Starting phenix.real_space_refine on Wed Sep 17 23:46:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gck_51231/09_2025/9gck_51231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gck_51231/09_2025/9gck_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_51231/09_2025/9gck_51231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gck_51231/09_2025/9gck_51231.map" model { file = "/net/cci-nas-00/data/ceres_data/9gck_51231/09_2025/9gck_51231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gck_51231/09_2025/9gck_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-2.0-5805/lib/python3.9/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: 2.83, per 1000 atoms: 0.23 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: 1.08 Conformation dependent library (CDL) restraints added in 488.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.66 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: 2.27 Time building geometry restraints manager: 1.42 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: 13894 2.31 - 4.62: 3344 4.62 - 6.93: 367 6.93 - 9.24: 21 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=" C4' DT E 30 " pdb=" C3' DT E 30 " pdb=" O3' DT E 30 " ideal model delta sigma weight residual 110.00 99.28 10.72 1.50e+00 4.44e-01 5.11e+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 - 0.128: 1610 0.128 - 0.255: 250 0.255 - 0.383: 43 0.383 - 0.510: 52 0.510 - 0.638: 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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.67e+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 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.29e+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: 2.050 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 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= 1.033 Angle : 1.892 11.545 17632 Z= 1.274 Chirality : 0.122 0.638 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 aren 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 covalent geometry : bond 0.01457 (12749) covalent geometry : angle 1.89227 (17632) hydrogen bonds : bond 0.19361 ( 497) hydrogen bonds : angle 8.39377 ( 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 : 0.438 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: 0.6571 (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: 0.8155 (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: 0.1512 time to fit residues: 42.9165 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 : 0.470 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: ** A1151 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 = 0.4884 r_free = 0.4884 target = 0.125272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.103598 restraints weight = 53544.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.105795 restraints weight = 25680.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.106823 restraints weight = 15875.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.107202 restraints weight = 11958.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.107464 restraints weight = 10998.676| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12749 Z= 0.211 Angle : 0.784 7.821 17632 Z= 0.435 Chirality : 0.046 0.241 1957 Planarity : 0.005 0.049 1931 Dihedral : 22.962 76.329 2487 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 1.96 % Allowed : 9.30 % Favored : 88.74 % 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 aren not related in a simple way. whole: -1.19 (0.22), residues: 1273 helix: -0.76 (0.20), residues: 568 sheet: 0.00 (0.59), residues: 66 loop : -0.78 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 983 TYR 0.035 0.003 TYR B1000 PHE 0.034 0.003 PHE B 839 TRP 0.025 0.002 TRP A 800 HIS 0.011 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00476 (12749) covalent geometry : angle 0.78426 (17632) hydrogen bonds : bond 0.05867 ( 497) hydrogen bonds : angle 5.54082 ( 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 165 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.446 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: A 784 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.7985 (ptp-170) REVERT: A 803 MET cc_start: 0.6089 (mtm) cc_final: 0.5295 (ttp) REVERT: A 826 LEU cc_start: 0.8659 (mm) cc_final: 0.8180 (pp) REVERT: A 830 TRP cc_start: 0.7615 (t60) cc_final: 0.7374 (t60) REVERT: A 833 PHE cc_start: 0.8802 (m-80) cc_final: 0.8177 (m-80) REVERT: A 1069 VAL cc_start: 0.6988 (t) cc_final: 0.6693 (m) REVERT: B 774 ARG cc_start: 0.7984 (mmp-170) cc_final: 0.7650 (mmp-170) REVERT: B 779 LYS cc_start: 0.8297 (mttt) cc_final: 0.8096 (mttm) REVERT: B 871 LYS cc_start: 0.8435 (mttt) cc_final: 0.8019 (pttp) REVERT: C 79 HIS cc_start: 0.7445 (m-70) cc_final: 0.7209 (m90) REVERT: C 204 GLN cc_start: 0.8731 (mt0) cc_final: 0.8220 (mp10) REVERT: D 158 TYR cc_start: 0.6049 (m-80) cc_final: 0.5237 (m-80) REVERT: D 188 MET cc_start: 0.0486 (mmm) cc_final: -0.1584 (tpt) REVERT: D 205 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7843 (p0) outliers start: 23 outliers final: 8 residues processed: 156 average time/residue: 0.1274 time to fit residues: 27.8749 Evaluate side-chains 122 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 781 TRP 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 C residue 212 LEU Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 7.9990 chunk 121 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 78 optimal weight: 0.2980 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.123155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.098582 restraints weight = 57898.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.101266 restraints weight = 31657.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.103059 restraints weight = 20764.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.104294 restraints weight = 15658.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.105120 restraints weight = 12952.746| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12749 Z= 0.169 Angle : 0.680 6.501 17632 Z= 0.378 Chirality : 0.042 0.222 1957 Planarity : 0.004 0.052 1931 Dihedral : 22.784 66.417 2485 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 2.39 % Allowed : 11.43 % Favored : 86.18 % 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 aren not related in a simple way. whole: -0.59 (0.23), residues: 1273 helix: -0.16 (0.21), residues: 573 sheet: 0.10 (0.56), residues: 83 loop : -0.57 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.030 0.002 TYR B1000 PHE 0.023 0.002 PHE B 839 TRP 0.042 0.002 TRP D 93 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00376 (12749) covalent geometry : angle 0.67997 (17632) hydrogen bonds : bond 0.04915 ( 497) hydrogen bonds : angle 5.07062 ( 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 159 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.418 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 803 MET cc_start: 0.6020 (mtm) cc_final: 0.5290 (ttp) REVERT: A 826 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8133 (pp) REVERT: A 830 TRP cc_start: 0.7656 (t60) cc_final: 0.7388 (t60) REVERT: A 833 PHE cc_start: 0.8849 (m-80) cc_final: 0.8256 (m-80) REVERT: A 949 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7880 (mp10) REVERT: A 1033 LEU cc_start: 0.7118 (mp) cc_final: 0.6669 (mt) REVERT: B 871 LYS cc_start: 0.8470 (mttt) cc_final: 0.7926 (pttp) REVERT: C 79 HIS cc_start: 0.7457 (m-70) cc_final: 0.7193 (m90) REVERT: C 116 ILE cc_start: 0.7774 (mm) cc_final: 0.7516 (mm) REVERT: C 204 GLN cc_start: 0.8455 (mt0) cc_final: 0.8025 (mp10) REVERT: D 141 MET cc_start: 0.8241 (mtt) cc_final: 0.8021 (mpp) REVERT: D 158 TYR cc_start: 0.6825 (m-80) cc_final: 0.6067 (m-80) REVERT: D 188 MET cc_start: 0.0072 (mmm) cc_final: -0.1293 (tpt) outliers start: 28 outliers final: 14 residues processed: 150 average time/residue: 0.1284 time to fit residues: 27.2714 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 : 0.303 ------------------------------------------------------------------------------- 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 1120 VAL Chi-restraints excluded: chain A residue 1129 ILE 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 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 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 107 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 0.0020 chunk 2 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 946 HIS ** 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 = 0.4763 r_free = 0.4763 target = 0.124584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.100126 restraints weight = 56061.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.102859 restraints weight = 30502.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.104714 restraints weight = 19880.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.105991 restraints weight = 14902.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.106789 restraints weight = 12302.074| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12749 Z= 0.145 Angle : 0.647 8.159 17632 Z= 0.357 Chirality : 0.041 0.241 1957 Planarity : 0.004 0.054 1931 Dihedral : 22.727 68.712 2485 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 1.79 % Allowed : 12.03 % Favored : 86.18 % 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 aren not related in a simple way. whole: -0.33 (0.23), residues: 1273 helix: 0.09 (0.21), residues: 570 sheet: -0.09 (0.60), residues: 79 loop : -0.41 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 784 TYR 0.027 0.002 TYR B 943 PHE 0.022 0.002 PHE D 150 TRP 0.015 0.002 TRP A 800 HIS 0.009 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00327 (12749) covalent geometry : angle 0.64676 (17632) hydrogen bonds : bond 0.04307 ( 497) hydrogen bonds : angle 4.89595 ( 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 141 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.456 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 803 MET cc_start: 0.5953 (mtm) cc_final: 0.5045 (ttt) REVERT: A 826 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8143 (pp) REVERT: A 833 PHE cc_start: 0.8859 (m-80) cc_final: 0.8109 (m-80) REVERT: A 1033 LEU cc_start: 0.6931 (mp) cc_final: 0.6625 (mt) REVERT: A 1104 PHE cc_start: 0.7127 (m-80) cc_final: 0.6476 (m-80) REVERT: A 1131 LYS cc_start: 0.7564 (mmmm) cc_final: 0.6934 (tmmt) REVERT: A 1135 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7426 (mt-10) REVERT: B 871 LYS cc_start: 0.8434 (mttt) cc_final: 0.7869 (pttp) REVERT: B 927 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.5040 (mt) REVERT: C 79 HIS cc_start: 0.7405 (m-70) cc_final: 0.7097 (m90) REVERT: C 204 GLN cc_start: 0.8313 (mt0) cc_final: 0.7894 (mp10) REVERT: D 141 MET cc_start: 0.8136 (mtt) cc_final: 0.7852 (mmt) REVERT: D 188 MET cc_start: 0.0100 (mmm) cc_final: -0.1473 (tpt) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.1211 time to fit residues: 23.1971 Evaluate side-chains 116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.121851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.097371 restraints weight = 55494.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.100824 restraints weight = 32908.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.101742 restraints weight = 17633.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.101936 restraints weight = 15062.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.102096 restraints weight = 13731.330| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12749 Z= 0.165 Angle : 0.653 9.182 17632 Z= 0.355 Chirality : 0.042 0.212 1957 Planarity : 0.005 0.060 1931 Dihedral : 22.749 69.229 2482 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 2.05 % Allowed : 14.42 % Favored : 83.53 % 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 aren not related in a simple way. whole: -0.29 (0.23), residues: 1273 helix: 0.15 (0.21), residues: 574 sheet: -0.08 (0.59), residues: 82 loop : -0.41 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 983 TYR 0.028 0.002 TYR B 818 PHE 0.019 0.002 PHE C 166 TRP 0.014 0.001 TRP A 800 HIS 0.008 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00382 (12749) covalent geometry : angle 0.65311 (17632) hydrogen bonds : bond 0.04500 ( 497) hydrogen bonds : angle 4.89442 ( 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 135 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 ARG cc_start: 0.7694 (ptt90) cc_final: 0.7239 (ptt90) REVERT: A 788 MET cc_start: 0.7208 (ppp) cc_final: 0.5577 (tpp) REVERT: A 803 MET cc_start: 0.5907 (mtm) cc_final: 0.5016 (ttt) REVERT: A 826 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8200 (pp) REVERT: A 833 PHE cc_start: 0.8918 (m-80) cc_final: 0.7933 (m-80) REVERT: A 1033 LEU cc_start: 0.7104 (mp) cc_final: 0.6879 (mp) REVERT: A 1104 PHE cc_start: 0.7081 (m-80) cc_final: 0.6369 (m-80) REVERT: A 1131 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7021 (tmmt) REVERT: A 1135 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7525 (mt-10) REVERT: B 774 ARG cc_start: 0.7829 (mmp-170) cc_final: 0.7307 (mmp80) REVERT: B 779 LYS cc_start: 0.8196 (mttt) cc_final: 0.7966 (mtpp) REVERT: B 871 LYS cc_start: 0.8521 (mttt) cc_final: 0.7992 (pttp) REVERT: B 927 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5654 (mt) REVERT: B 1019 MET cc_start: 0.8400 (ptp) cc_final: 0.8054 (ptp) REVERT: C 79 HIS cc_start: 0.7330 (m-70) cc_final: 0.7092 (m90) REVERT: C 204 GLN cc_start: 0.8428 (mt0) cc_final: 0.7980 (mp10) REVERT: C 215 ASP cc_start: 0.6961 (t0) cc_final: 0.6595 (m-30) REVERT: D 140 TYR cc_start: 0.6817 (t80) cc_final: 0.6611 (t80) REVERT: D 141 MET cc_start: 0.8276 (mtt) cc_final: 0.7925 (mpp) REVERT: D 188 MET cc_start: 0.0541 (mmm) cc_final: -0.0031 (tpt) outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 0.1264 time to fit residues: 22.9435 Evaluate side-chains 117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU 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 56 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4731 r_free = 0.4731 target = 0.122932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.097364 restraints weight = 55705.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.099778 restraints weight = 31683.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.100733 restraints weight = 20959.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.102153 restraints weight = 16680.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 74)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.103181 restraints weight = 13824.612| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12749 Z= 0.149 Angle : 0.636 10.665 17632 Z= 0.344 Chirality : 0.041 0.197 1957 Planarity : 0.004 0.057 1931 Dihedral : 22.654 70.561 2482 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.05 % Allowed : 14.51 % Favored : 83.45 % 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 aren not related in a simple way. whole: -0.07 (0.24), residues: 1273 helix: 0.39 (0.22), residues: 570 sheet: -0.18 (0.59), residues: 79 loop : -0.32 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.025 0.002 TYR B 818 PHE 0.030 0.002 PHE C 166 TRP 0.015 0.001 TRP A1008 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00341 (12749) covalent geometry : angle 0.63614 (17632) hydrogen bonds : bond 0.04107 ( 497) hydrogen bonds : angle 4.77609 ( 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 136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.5128 (mpp) cc_final: 0.4295 (pmm) REVERT: A 788 MET cc_start: 0.7152 (ppp) cc_final: 0.6014 (ppp) REVERT: A 803 MET cc_start: 0.6006 (mtm) cc_final: 0.5127 (ttt) REVERT: A 826 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8216 (pp) REVERT: A 833 PHE cc_start: 0.8916 (m-80) cc_final: 0.7907 (m-80) REVERT: A 1033 LEU cc_start: 0.6867 (mp) cc_final: 0.6636 (mp) REVERT: A 1104 PHE cc_start: 0.7024 (m-80) cc_final: 0.6358 (m-80) REVERT: A 1131 LYS cc_start: 0.7556 (mmmm) cc_final: 0.6954 (tmmt) REVERT: A 1135 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7491 (mt-10) REVERT: B 779 LYS cc_start: 0.8214 (mttt) cc_final: 0.7919 (mtpp) REVERT: B 871 LYS cc_start: 0.8503 (mttt) cc_final: 0.7997 (pttp) REVERT: B 927 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5487 (mt) REVERT: C 36 ILE cc_start: 0.7514 (mm) cc_final: 0.7250 (mm) REVERT: C 79 HIS cc_start: 0.7291 (m-70) cc_final: 0.7076 (m90) REVERT: C 204 GLN cc_start: 0.8360 (mt0) cc_final: 0.7925 (mp10) REVERT: D 140 TYR cc_start: 0.6578 (t80) cc_final: 0.6310 (t80) REVERT: D 178 MET cc_start: 0.7211 (mmm) cc_final: 0.6693 (mmm) REVERT: D 188 MET cc_start: 0.0241 (mmm) cc_final: -0.1318 (tpt) outliers start: 24 outliers final: 17 residues processed: 128 average time/residue: 0.1204 time to fit residues: 22.2743 Evaluate side-chains 121 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 840 LEU 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 C residue 56 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 0.0000 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1114 GLN B 946 HIS ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.121165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.096904 restraints weight = 55453.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.100049 restraints weight = 34176.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.100426 restraints weight = 19300.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.100746 restraints weight = 16488.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.101136 restraints weight = 14842.126| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12749 Z= 0.171 Angle : 0.646 10.418 17632 Z= 0.349 Chirality : 0.041 0.202 1957 Planarity : 0.004 0.062 1931 Dihedral : 22.634 70.527 2482 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 2.56 % Allowed : 15.10 % Favored : 82.34 % 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 aren not related in a simple way. whole: -0.24 (0.24), residues: 1273 helix: 0.23 (0.21), residues: 578 sheet: -0.58 (0.54), residues: 90 loop : -0.35 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.027 0.002 TYR B 818 PHE 0.020 0.002 PHE C 166 TRP 0.018 0.002 TRP C 188 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00400 (12749) covalent geometry : angle 0.64639 (17632) hydrogen bonds : bond 0.04489 ( 497) hydrogen bonds : angle 4.80924 ( 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 133 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 MET cc_start: 0.7366 (ppp) cc_final: 0.6364 (ppp) REVERT: A 803 MET cc_start: 0.5964 (mtm) cc_final: 0.5179 (ttt) REVERT: A 826 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8285 (pp) REVERT: A 833 PHE cc_start: 0.9002 (m-80) cc_final: 0.8019 (m-80) REVERT: A 1033 LEU cc_start: 0.7185 (mp) cc_final: 0.6899 (mp) REVERT: A 1104 PHE cc_start: 0.7072 (m-80) cc_final: 0.6448 (m-80) REVERT: A 1131 LYS cc_start: 0.7713 (mmmm) cc_final: 0.7058 (tmmt) REVERT: A 1135 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7577 (mt-10) REVERT: B 871 LYS cc_start: 0.8621 (mttt) cc_final: 0.8106 (pttp) REVERT: B 927 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5791 (mt) REVERT: C 79 HIS cc_start: 0.7338 (m-70) cc_final: 0.7107 (m-70) REVERT: C 204 GLN cc_start: 0.8508 (mt0) cc_final: 0.8038 (mp10) REVERT: D 137 GLN cc_start: 0.7174 (mp10) cc_final: 0.6936 (mp10) REVERT: D 141 MET cc_start: 0.7011 (mmt) cc_final: 0.6544 (mpp) REVERT: D 188 MET cc_start: 0.0862 (mmm) cc_final: -0.0753 (tpt) outliers start: 30 outliers final: 17 residues processed: 123 average time/residue: 0.1142 time to fit residues: 20.8331 Evaluate side-chains 117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU 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 56 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 165 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: 3.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 946 HIS ** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4728 r_free = 0.4728 target = 0.122818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.097182 restraints weight = 55803.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.099908 restraints weight = 31054.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.101559 restraints weight = 20724.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.102660 restraints weight = 15832.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.103036 restraints weight = 13421.291| |-----------------------------------------------------------------------------| r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12749 Z= 0.143 Angle : 0.622 10.031 17632 Z= 0.336 Chirality : 0.041 0.184 1957 Planarity : 0.004 0.061 1931 Dihedral : 22.399 71.005 2482 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 1.88 % Allowed : 16.89 % Favored : 81.23 % 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 aren not related in a simple way. whole: -0.11 (0.24), residues: 1273 helix: 0.41 (0.21), residues: 577 sheet: -0.64 (0.53), residues: 91 loop : -0.32 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A1043 TYR 0.025 0.002 TYR B 818 PHE 0.025 0.002 PHE C 166 TRP 0.015 0.002 TRP A1008 HIS 0.009 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00332 (12749) covalent geometry : angle 0.62160 (17632) hydrogen bonds : bond 0.04020 ( 497) hydrogen bonds : angle 4.73167 ( 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 131 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.5235 (mpp) cc_final: 0.4530 (pmm) REVERT: A 788 MET cc_start: 0.7378 (ppp) cc_final: 0.6412 (ppp) REVERT: A 803 MET cc_start: 0.5941 (mtm) cc_final: 0.5354 (ttp) REVERT: A 826 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8171 (pp) REVERT: A 827 LEU cc_start: 0.8571 (mt) cc_final: 0.8084 (mt) REVERT: A 833 PHE cc_start: 0.9049 (m-80) cc_final: 0.8563 (m-80) REVERT: A 849 GLU cc_start: 0.8360 (mp0) cc_final: 0.8030 (pm20) REVERT: A 1033 LEU cc_start: 0.7052 (mp) cc_final: 0.6768 (mp) REVERT: A 1104 PHE cc_start: 0.7003 (m-80) cc_final: 0.6403 (m-80) REVERT: A 1131 LYS cc_start: 0.7534 (mmmm) cc_final: 0.6965 (tmmt) REVERT: A 1135 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7494 (mt-10) REVERT: B 774 ARG cc_start: 0.7915 (mmp-170) cc_final: 0.7587 (mmp80) REVERT: B 779 LYS cc_start: 0.8216 (mttm) cc_final: 0.7986 (mtpp) REVERT: B 871 LYS cc_start: 0.8564 (mttt) cc_final: 0.8080 (pttp) REVERT: B 927 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5670 (mt) REVERT: C 36 ILE cc_start: 0.7751 (mm) cc_final: 0.7520 (mm) REVERT: C 79 HIS cc_start: 0.7227 (m-70) cc_final: 0.6954 (m-70) REVERT: C 204 GLN cc_start: 0.8419 (mt0) cc_final: 0.8001 (mp10) REVERT: D 93 TRP cc_start: 0.6961 (t60) cc_final: 0.6420 (t60) REVERT: D 139 MET cc_start: -0.0398 (ptm) cc_final: -0.0772 (ptm) REVERT: D 141 MET cc_start: 0.6991 (mmt) cc_final: 0.6672 (mpp) REVERT: D 188 MET cc_start: 0.0050 (mmm) cc_final: -0.1341 (tpt) REVERT: D 233 ASP cc_start: 0.4236 (t0) cc_final: 0.3850 (t0) REVERT: D 426 ARG cc_start: 0.7601 (ptm160) cc_final: 0.7007 (ptm160) outliers start: 22 outliers final: 16 residues processed: 123 average time/residue: 0.1035 time to fit residues: 19.1799 Evaluate side-chains 117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 866 VAL 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 58 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 165 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: 6.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 132 optimal weight: 10.0000 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4813 r_free = 0.4813 target = 0.125040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.100169 restraints weight = 57749.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.103051 restraints weight = 30646.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.104841 restraints weight = 19991.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.106154 restraints weight = 15220.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.106684 restraints weight = 12721.547| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12749 Z= 0.151 Angle : 0.638 11.825 17632 Z= 0.343 Chirality : 0.041 0.203 1957 Planarity : 0.004 0.064 1931 Dihedral : 22.291 71.231 2482 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 1.62 % Allowed : 17.32 % Favored : 81.06 % 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 aren not related in a simple way. whole: -0.07 (0.24), residues: 1273 helix: 0.41 (0.21), residues: 579 sheet: -0.56 (0.59), residues: 79 loop : -0.30 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1043 TYR 0.031 0.002 TYR B1000 PHE 0.030 0.002 PHE C 166 TRP 0.033 0.002 TRP A 830 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00352 (12749) covalent geometry : angle 0.63798 (17632) hydrogen bonds : bond 0.04159 ( 497) hydrogen bonds : angle 4.79367 ( 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 121 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.5341 (mpp) cc_final: 0.4687 (pmm) REVERT: A 788 MET cc_start: 0.7297 (ppp) cc_final: 0.6275 (ppp) REVERT: A 803 MET cc_start: 0.6014 (mtm) cc_final: 0.5292 (ttp) REVERT: A 826 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 827 LEU cc_start: 0.8517 (mt) cc_final: 0.8013 (mt) REVERT: A 833 PHE cc_start: 0.9007 (m-80) cc_final: 0.8537 (m-80) REVERT: A 849 GLU cc_start: 0.8334 (mp0) cc_final: 0.8020 (pm20) REVERT: A 1033 LEU cc_start: 0.6868 (mp) cc_final: 0.6599 (mp) REVERT: A 1104 PHE cc_start: 0.6953 (m-80) cc_final: 0.6388 (m-80) REVERT: A 1131 LYS cc_start: 0.7545 (mmmm) cc_final: 0.6958 (tmmt) REVERT: A 1135 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7556 (mt-10) REVERT: B 774 ARG cc_start: 0.7901 (mmp-170) cc_final: 0.7618 (mmp80) REVERT: B 871 LYS cc_start: 0.8451 (mttt) cc_final: 0.8037 (pttp) REVERT: B 927 LEU cc_start: 0.5976 (OUTLIER) cc_final: 0.5669 (mt) REVERT: C 204 GLN cc_start: 0.8412 (mt0) cc_final: 0.8004 (mp10) REVERT: C 235 MET cc_start: 0.2896 (mmm) cc_final: 0.2551 (mmm) REVERT: D 93 TRP cc_start: 0.6991 (t60) cc_final: 0.6489 (t60) REVERT: D 139 MET cc_start: -0.0265 (ptm) cc_final: -0.0555 (ptt) REVERT: D 141 MET cc_start: 0.6898 (mmt) cc_final: 0.6512 (mpp) REVERT: D 178 MET cc_start: 0.7266 (mmm) cc_final: 0.6824 (mmm) REVERT: D 188 MET cc_start: 0.0286 (mmm) cc_final: -0.1111 (tpt) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.1127 time to fit residues: 19.4745 Evaluate side-chains 112 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 866 VAL 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 173 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 127 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 946 HIS ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** 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 = 0.4773 r_free = 0.4773 target = 0.122590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.098421 restraints weight = 57760.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.101802 restraints weight = 31341.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.102234 restraints weight = 17085.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.102602 restraints weight = 15220.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.102677 restraints weight = 14205.353| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12749 Z= 0.189 Angle : 0.678 10.754 17632 Z= 0.364 Chirality : 0.043 0.264 1957 Planarity : 0.005 0.066 1931 Dihedral : 22.310 71.347 2482 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 1.37 % Allowed : 17.83 % 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 aren not related in a simple way. whole: -0.32 (0.23), residues: 1273 helix: 0.13 (0.21), residues: 588 sheet: -0.53 (0.63), residues: 70 loop : -0.38 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1043 TYR 0.029 0.002 TYR B 818 PHE 0.025 0.002 PHE C 166 TRP 0.063 0.003 TRP A 830 HIS 0.011 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00440 (12749) covalent geometry : angle 0.67791 (17632) hydrogen bonds : bond 0.04775 ( 497) hydrogen bonds : angle 4.99487 ( 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 110 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.5515 (mpp) cc_final: 0.4819 (pmm) REVERT: A 788 MET cc_start: 0.7295 (ppp) cc_final: 0.6335 (ppp) REVERT: A 803 MET cc_start: 0.5696 (mtm) cc_final: 0.4859 (ptm) REVERT: A 826 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8358 (pp) REVERT: A 827 LEU cc_start: 0.8658 (mt) cc_final: 0.8038 (mt) REVERT: A 833 PHE cc_start: 0.9126 (m-80) cc_final: 0.8909 (m-80) REVERT: A 849 GLU cc_start: 0.8353 (mp0) cc_final: 0.8040 (pm20) REVERT: A 1033 LEU cc_start: 0.7227 (mp) cc_final: 0.6963 (mp) REVERT: A 1104 PHE cc_start: 0.7026 (m-80) cc_final: 0.6443 (m-80) REVERT: A 1135 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7665 (mt-10) REVERT: B 774 ARG cc_start: 0.8120 (mmp-170) cc_final: 0.7766 (mmp80) REVERT: B 871 LYS cc_start: 0.8542 (mttt) cc_final: 0.8142 (pttp) REVERT: B 927 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5877 (mt) REVERT: C 204 GLN cc_start: 0.8629 (mt0) cc_final: 0.8145 (mp10) REVERT: C 235 MET cc_start: 0.3139 (mmm) cc_final: 0.2836 (mmm) REVERT: D 141 MET cc_start: 0.6860 (mmt) cc_final: 0.6410 (mpp) REVERT: D 188 MET cc_start: 0.0997 (mmm) cc_final: -0.0709 (tpt) outliers start: 16 outliers final: 12 residues processed: 105 average time/residue: 0.1142 time to fit residues: 18.0093 Evaluate side-chains 106 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 1086 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 818 TYR Chi-restraints excluded: chain B residue 866 VAL 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 173 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 49 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4797 r_free = 0.4797 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.098747 restraints weight = 55670.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.101636 restraints weight = 29144.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.103395 restraints weight = 18931.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.104460 restraints weight = 14282.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.104786 restraints weight = 12023.653| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12749 Z= 0.156 Angle : 0.650 10.576 17632 Z= 0.348 Chirality : 0.042 0.262 1957 Planarity : 0.004 0.062 1931 Dihedral : 22.147 70.651 2482 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.54 % Allowed : 18.00 % 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 aren not related in a simple way. whole: -0.15 (0.24), residues: 1273 helix: 0.34 (0.21), residues: 587 sheet: -0.60 (0.65), residues: 62 loop : -0.35 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1043 TYR 0.025 0.002 TYR B 818 PHE 0.025 0.002 PHE C 166 TRP 0.053 0.002 TRP A 830 HIS 0.010 0.001 HIS B 919 Details of bonding type rmsd covalent geometry : bond 0.00362 (12749) covalent geometry : angle 0.64962 (17632) hydrogen bonds : bond 0.04274 ( 497) hydrogen bonds : angle 4.86855 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.14 seconds wall clock time: 52 minutes 54.78 seconds (3174.78 seconds total)