Starting phenix.real_space_refine on Wed Feb 12 14:16:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j88_36063/02_2025/8j88_36063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j88_36063/02_2025/8j88_36063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j88_36063/02_2025/8j88_36063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j88_36063/02_2025/8j88_36063.map" model { file = "/net/cci-nas-00/data/ceres_data/8j88_36063/02_2025/8j88_36063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j88_36063/02_2025/8j88_36063.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 5058 2.51 5 N 1346 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7846 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3923 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Restraints were copied for chains: B Time building chain proxies: 7.07, per 1000 atoms: 0.90 Number of scatterers: 7846 At special positions: 0 Unit cell: (148.57, 77.19, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1420 8.00 N 1346 7.00 C 5058 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 47.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.720A pdb=" N LYS A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 725 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.668A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.594A pdb=" N LEU A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.695A pdb=" N TYR A 946 " --> pdb=" O PRO A 942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 removed outlier: 3.572A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 981 No H-bonds generated for 'chain 'A' and resid 979 through 981' Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.381A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1028 through 1070 Proline residue: A1037 - end of helix removed outlier: 3.771A pdb=" N GLN A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1056 " --> pdb=" O ALA A1052 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 3.604A pdb=" N LEU A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.502A pdb=" N ASN A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A1115 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.805A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1158 removed outlier: 3.674A pdb=" N ILE A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 removed outlier: 3.518A pdb=" N LEU A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 729 removed outlier: 3.673A pdb=" N GLY B 724 " --> pdb=" O LYS B 720 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 725 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 754 through 766 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.669A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.594A pdb=" N LEU B 886 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 892 " --> pdb=" O TYR B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.695A pdb=" N TYR B 946 " --> pdb=" O PRO B 942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 947 " --> pdb=" O THR B 943 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 948 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 951 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 960 removed outlier: 3.572A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 981 No H-bonds generated for 'chain 'B' and resid 979 through 981' Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.381A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 Processing helix chain 'B' and resid 1028 through 1070 Proline residue: B1037 - end of helix removed outlier: 3.771A pdb=" N GLN B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B1056 " --> pdb=" O ALA B1052 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B1069 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1089 removed outlier: 3.603A pdb=" N LEU B1089 " --> pdb=" O ALA B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1119 removed outlier: 3.502A pdb=" N ASN B1114 " --> pdb=" O ILE B1110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B1115 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.805A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1158 removed outlier: 3.673A pdb=" N ILE B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B1146 " --> pdb=" O VAL B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.519A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.951A pdb=" N GLN A 804 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.689A pdb=" N PHE A 913 " --> pdb=" O TYR A 916 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 919 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A1007 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.120A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 926 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 931 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 934 " --> pdb=" O ILE A 974 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 974 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1015 through 1016 Processing sheet with id=AA6, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.951A pdb=" N GLN B 804 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.689A pdb=" N PHE B 913 " --> pdb=" O TYR B 916 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 919 " --> pdb=" O ASN B1007 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B1007 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.121A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 926 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 931 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 934 " --> pdb=" O ILE B 974 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 974 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1015 through 1016 288 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2524 1.35 - 1.46: 1928 1.46 - 1.58: 3554 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8044 Sorted by residual: bond pdb=" C SER B1162 " pdb=" N PRO B1163 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.69e+00 bond pdb=" C SER A1162 " pdb=" N PRO A1163 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.59e+00 bond pdb=" C ARG A 900 " pdb=" N PRO A 901 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.25e-02 6.40e+03 9.81e-01 bond pdb=" C ARG B 900 " pdb=" N PRO B 901 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.25e-02 6.40e+03 9.29e-01 bond pdb=" C LEU A 937 " pdb=" N PRO A 938 " ideal model delta sigma weight residual 1.331 1.343 -0.011 1.21e-02 6.83e+03 8.76e-01 ... (remaining 8039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 10710 1.85 - 3.70: 138 3.70 - 5.55: 16 5.55 - 7.41: 2 7.41 - 9.26: 8 Bond angle restraints: 10874 Sorted by residual: angle pdb=" CB MET B 957 " pdb=" CG MET B 957 " pdb=" SD MET B 957 " ideal model delta sigma weight residual 112.70 121.96 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" CB MET A 957 " pdb=" CG MET A 957 " pdb=" SD MET A 957 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.48e+00 angle pdb=" CA LEU B1159 " pdb=" CB LEU B1159 " pdb=" CG LEU B1159 " ideal model delta sigma weight residual 116.30 125.37 -9.07 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU A1159 " pdb=" CB LEU A1159 " pdb=" CG LEU A1159 " ideal model delta sigma weight residual 116.30 125.34 -9.04 3.50e+00 8.16e-02 6.68e+00 angle pdb=" CA LEU B1126 " pdb=" CB LEU B1126 " pdb=" CG LEU B1126 " ideal model delta sigma weight residual 116.30 125.00 -8.70 3.50e+00 8.16e-02 6.18e+00 ... (remaining 10869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 4413 15.66 - 31.31: 353 31.31 - 46.97: 74 46.97 - 62.62: 4 62.62 - 78.28: 6 Dihedral angle restraints: 4850 sinusoidal: 2026 harmonic: 2824 Sorted by residual: dihedral pdb=" CA THR A1123 " pdb=" C THR A1123 " pdb=" N TYR A1124 " pdb=" CA TYR A1124 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR B1123 " pdb=" C THR B1123 " pdb=" N TYR B1124 " pdb=" CA TYR B1124 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO B 938 " pdb=" C PRO B 938 " pdb=" N LEU B 939 " pdb=" CA LEU B 939 " ideal model delta harmonic sigma weight residual -180.00 -164.90 -15.10 0 5.00e+00 4.00e-02 9.12e+00 ... (remaining 4847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 676 0.028 - 0.056: 314 0.056 - 0.084: 103 0.084 - 0.112: 50 0.112 - 0.141: 17 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CB VAL A 838 " pdb=" CA VAL A 838 " pdb=" CG1 VAL A 838 " pdb=" CG2 VAL A 838 " both_signs ideal model delta sigma weight residual False -2.63 -2.77 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CB VAL B 838 " pdb=" CA VAL B 838 " pdb=" CG1 VAL B 838 " pdb=" CG2 VAL B 838 " both_signs ideal model delta sigma weight residual False -2.63 -2.77 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA SER B1162 " pdb=" N SER B1162 " pdb=" C SER B1162 " pdb=" CB SER B1162 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1157 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 938 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 938 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 900 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 901 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 901 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 901 " -0.022 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 662 2.74 - 3.28: 7950 3.28 - 3.82: 12752 3.82 - 4.36: 14599 4.36 - 4.90: 24565 Nonbonded interactions: 60528 Sorted by model distance: nonbonded pdb=" OG SER B1071 " pdb=" OE1 GLU B1073 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A1071 " pdb=" OE1 GLU A1073 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.272 3.040 nonbonded pdb=" O THR A1100 " pdb=" OG SER A1104 " model vdw 2.285 3.040 ... (remaining 60523 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.300 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8044 Z= 0.129 Angle : 0.562 9.258 10874 Z= 0.290 Chirality : 0.040 0.141 1160 Planarity : 0.004 0.047 1388 Dihedral : 11.869 78.275 3038 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 950 helix: -0.25 (0.27), residues: 374 sheet: -0.36 (0.53), residues: 124 loop : -0.94 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1189 HIS 0.002 0.001 HIS A1078 PHE 0.017 0.001 PHE B 913 TYR 0.019 0.001 TYR B1079 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.832 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2074 time to fit residues: 21.0899 Evaluate side-chains 51 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 HIS B1014 ASN ** B1192 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 = 0.4755 r_free = 0.4755 target = 0.123961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.107436 restraints weight = 41652.064| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 6.83 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8044 Z= 0.203 Angle : 0.602 8.717 10874 Z= 0.307 Chirality : 0.043 0.137 1160 Planarity : 0.005 0.043 1388 Dihedral : 4.147 19.094 1072 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.59 % Allowed : 6.40 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 950 helix: 0.63 (0.27), residues: 390 sheet: -0.25 (0.52), residues: 126 loop : -1.13 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 856 HIS 0.006 0.001 HIS A1051 PHE 0.014 0.001 PHE B 913 TYR 0.013 0.002 TYR B1043 ARG 0.014 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.955 Fit side-chains REVERT: B 903 ASN cc_start: 0.8069 (m-40) cc_final: 0.7785 (t0) outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 0.1699 time to fit residues: 15.7716 Evaluate side-chains 53 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain B residue 750 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS B 753 HIS ** B1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.120274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.102956 restraints weight = 41752.011| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 7.16 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8044 Z= 0.227 Angle : 0.602 8.758 10874 Z= 0.312 Chirality : 0.044 0.137 1160 Planarity : 0.005 0.042 1388 Dihedral : 4.604 24.503 1072 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.95 % Allowed : 9.60 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.28), residues: 950 helix: 0.72 (0.27), residues: 392 sheet: -0.69 (0.49), residues: 128 loop : -1.26 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.007 0.001 HIS A1051 PHE 0.020 0.001 PHE B 913 TYR 0.020 0.002 TYR A1038 ARG 0.004 0.001 ARG A 736 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 775 LEU cc_start: 0.6343 (mp) cc_final: 0.5966 (tp) REVERT: A 957 MET cc_start: 0.6353 (tpt) cc_final: 0.5843 (tpt) REVERT: B 1026 ASN cc_start: 0.8258 (p0) cc_final: 0.7977 (p0) outliers start: 8 outliers final: 3 residues processed: 64 average time/residue: 0.1945 time to fit residues: 18.8290 Evaluate side-chains 51 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain B residue 1047 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 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 = 0.4747 r_free = 0.4747 target = 0.122905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.105730 restraints weight = 40610.672| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 7.12 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8044 Z= 0.134 Angle : 0.509 8.664 10874 Z= 0.259 Chirality : 0.041 0.142 1160 Planarity : 0.004 0.041 1388 Dihedral : 4.112 22.669 1072 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.18 % Allowed : 11.37 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 950 helix: 1.25 (0.28), residues: 380 sheet: -0.55 (0.50), residues: 128 loop : -1.31 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 856 HIS 0.005 0.001 HIS A1051 PHE 0.027 0.001 PHE B 750 TYR 0.010 0.001 TYR A 769 ARG 0.003 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 775 LEU cc_start: 0.6372 (mp) cc_final: 0.5753 (tp) REVERT: A 957 MET cc_start: 0.6368 (tpt) cc_final: 0.5969 (tpt) REVERT: A 1076 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7169 (pp) REVERT: B 1026 ASN cc_start: 0.8197 (p0) cc_final: 0.7986 (p0) outliers start: 10 outliers final: 3 residues processed: 64 average time/residue: 0.1804 time to fit residues: 16.9453 Evaluate side-chains 55 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1076 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 0.0070 chunk 52 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS ** B1001 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 = 0.4756 r_free = 0.4756 target = 0.123530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.106669 restraints weight = 40262.730| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 7.03 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8044 Z= 0.128 Angle : 0.503 8.622 10874 Z= 0.255 Chirality : 0.041 0.146 1160 Planarity : 0.004 0.043 1388 Dihedral : 3.873 21.470 1072 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.42 % Allowed : 11.85 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 950 helix: 1.40 (0.28), residues: 382 sheet: -0.25 (0.49), residues: 136 loop : -1.38 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.004 0.001 HIS B1051 PHE 0.016 0.001 PHE B 913 TYR 0.022 0.001 TYR A 888 ARG 0.004 0.000 ARG B1087 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.867 Fit side-chains REVERT: A 775 LEU cc_start: 0.6344 (mp) cc_final: 0.5770 (tp) REVERT: A 957 MET cc_start: 0.6304 (tpt) cc_final: 0.5923 (tpt) REVERT: A 1073 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5383 (tt0) outliers start: 12 outliers final: 5 residues processed: 67 average time/residue: 0.2012 time to fit residues: 19.2290 Evaluate side-chains 55 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 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 = 0.4640 r_free = 0.4640 target = 0.117395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.100603 restraints weight = 40672.863| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 6.96 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 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 0.034 8044 Z= 0.265 Angle : 0.651 9.211 10874 Z= 0.333 Chirality : 0.045 0.169 1160 Planarity : 0.005 0.052 1388 Dihedral : 4.688 25.951 1072 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.90 % Allowed : 11.85 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.28), residues: 950 helix: 0.69 (0.27), residues: 388 sheet: -0.64 (0.48), residues: 132 loop : -1.47 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1189 HIS 0.005 0.001 HIS A1051 PHE 0.013 0.002 PHE B 913 TYR 0.023 0.002 TYR A1038 ARG 0.008 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.857 Fit side-chains REVERT: A 1073 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6509 (mm-30) REVERT: B 1073 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.5998 (tt0) outliers start: 16 outliers final: 8 residues processed: 64 average time/residue: 0.1541 time to fit residues: 15.1008 Evaluate side-chains 56 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 72 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 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 = 0.4688 r_free = 0.4688 target = 0.119791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.103109 restraints weight = 40506.796| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 6.98 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8044 Z= 0.155 Angle : 0.558 8.861 10874 Z= 0.280 Chirality : 0.042 0.142 1160 Planarity : 0.004 0.044 1388 Dihedral : 4.233 23.387 1072 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.66 % Allowed : 12.80 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.28), residues: 950 helix: 1.04 (0.28), residues: 378 sheet: -0.13 (0.51), residues: 124 loop : -1.52 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1170 HIS 0.005 0.001 HIS B1051 PHE 0.013 0.001 PHE B 913 TYR 0.012 0.001 TYR A1029 ARG 0.005 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.913 Fit side-chains REVERT: A 775 LEU cc_start: 0.5907 (mp) cc_final: 0.5454 (tp) REVERT: A 1073 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5659 (tt0) REVERT: B 1026 ASN cc_start: 0.8399 (p0) cc_final: 0.7995 (p0) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1859 time to fit residues: 17.8022 Evaluate side-chains 60 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 776 TYR Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1001 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 = 0.4688 r_free = 0.4688 target = 0.119708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.103184 restraints weight = 40761.241| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 6.93 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8044 Z= 0.156 Angle : 0.573 9.945 10874 Z= 0.286 Chirality : 0.042 0.165 1160 Planarity : 0.004 0.042 1388 Dihedral : 4.177 23.426 1072 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.66 % Allowed : 13.27 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 950 helix: 1.24 (0.29), residues: 374 sheet: 0.30 (0.54), residues: 114 loop : -1.49 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.005 0.001 HIS B1051 PHE 0.018 0.001 PHE A 913 TYR 0.027 0.001 TYR A1029 ARG 0.004 0.000 ARG B1087 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.898 Fit side-chains REVERT: A 775 LEU cc_start: 0.5964 (mp) cc_final: 0.5466 (tp) REVERT: A 1073 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5442 (tt0) REVERT: B 893 LYS cc_start: 0.9068 (mptt) cc_final: 0.8720 (mptt) REVERT: B 900 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7777 (ptp-170) REVERT: B 962 GLU cc_start: 0.7603 (tp30) cc_final: 0.7106 (tp30) REVERT: B 1026 ASN cc_start: 0.8301 (p0) cc_final: 0.7906 (p0) REVERT: B 1073 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6090 (tt0) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.1627 time to fit residues: 15.6792 Evaluate side-chains 64 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 776 TYR Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 HIS ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS B 789 HIS ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.114002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.097486 restraints weight = 41508.923| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 6.86 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8044 Z= 0.318 Angle : 0.722 8.719 10874 Z= 0.374 Chirality : 0.047 0.190 1160 Planarity : 0.006 0.094 1388 Dihedral : 5.265 27.760 1072 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.66 % Allowed : 13.74 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 950 helix: 0.15 (0.26), residues: 388 sheet: -0.21 (0.52), residues: 106 loop : -1.78 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 856 HIS 0.007 0.002 HIS B1078 PHE 0.023 0.002 PHE B 913 TYR 0.026 0.003 TYR A1029 ARG 0.008 0.001 ARG B1087 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 1073 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.5940 (tt0) REVERT: B 893 LYS cc_start: 0.9009 (mptt) cc_final: 0.8742 (mptt) REVERT: B 1026 ASN cc_start: 0.8390 (p0) cc_final: 0.7971 (p0) REVERT: B 1073 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.5496 (mm-30) REVERT: B 1101 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7425 (tp) outliers start: 14 outliers final: 8 residues processed: 63 average time/residue: 0.1650 time to fit residues: 15.3656 Evaluate side-chains 58 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 0.0030 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.118091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.101878 restraints weight = 40876.202| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 6.89 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8044 Z= 0.160 Angle : 0.597 8.831 10874 Z= 0.300 Chirality : 0.043 0.157 1160 Planarity : 0.004 0.046 1388 Dihedral : 4.448 24.209 1072 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.30 % Allowed : 14.57 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 950 helix: 0.69 (0.27), residues: 390 sheet: 0.06 (0.54), residues: 98 loop : -1.53 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1170 HIS 0.005 0.001 HIS B1051 PHE 0.022 0.001 PHE B 913 TYR 0.025 0.001 TYR A 769 ARG 0.018 0.001 ARG B1087 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 775 LEU cc_start: 0.5904 (mp) cc_final: 0.5474 (tp) REVERT: B 893 LYS cc_start: 0.9090 (mptt) cc_final: 0.8779 (mptt) REVERT: B 900 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7758 (ptp-170) REVERT: B 1026 ASN cc_start: 0.8299 (p0) cc_final: 0.7896 (p0) REVERT: B 1073 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.5909 (tt0) REVERT: B 1087 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8349 (pmt-80) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.2087 time to fit residues: 20.0654 Evaluate side-chains 67 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 1073 GLU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 776 TYR Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.115161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.098897 restraints weight = 40962.062| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 6.92 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8044 Z= 0.247 Angle : 0.660 9.659 10874 Z= 0.337 Chirality : 0.045 0.187 1160 Planarity : 0.005 0.058 1388 Dihedral : 4.698 24.466 1072 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.95 % Allowed : 15.05 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 950 helix: 0.53 (0.27), residues: 388 sheet: -0.19 (0.52), residues: 98 loop : -1.62 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 856 HIS 0.005 0.001 HIS B1078 PHE 0.026 0.002 PHE B 913 TYR 0.018 0.002 TYR A1038 ARG 0.011 0.001 ARG B1087 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.78 seconds wall clock time: 65 minutes 15.76 seconds (3915.76 seconds total)