cc_start: 0.6838 (m-80) cc_final: 0.6435 (m-80) REVERT: A 1129 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7465 (tp) REVERT: B 871 LYS cc_start: 0.8401 (mttt) cc_final: 0.7983 (pttp) REVERT: C 204 GLN cc_start: 0.8603 (mt0) cc_final: 0.8054 (mp10) REVERT: D 93 TRP cc_start: 0.6533 (t60) cc_final: 0.6247 (t60) REVERT: D 141 MET cc_start: 0.8127 (mtt) cc_final: 0.7803 (mpp) REVERT: D 158 TYR cc_start: 0.6585 (m-80) cc_final: 0.5897 (m-80) REVERT: D 188 MET cc_start: 0.0085 (mmm) cc_final: -0.0569 (mmm) outliers start: 26 outliers final: 14 residues processed: 120 average time/residue: 0.0955 time to fit residues: 17.4415 Evaluate side-chains 114 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.120907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.096191 restraints weight = 56798.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.098759 restraints weight = 31628.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.099702 restraints weight = 21261.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.101408 restraints weight = 17090.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.102143 restraints weight = 14026.106| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12749 Z= 0.167 Angle : 0.729 13.248 17632 Z= 0.386 Chirality : 0.045 0.238 1957 Planarity : 0.005 0.061 1931 Dihedral : 23.192 69.450 2482 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 2.56 % Allowed : 16.04 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.71 (0.23), residues: 1273 helix: -0.23 (0.21), residues: 568 sheet: -0.11 (0.64), residues: 71 loop : -0.62 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 774 TYR 0.037 0.002 TYR B 818 PHE 0.033 0.002 PHE B 736 TRP 0.023 0.002 TRP D 93 HIS 0.009 0.001 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (12749) covalent geometry : angle 0.72889 / 0.39 (17632) hydrogen bonds : bond 0.04830 / 3.29 ( 497) hydrogen bonds : angle 5.08795 / 3.55 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6113 (mtm) cc_final: 0.5179 (ttt) REVERT: A 826 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8179 (pp) REVERT: A 833 PHE cc_start: 0.8876 (m-10) cc_final: 0.8109 (m-80) REVERT: A 1104 PHE cc_start: 0.6871 (m-80) cc_final: 0.6479 (m-80) REVERT: A 1129 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7508 (tp) REVERT: B 871 LYS cc_start: 0.8406 (mttt) cc_final: 0.7982 (pttp) REVERT: C 204 GLN cc_start: 0.8612 (mt0) cc_final: 0.8040 (mp10) REVERT: D 93 TRP cc_start: 0.6565 (t60) cc_final: 0.6335 (t60) REVERT: D 141 MET cc_start: 0.8166 (mtt) cc_final: 0.7834 (mpp) REVERT: D 158 TYR cc_start: 0.6567 (m-80) cc_final: 0.5810 (m-80) REVERT: D 178 MET cc_start: 0.7174 (mmm) cc_final: 0.6231 (mmt) REVERT: D 188 MET cc_start: 0.0327 (mmm) cc_final: 0.0081 (mmm) outliers start: 30 outliers final: 21 residues processed: 127 average time/residue: 0.0882 time to fit residues: 17.2972 Evaluate side-chains 123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1012 ASP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.0270 chunk 115 optimal weight: 7.9990 chunk 107 optimal weight: 0.0470 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.122644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.097926 restraints weight = 56622.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.100590 restraints weight = 30828.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.102335 restraints weight = 20555.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.103509 restraints weight = 15589.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.104224 restraints weight = 12963.103| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12749 Z= 0.145 Angle : 0.697 10.712 17632 Z= 0.372 Chirality : 0.044 0.221 1957 Planarity : 0.005 0.061 1931 Dihedral : 23.096 69.834 2482 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 1.79 % Allowed : 17.24 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.58 (0.23), residues: 1273 helix: -0.07 (0.21), residues: 571 sheet: -0.19 (0.64), residues: 72 loop : -0.59 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 967 TYR 0.034 0.002 TYR B 818 PHE 0.041 0.002 PHE B 736 TRP 0.017 0.001 TRP D 93 HIS 0.008 0.001 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12749) covalent geometry : angle 0.69677 / 0.37 (17632) hydrogen bonds : bond 0.04502 / 3.05 ( 497) hydrogen bonds : angle 4.98474 / 3.48 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6074 (mtm) cc_final: 0.5374 (ttt) REVERT: A 826 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8151 (pp) REVERT: A 830 TRP cc_start: 0.7707 (t60) cc_final: 0.7440 (t60) REVERT: A 833 PHE cc_start: 0.8863 (m-10) cc_final: 0.8102 (m-80) REVERT: A 1104 PHE cc_start: 0.6744 (m-80) cc_final: 0.6435 (m-80) REVERT: B 779 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7584 (ttmt) REVERT: B 871 LYS cc_start: 0.8381 (mttt) cc_final: 0.7952 (pttp) REVERT: C 204 GLN cc_start: 0.8491 (mt0) cc_final: 0.7930 (mp10) REVERT: D 137 GLN cc_start: 0.7051 (mp10) cc_final: 0.6833 (mp10) REVERT: D 141 MET cc_start: 0.8152 (mtt) cc_final: 0.7806 (mpp) REVERT: D 158 TYR cc_start: 0.6568 (m-80) cc_final: 0.5722 (m-80) REVERT: D 178 MET cc_start: 0.7327 (mmm) cc_final: 0.6257 (mmt) REVERT: D 188 MET cc_start: 0.0461 (mmm) cc_final: 0.0227 (mmm) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.1028 time to fit residues: 19.0485 Evaluate side-chains 120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 39 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 132 optimal weight: 50.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.123090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.098694 restraints weight = 56143.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.101261 restraints weight = 30225.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.102978 restraints weight = 20145.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.104168 restraints weight = 15264.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.104696 restraints weight = 12737.615| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12749 Z= 0.143 Angle : 0.686 12.539 17632 Z= 0.366 Chirality : 0.044 0.252 1957 Planarity : 0.004 0.062 1931 Dihedral : 23.015 69.632 2482 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.88 % Allowed : 17.49 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.37 (0.24), residues: 1273 helix: 0.10 (0.21), residues: 574 sheet: -0.16 (0.61), residues: 78 loop : -0.48 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 107 TYR 0.045 0.002 TYR B1000 PHE 0.050 0.002 PHE B 736 TRP 0.019 0.001 TRP D 93 HIS 0.008 0.001 HIS B 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12749) covalent geometry : angle 0.68627 / 0.37 (17632) hydrogen bonds : bond 0.04313 / 2.92 ( 497) hydrogen bonds : angle 4.92204 / 3.45 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.6035 (mtm) cc_final: 0.5354 (ttt) REVERT: A 826 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 830 TRP cc_start: 0.7689 (t60) cc_final: 0.7477 (t60) REVERT: A 833 PHE cc_start: 0.8848 (m-10) cc_final: 0.8113 (m-80) REVERT: A 949 GLN cc_start: 0.7918 (mp10) cc_final: 0.7171 (tp-100) REVERT: A 1104 PHE cc_start: 0.6753 (m-80) cc_final: 0.6447 (m-80) REVERT: A 1129 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7231 (tp) REVERT: B 779 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7601 (ttmt) REVERT: B 871 LYS cc_start: 0.8391 (mttt) cc_final: 0.7953 (pttp) REVERT: B 927 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.5116 (mt) REVERT: C 204 GLN cc_start: 0.8492 (mt0) cc_final: 0.7994 (mp10) REVERT: D 137 GLN cc_start: 0.7086 (mp10) cc_final: 0.6471 (mm-40) REVERT: D 141 MET cc_start: 0.8100 (mtt) cc_final: 0.7813 (mpp) REVERT: D 158 TYR cc_start: 0.6569 (m-80) cc_final: 0.5676 (m-80) REVERT: D 178 MET cc_start: 0.7313 (mmm) cc_final: 0.6303 (mmt) REVERT: D 188 MET cc_start: 0.0399 (mmm) cc_final: -0.0514 (tpt) outliers start: 22 outliers final: 16 residues processed: 122 average time/residue: 0.1082 time to fit residues: 19.7669 Evaluate side-chains 116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 970 HIS Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 0.4980 chunk 32 optimal weight: 0.3980 chunk 127 optimal weight: 50.0000 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.123537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.099207 restraints weight = 56636.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.101847 restraints weight = 30192.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.103572 restraints weight = 19843.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.104154 restraints weight = 14961.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.105394 restraints weight = 12806.069| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12749 Z= 0.141 Angle : 0.695 12.494 17632 Z= 0.369 Chirality : 0.044 0.194 1957 Planarity : 0.005 0.064 1931 Dihedral : 22.965 69.486 2482 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.79 % Allowed : 17.41 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.32 (0.24), residues: 1273 helix: 0.13 (0.21), residues: 575 sheet: -0.23 (0.59), residues: 78 loop : -0.41 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 967 TYR 0.034 0.002 TYR B1000 PHE 0.053 0.002 PHE B 736 TRP 0.058 0.002 TRP D 93 HIS 0.007 0.001 HIS B 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12749) covalent geometry : angle 0.69475 / 0.37 (17632) hydrogen bonds : bond 0.04266 / 2.88 ( 497) hydrogen bonds : angle 4.87595 / 3.42 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 MET cc_start: 0.5996 (mtm) cc_final: 0.5350 (ttt) REVERT: A 826 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8205 (pp) REVERT: A 830 TRP cc_start: 0.7668 (t60) cc_final: 0.7467 (t60) REVERT: A 833 PHE cc_start: 0.8840 (m-10) cc_final: 0.8097 (m-80) REVERT: A 849 GLU cc_start: 0.8348 (mp0) cc_final: 0.7910 (tp30) REVERT: A 949 GLN cc_start: 0.7852 (mp10) cc_final: 0.7159 (tp-100) REVERT: A 1104 PHE cc_start: 0.6755 (m-80) cc_final: 0.6475 (m-80) REVERT: A 1129 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7171 (tp) REVERT: A 1154 TYR cc_start: 0.7227 (p90) cc_final: 0.6908 (p90) REVERT: B 779 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7578 (ttmt) REVERT: B 871 LYS cc_start: 0.8431 (mttt) cc_final: 0.7934 (pttp) REVERT: B 927 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5124 (mt) REVERT: C 59 CYS cc_start: 0.7858 (p) cc_final: 0.7423 (p) REVERT: C 204 GLN cc_start: 0.8485 (mt0) cc_final: 0.7994 (mp10) REVERT: D 137 GLN cc_start: 0.6938 (mp10) cc_final: 0.6708 (mp10) REVERT: D 141 MET cc_start: 0.8147 (mtt) cc_final: 0.7808 (mpp) REVERT: D 158 TYR cc_start: 0.6484 (m-80) cc_final: 0.5544 (m-80) REVERT: D 188 MET cc_start: 0.0522 (mmm) cc_final: -0.1002 (tpt) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.1055 time to fit residues: 18.8271 Evaluate side-chains 116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 970 HIS Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain B residue 1017 HIS Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.122215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.097384 restraints weight = 56253.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.100036 restraints weight = 30918.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.101778 restraints weight = 20342.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.103015 restraints weight = 15389.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.103440 restraints weight = 12721.423| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12749 Z= 0.167 Angle : 0.708 12.034 17632 Z= 0.372 Chirality : 0.045 0.250 1957 Planarity : 0.005 0.066 1931 Dihedral : 22.972 69.342 2482 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.79 % Allowed : 17.75 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.37 (0.24), residues: 1273 helix: 0.16 (0.21), residues: 575 sheet: -0.39 (0.62), residues: 69 loop : -0.51 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 983 TYR 0.032 0.002 TYR B 818 PHE 0.052 0.002 PHE B 736 TRP 0.080 0.002 TRP D 93 HIS 0.010 0.001 HIS B 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (12749) covalent geometry : angle 0.70789 / 0.37 (17632) hydrogen bonds : bond 0.04522 / 3.04 ( 497) hydrogen bonds : angle 4.92372 / 3.46 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.52 seconds wall clock time: 50 minutes 49.57 seconds (3049.57 seconds total)