Starting phenix.real_space_refine on Wed Mar 12 14:35:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j87_36062/03_2025/8j87_36062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j87_36062/03_2025/8j87_36062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j87_36062/03_2025/8j87_36062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j87_36062/03_2025/8j87_36062.map" model { file = "/net/cci-nas-00/data/ceres_data/8j87_36062/03_2025/8j87_36062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j87_36062/03_2025/8j87_36062.cif" } resolution = 3.42 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 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7846 Number of models: 1 Model: "" Number of chains: 2 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} Chain: "B" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3923 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Time building chain proxies: 5.28, per 1000 atoms: 0.67 Number of scatterers: 7846 At special positions: 0 Unit cell: (153.55, 72.21, 107.9, 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: 1.79 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: 38 helices and 12 sheets defined 49.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.519A pdb=" N LYS A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 818 through 822 removed outlier: 3.518A pdb=" N LEU A 822 " --> pdb=" O SER A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.841A pdb=" N MET A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 883 through 893 removed outlier: 3.847A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 954 through 960 removed outlier: 4.009A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.992A pdb=" N LEU A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 979 through 984' Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.839A pdb=" N GLU A 988 " --> pdb=" O ARG A 985 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 989 " --> pdb=" O ILE A 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 989' Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.963A pdb=" N LEU A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1070 removed outlier: 3.726A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 3.708A pdb=" N LEU A1056 " --> pdb=" O ALA A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1092 removed outlier: 4.027A pdb=" N ARG A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A1088 " --> pdb=" O GLU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.715A pdb=" N ASN A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A1115 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A1116 " --> pdb=" O GLU A1112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.913A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1158 removed outlier: 3.874A pdb=" N LYS A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 removed outlier: 3.524A pdb=" N TRP A1170 " --> pdb=" O GLY A1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 729 Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.519A pdb=" N LEU B 822 " --> pdb=" O SER B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.840A pdb=" N MET B 846 " --> pdb=" O PRO B 842 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 847' Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 883 through 893 removed outlier: 3.847A pdb=" N LYS B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 892 " --> pdb=" O TYR B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 954 through 960 removed outlier: 4.008A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.992A pdb=" N LEU B 983 " --> pdb=" O LYS B 979 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 979 through 984' Processing helix chain 'B' and resid 985 through 989 removed outlier: 3.839A pdb=" N GLU B 988 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU B 989 " --> pdb=" O ILE B 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 985 through 989' Processing helix chain 'B' and resid 997 through 1003 removed outlier: 3.963A pdb=" N LEU B1003 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1070 removed outlier: 3.726A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 3.706A pdb=" N LEU B1056 " --> pdb=" O ALA B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1092 removed outlier: 4.028A pdb=" N ARG B1087 " --> pdb=" O LYS B1083 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B1088 " --> pdb=" O GLU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1119 removed outlier: 3.716A pdb=" N ASN B1114 " --> pdb=" O ILE B1110 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B1115 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B1116 " --> pdb=" O GLU B1112 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.914A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1158 removed outlier: 3.875A pdb=" N LYS B1146 " --> pdb=" O VAL B1142 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B1147 " --> pdb=" O GLU B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.524A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.615A pdb=" N GLN A 804 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.894A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.519A pdb=" N SER A 919 " --> pdb=" O ASN A1007 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.146A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 931 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 974 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 977 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 967 through 968 Processing sheet with id=AA6, first strand: chain 'A' and resid 1014 through 1016 removed outlier: 3.569A pdb=" N PHE A1015 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.614A pdb=" N GLN B 804 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.894A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.520A pdb=" N SER B 919 " --> pdb=" O ASN B1007 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.145A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 931 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 974 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 977 " --> pdb=" O GLU B 962 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 967 through 968 Processing sheet with id=AB3, first strand: chain 'B' and resid 1014 through 1016 removed outlier: 3.569A pdb=" N PHE B1015 " --> pdb=" O ILE B1023 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 900 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: 1.99 Time building geometry restraints manager: 2.14 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: 1914 1.46 - 1.58: 3568 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 1.362 -0.028 2.34e-02 1.83e+03 1.45e+00 bond pdb=" C SER A1162 " pdb=" N PRO A1163 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.39e+00 bond pdb=" C LEU A1036 " pdb=" N PRO A1037 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.00e-01 bond pdb=" N THR A1123 " pdb=" CA THR A1123 " ideal model delta sigma weight residual 1.458 1.470 -0.012 1.77e-02 3.19e+03 4.31e-01 bond pdb=" N LEU B1126 " pdb=" CA LEU B1126 " ideal model delta sigma weight residual 1.462 1.471 -0.009 1.48e-02 4.57e+03 3.93e-01 ... (remaining 8039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 10732 1.88 - 3.77: 118 3.77 - 5.65: 14 5.65 - 7.54: 4 7.54 - 9.42: 6 Bond angle restraints: 10874 Sorted by residual: angle pdb=" C HIS B1099 " pdb=" N THR B1100 " pdb=" CA THR B1100 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.37e+00 angle pdb=" C HIS A1099 " pdb=" N THR A1100 " pdb=" CA THR A1100 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 angle pdb=" CA LEU B1126 " pdb=" CB LEU B1126 " pdb=" CG LEU B1126 " ideal model delta sigma weight residual 116.30 125.72 -9.42 3.50e+00 8.16e-02 7.24e+00 angle pdb=" CA LEU A1159 " pdb=" CB LEU A1159 " pdb=" CG LEU A1159 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 angle pdb=" CA LEU B1159 " pdb=" CB LEU B1159 " pdb=" CG LEU B1159 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 ... (remaining 10869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.38: 4190 10.38 - 20.76: 409 20.76 - 31.15: 161 31.15 - 41.53: 72 41.53 - 51.91: 18 Dihedral angle restraints: 4850 sinusoidal: 2026 harmonic: 2824 Sorted by residual: dihedral pdb=" CA THR B1123 " pdb=" C THR B1123 " pdb=" N TYR B1124 " pdb=" CA TYR B1124 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA THR A1123 " pdb=" C THR A1123 " pdb=" N TYR A1124 " pdb=" CA TYR A1124 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+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 -164.22 -15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 4847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 737 0.030 - 0.060: 279 0.060 - 0.089: 89 0.089 - 0.119: 48 0.119 - 0.149: 7 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA LEU B 865 " pdb=" N LEU B 865 " pdb=" C LEU B 865 " pdb=" CB LEU B 865 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA LEU A 865 " pdb=" N LEU A 865 " pdb=" C LEU A 865 " pdb=" CB LEU A 865 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE A1125 " pdb=" N ILE A1125 " pdb=" C ILE A1125 " pdb=" CB ILE A1125 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1157 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 769 " 0.011 2.00e-02 2.50e+03 1.16e-02 2.69e+00 pdb=" CG TYR A 769 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 769 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 769 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 769 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 769 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 769 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 769 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 769 " 0.010 2.00e-02 2.50e+03 1.14e-02 2.61e+00 pdb=" CG TYR B 769 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 769 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 769 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 769 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 769 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 769 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 769 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO B 938 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.020 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 472 2.74 - 3.28: 8024 3.28 - 3.82: 12438 3.82 - 4.36: 14640 4.36 - 4.90: 24614 Nonbonded interactions: 60188 Sorted by model distance: nonbonded pdb=" OG SER A1109 " pdb=" OE1 GLU A1112 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B1109 " pdb=" OE1 GLU B1112 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 953 " pdb=" OD1 ASN A 955 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 953 " pdb=" OD1 ASN B 955 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.298 3.040 ... (remaining 60183 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: 2.780 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 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 0.028 8044 Z= 0.109 Angle : 0.540 9.420 10874 Z= 0.276 Chirality : 0.039 0.149 1160 Planarity : 0.003 0.035 1388 Dihedral : 10.980 51.912 3038 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.40 (0.27), residues: 950 helix: 0.14 (0.27), residues: 380 sheet: 1.65 (0.63), residues: 78 loop : -0.88 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 861 HIS 0.002 0.000 HIS B1099 PHE 0.008 0.001 PHE B 913 TYR 0.029 0.001 TYR A 769 ARG 0.001 0.000 ARG B 863 *********************** 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 85 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.920 Fit side-chains REVERT: A 959 PHE cc_start: 0.8113 (m-80) cc_final: 0.7725 (m-80) REVERT: A 990 PHE cc_start: 0.6724 (m-80) cc_final: 0.6240 (m-10) REVERT: B 957 MET cc_start: 0.8326 (mmp) cc_final: 0.8029 (mmp) REVERT: B 959 PHE cc_start: 0.8252 (m-80) cc_final: 0.7851 (m-80) REVERT: B 990 PHE cc_start: 0.6862 (m-80) cc_final: 0.6437 (m-10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1758 time to fit residues: 21.9222 Evaluate side-chains 69 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN A1007 ASN B 930 ASN B1007 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.122510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.105760 restraints weight = 31407.817| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 5.43 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8044 Z= 0.172 Angle : 0.571 8.685 10874 Z= 0.291 Chirality : 0.042 0.140 1160 Planarity : 0.004 0.033 1388 Dihedral : 3.924 18.746 1072 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.95 % Allowed : 7.23 % Favored : 91.82 % 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: 0.28 (0.27), residues: 950 helix: 1.16 (0.27), residues: 390 sheet: 0.97 (0.63), residues: 78 loop : -0.76 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 820 HIS 0.005 0.001 HIS B1099 PHE 0.021 0.001 PHE B 913 TYR 0.021 0.002 TYR A 769 ARG 0.004 0.000 ARG A 873 *********************** 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 81 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 957 MET cc_start: 0.8595 (mmp) cc_final: 0.8252 (mmp) REVERT: A 990 PHE cc_start: 0.7004 (m-80) cc_final: 0.6289 (m-80) REVERT: B 756 MET cc_start: 0.6832 (tpp) cc_final: 0.6593 (tpp) REVERT: B 957 MET cc_start: 0.8494 (mmp) cc_final: 0.8271 (mmm) REVERT: B 959 PHE cc_start: 0.8211 (m-80) cc_final: 0.7736 (m-80) REVERT: B 990 PHE cc_start: 0.7081 (m-80) cc_final: 0.6405 (m-80) outliers start: 8 outliers final: 3 residues processed: 77 average time/residue: 0.1682 time to fit residues: 19.5978 Evaluate side-chains 71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 1053 VAL 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: 2.9990 chunk 13 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.122001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.105135 restraints weight = 32531.955| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 5.75 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8044 Z= 0.144 Angle : 0.536 8.698 10874 Z= 0.269 Chirality : 0.041 0.145 1160 Planarity : 0.003 0.032 1388 Dihedral : 3.890 20.653 1072 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.18 % Allowed : 9.60 % Favored : 89.22 % 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: 0.37 (0.28), residues: 950 helix: 1.44 (0.27), residues: 390 sheet: 0.56 (0.61), residues: 78 loop : -0.81 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 861 HIS 0.004 0.001 HIS B1099 PHE 0.010 0.001 PHE B 809 TYR 0.013 0.001 TYR A 888 ARG 0.007 0.000 ARG A1040 *********************** 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 84 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.858 Fit side-chains REVERT: A 869 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6476 (mp) REVERT: A 916 TYR cc_start: 0.8020 (m-80) cc_final: 0.7728 (m-80) REVERT: A 957 MET cc_start: 0.8655 (mmp) cc_final: 0.8435 (mmm) REVERT: A 959 PHE cc_start: 0.8193 (m-80) cc_final: 0.7813 (m-80) REVERT: A 990 PHE cc_start: 0.7011 (m-80) cc_final: 0.6418 (m-80) REVERT: B 957 MET cc_start: 0.8712 (mmp) cc_final: 0.8345 (mmm) REVERT: B 990 PHE cc_start: 0.6979 (m-80) cc_final: 0.6390 (m-80) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.1518 time to fit residues: 18.2117 Evaluate side-chains 75 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1053 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 0.0870 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 53 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.121536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.104490 restraints weight = 34519.434| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 5.94 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8044 Z= 0.124 Angle : 0.516 8.748 10874 Z= 0.258 Chirality : 0.040 0.144 1160 Planarity : 0.003 0.033 1388 Dihedral : 3.792 20.922 1072 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.42 % Allowed : 10.31 % Favored : 88.27 % 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: 0.39 (0.28), residues: 950 helix: 1.57 (0.27), residues: 390 sheet: 0.37 (0.60), residues: 78 loop : -0.87 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS B1099 PHE 0.015 0.001 PHE A 913 TYR 0.021 0.001 TYR B 769 ARG 0.003 0.000 ARG B1040 *********************** 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 90 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.941 Fit side-chains REVERT: A 869 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6251 (mp) REVERT: A 957 MET cc_start: 0.8661 (mmp) cc_final: 0.8190 (mmp) REVERT: A 959 PHE cc_start: 0.8192 (m-80) cc_final: 0.7751 (m-80) REVERT: A 990 PHE cc_start: 0.7098 (m-80) cc_final: 0.6478 (m-80) REVERT: B 957 MET cc_start: 0.8697 (mmp) cc_final: 0.8317 (mmm) REVERT: B 990 PHE cc_start: 0.7071 (m-80) cc_final: 0.6365 (m-80) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.1447 time to fit residues: 19.0304 Evaluate side-chains 76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1053 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.119241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.102461 restraints weight = 35163.784| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 5.85 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8044 Z= 0.158 Angle : 0.548 8.352 10874 Z= 0.274 Chirality : 0.042 0.163 1160 Planarity : 0.003 0.034 1388 Dihedral : 3.970 21.434 1072 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.78 % Allowed : 11.73 % Favored : 86.49 % 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: 0.33 (0.27), residues: 950 helix: 1.56 (0.27), residues: 388 sheet: 0.16 (0.59), residues: 78 loop : -0.91 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 861 HIS 0.004 0.001 HIS B 748 PHE 0.021 0.001 PHE A 906 TYR 0.014 0.001 TYR A1029 ARG 0.002 0.000 ARG B1131 *********************** 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 87 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.853 Fit side-chains REVERT: A 957 MET cc_start: 0.8758 (mmp) cc_final: 0.8470 (mmm) REVERT: A 959 PHE cc_start: 0.8290 (m-80) cc_final: 0.8018 (m-80) REVERT: A 990 PHE cc_start: 0.7084 (m-80) cc_final: 0.6586 (m-80) REVERT: B 749 MET cc_start: 0.6153 (mpp) cc_final: 0.5951 (mpp) REVERT: B 957 MET cc_start: 0.8783 (mmp) cc_final: 0.8350 (mmm) REVERT: B 959 PHE cc_start: 0.8289 (m-80) cc_final: 0.8034 (m-80) REVERT: B 990 PHE cc_start: 0.7018 (m-80) cc_final: 0.6421 (m-80) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.1383 time to fit residues: 17.4800 Evaluate side-chains 77 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.118914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.102508 restraints weight = 35360.452| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 5.75 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8044 Z= 0.148 Angle : 0.539 8.648 10874 Z= 0.267 Chirality : 0.041 0.151 1160 Planarity : 0.003 0.036 1388 Dihedral : 3.948 21.853 1072 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.18 % Allowed : 13.39 % Favored : 85.43 % 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: 0.35 (0.27), residues: 950 helix: 1.64 (0.27), residues: 388 sheet: 0.14 (0.58), residues: 78 loop : -0.95 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS B1099 PHE 0.017 0.001 PHE A 906 TYR 0.022 0.001 TYR B 769 ARG 0.002 0.000 ARG A 985 *********************** 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 82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.875 Fit side-chains REVERT: A 957 MET cc_start: 0.8730 (mmp) cc_final: 0.8465 (mmm) REVERT: A 959 PHE cc_start: 0.8266 (m-80) cc_final: 0.7989 (m-80) REVERT: A 990 PHE cc_start: 0.7138 (m-80) cc_final: 0.6537 (m-80) REVERT: A 1097 LEU cc_start: 0.2755 (OUTLIER) cc_final: 0.2088 (mt) REVERT: B 749 MET cc_start: 0.6195 (mpp) cc_final: 0.5708 (mpp) REVERT: B 957 MET cc_start: 0.8719 (mmp) cc_final: 0.8238 (mmm) REVERT: B 959 PHE cc_start: 0.8118 (m-80) cc_final: 0.7818 (m-80) REVERT: B 990 PHE cc_start: 0.6982 (m-80) cc_final: 0.6393 (m-80) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.1408 time to fit residues: 17.4515 Evaluate side-chains 74 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.118908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.102534 restraints weight = 35721.049| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 5.82 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8044 Z= 0.155 Angle : 0.553 8.781 10874 Z= 0.274 Chirality : 0.041 0.167 1160 Planarity : 0.003 0.035 1388 Dihedral : 4.034 22.051 1072 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.66 % Allowed : 13.51 % Favored : 84.83 % 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: 0.35 (0.27), residues: 950 helix: 1.63 (0.27), residues: 388 sheet: 0.47 (0.56), residues: 88 loop : -1.03 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 861 HIS 0.004 0.001 HIS A1099 PHE 0.015 0.001 PHE A 906 TYR 0.021 0.001 TYR B1029 ARG 0.002 0.000 ARG B 985 *********************** 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 82 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.873 Fit side-chains REVERT: A 749 MET cc_start: 0.6175 (mpp) cc_final: 0.5861 (mpp) REVERT: A 957 MET cc_start: 0.8787 (mmp) cc_final: 0.8516 (mmm) REVERT: A 959 PHE cc_start: 0.8214 (m-80) cc_final: 0.7895 (m-80) REVERT: A 990 PHE cc_start: 0.7153 (m-80) cc_final: 0.6518 (m-80) REVERT: A 1097 LEU cc_start: 0.2791 (OUTLIER) cc_final: 0.2092 (mt) REVERT: B 749 MET cc_start: 0.6451 (mpp) cc_final: 0.6134 (mpp) REVERT: B 957 MET cc_start: 0.8823 (mmp) cc_final: 0.8312 (mmm) REVERT: B 959 PHE cc_start: 0.8127 (m-80) cc_final: 0.7780 (m-80) REVERT: B 990 PHE cc_start: 0.6914 (m-80) cc_final: 0.6330 (m-80) REVERT: B 1097 LEU cc_start: 0.2776 (OUTLIER) cc_final: 0.2153 (mt) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.1371 time to fit residues: 16.8370 Evaluate side-chains 79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 92 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 89 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN B1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.119318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.103052 restraints weight = 35900.629| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 5.72 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8044 Z= 0.129 Angle : 0.541 8.885 10874 Z= 0.264 Chirality : 0.041 0.150 1160 Planarity : 0.003 0.035 1388 Dihedral : 3.879 21.803 1072 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.30 % Allowed : 14.34 % Favored : 84.36 % 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 (0.27), residues: 950 helix: 1.70 (0.27), residues: 390 sheet: 0.48 (0.55), residues: 88 loop : -0.99 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 861 HIS 0.003 0.001 HIS B1099 PHE 0.014 0.001 PHE A 906 TYR 0.023 0.001 TYR B 769 ARG 0.001 0.000 ARG B1141 *********************** 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 78 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.987 Fit side-chains REVERT: A 957 MET cc_start: 0.8632 (mmp) cc_final: 0.8362 (mmm) REVERT: A 959 PHE cc_start: 0.8161 (m-80) cc_final: 0.7862 (m-80) REVERT: A 990 PHE cc_start: 0.7171 (m-80) cc_final: 0.6542 (m-80) REVERT: A 1097 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2044 (mt) REVERT: B 749 MET cc_start: 0.6445 (mpp) cc_final: 0.6218 (mpp) REVERT: B 957 MET cc_start: 0.8659 (mmp) cc_final: 0.8168 (mmm) REVERT: B 959 PHE cc_start: 0.8111 (m-80) cc_final: 0.7788 (m-80) REVERT: B 990 PHE cc_start: 0.6960 (m-80) cc_final: 0.6375 (m-80) REVERT: B 1097 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2071 (mt) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1437 time to fit residues: 16.8776 Evaluate side-chains 78 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 83 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.118544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.102203 restraints weight = 36300.298| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 5.86 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8044 Z= 0.146 Angle : 0.552 9.724 10874 Z= 0.271 Chirality : 0.041 0.148 1160 Planarity : 0.003 0.035 1388 Dihedral : 3.917 21.637 1072 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.54 % Allowed : 13.98 % Favored : 84.48 % 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: 0.48 (0.27), residues: 950 helix: 1.75 (0.27), residues: 390 sheet: 0.47 (0.56), residues: 88 loop : -0.96 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 861 HIS 0.004 0.001 HIS A1099 PHE 0.014 0.001 PHE A 906 TYR 0.021 0.001 TYR A 888 ARG 0.001 0.000 ARG B 985 *********************** 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 83 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.973 Fit side-chains REVERT: A 957 MET cc_start: 0.8725 (mmp) cc_final: 0.8460 (mmm) REVERT: A 959 PHE cc_start: 0.8194 (m-80) cc_final: 0.7772 (m-80) REVERT: A 990 PHE cc_start: 0.7074 (m-80) cc_final: 0.6501 (m-80) REVERT: A 1097 LEU cc_start: 0.2788 (OUTLIER) cc_final: 0.2495 (pp) REVERT: B 957 MET cc_start: 0.8758 (mmp) cc_final: 0.8255 (mmm) REVERT: B 959 PHE cc_start: 0.8061 (m-80) cc_final: 0.7702 (m-80) REVERT: B 990 PHE cc_start: 0.6932 (m-80) cc_final: 0.6317 (m-80) REVERT: B 1097 LEU cc_start: 0.2785 (OUTLIER) cc_final: 0.2074 (mt) outliers start: 13 outliers final: 11 residues processed: 79 average time/residue: 0.1493 time to fit residues: 18.4402 Evaluate side-chains 80 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 ASN B1014 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.113138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.096772 restraints weight = 32051.592| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 5.24 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.4580 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= 0.331 Angle : 0.751 10.321 10874 Z= 0.372 Chirality : 0.047 0.163 1160 Planarity : 0.005 0.041 1388 Dihedral : 5.142 26.167 1072 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.78 % Allowed : 14.10 % 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: -0.38 (0.27), residues: 950 helix: 0.80 (0.26), residues: 388 sheet: 0.25 (0.55), residues: 88 loop : -1.26 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 861 HIS 0.005 0.001 HIS A1099 PHE 0.017 0.002 PHE A 906 TYR 0.032 0.002 TYR B 769 ARG 0.004 0.001 ARG B 985 ********************** 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 81 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.927 Fit side-chains REVERT: A 749 MET cc_start: 0.6609 (mpp) cc_final: 0.6130 (mpp) REVERT: A 957 MET cc_start: 0.9005 (mmp) cc_final: 0.8654 (mmm) REVERT: A 990 PHE cc_start: 0.7319 (m-80) cc_final: 0.6653 (m-80) REVERT: B 959 PHE cc_start: 0.8147 (m-80) cc_final: 0.7822 (m-80) REVERT: B 990 PHE cc_start: 0.7199 (m-80) cc_final: 0.6518 (m-80) REVERT: B 1097 LEU cc_start: 0.2807 (OUTLIER) cc_final: 0.2597 (pp) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1503 time to fit residues: 18.3358 Evaluate side-chains 71 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 19 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1192 HIS ** 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 = 0.4489 r_free = 0.4489 target = 0.116430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.100499 restraints weight = 36177.147| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 5.61 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4247 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= 0.160 Angle : 0.604 10.076 10874 Z= 0.299 Chirality : 0.042 0.158 1160 Planarity : 0.003 0.038 1388 Dihedral : 4.372 23.517 1072 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.42 % Allowed : 15.17 % Favored : 83.41 % 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: 0.04 (0.27), residues: 950 helix: 1.42 (0.27), residues: 388 sheet: 0.15 (0.54), residues: 88 loop : -1.23 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 861 HIS 0.003 0.001 HIS A1051 PHE 0.014 0.001 PHE A 906 TYR 0.022 0.001 TYR A 888 ARG 0.004 0.000 ARG B 985 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.07 seconds wall clock time: 65 minutes 37.47 seconds (3937.47 seconds total)