Starting phenix.real_space_refine on Wed Feb 12 14:08:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j87_36062/02_2025/8j87_36062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j87_36062/02_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_36062/02_2025/8j87_36062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j87_36062/02_2025/8j87_36062.map" model { file = "/net/cci-nas-00/data/ceres_data/8j87_36062/02_2025/8j87_36062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j87_36062/02_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-5592/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: 5.71, per 1000 atoms: 0.73 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: 1.57 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 2.22 Time building geometry restraints manager: 1.91 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: 3.810 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- 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 : 0.997 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: 0.1709 time to fit residues: 21.5360 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 : 0.837 ------------------------------------------------------------------------------- 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 = 0.105759 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 : 0.883 Fit side-chains revert: symmetry clash REVERT: A 957 MET cc_start: 0.8596 (mmp) cc_final: 0.8253 (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: 0.8498 (mmp) cc_final: 0.8274 (mmm) REVERT: B 959 PHE cc_start: 0.8213 (m-80) cc_final: 0.7737 (m-80) REVERT: B 990 PHE cc_start: 0.7082 (m-80) cc_final: 0.6406 (m-80) outliers start: 8 outliers final: 3 residues processed: 77 average time/residue: 0.1688 time to fit residues: 19.3370 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 : 0.929 ------------------------------------------------------------------------------- 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: 8.9990 chunk 13 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.122222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.105391 restraints weight = 33016.587| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 5.79 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.2286 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= 0.142 Angle : 0.530 8.767 10874 Z= 0.266 Chirality : 0.041 0.144 1160 Planarity : 0.003 0.032 1388 Dihedral : 3.867 20.594 1072 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.18 % Allowed : 9.36 % 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: 0.38 (0.28), residues: 950 helix: 1.44 (0.27), residues: 390 sheet: 0.57 (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 0.009 0.001 PHE A1164 TYR 0.012 0.001 TYR A 888 ARG 0.006 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 85 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.941 Fit side-chains REVERT: A 869 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6470 (mp) REVERT: A 916 TYR cc_start: 0.8018 (m-80) cc_final: 0.7727 (m-80) REVERT: A 957 MET cc_start: 0.8638 (mmp) cc_final: 0.8152 (mmp) REVERT: A 959 PHE cc_start: 0.8188 (m-80) cc_final: 0.7803 (m-80) REVERT: A 990 PHE cc_start: 0.7033 (m-80) cc_final: 0.6443 (m-80) REVERT: B 957 MET cc_start: 0.8691 (mmp) cc_final: 0.8325 (mmm) REVERT: B 990 PHE cc_start: 0.6975 (m-80) cc_final: 0.6386 (m-80) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.1639 time to fit residues: 19.8244 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 : 0.872 ------------------------------------------------------------------------------- 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: 0.0470 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 = 0.4581 r_free = 0.4581 target = 0.121814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.104905 restraints weight = 34711.649| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 5.92 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.2535 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= 0.116 Angle : 0.507 8.603 10874 Z= 0.253 Chirality : 0.040 0.142 1160 Planarity : 0.003 0.033 1388 Dihedral : 3.723 20.693 1072 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.42 % Allowed : 10.07 % Favored : 88.51 % 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: 0.45 (0.28), residues: 950 helix: 1.59 (0.27), residues: 392 sheet: 0.45 (0.61), residues: 78 loop : -0.83 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 861 HIS 0.003 0.001 HIS B1099 PHE 0.017 0.001 PHE A 913 TYR 0.020 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 91 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.083 Fit side-chains REVERT: A 957 MET cc_start: 0.8596 (mmp) cc_final: 0.8125 (mmp) REVERT: A 959 PHE cc_start: 0.8168 (m-80) cc_final: 0.7945 (m-80) REVERT: A 990 PHE cc_start: 0.7097 (m-80) cc_final: 0.6571 (m-80) REVERT: B 957 MET cc_start: 0.8628 (mmp) cc_final: 0.8246 (mmm) REVERT: B 959 PHE cc_start: 0.8219 (m-80) cc_final: 0.7961 (m-80) REVERT: B 990 PHE cc_start: 0.7038 (m-80) cc_final: 0.6341 (m-80) outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 0.1434 time to fit residues: 19.1539 Evaluate side-chains 77 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 1053 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.121830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.105599 restraints weight = 34706.850| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 5.66 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.2816 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= 0.139 Angle : 0.532 8.394 10874 Z= 0.265 Chirality : 0.041 0.146 1160 Planarity : 0.003 0.033 1388 Dihedral : 3.818 20.964 1072 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.54 % Allowed : 11.73 % 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: 0.42 (0.28), residues: 950 helix: 1.64 (0.27), residues: 390 sheet: 0.26 (0.59), residues: 78 loop : -0.88 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 861 HIS 0.004 0.001 HIS B 748 PHE 0.022 0.001 PHE A 906 TYR 0.013 0.001 TYR A1029 ARG 0.001 0.000 ARG B 736 *********************** 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 85 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.938 Fit side-chains REVERT: A 749 MET cc_start: 0.6119 (mpp) cc_final: 0.5882 (mpp) REVERT: A 957 MET cc_start: 0.8652 (mmp) cc_final: 0.8137 (mmp) REVERT: A 959 PHE cc_start: 0.8250 (m-80) cc_final: 0.7822 (m-80) REVERT: A 990 PHE cc_start: 0.7052 (m-80) cc_final: 0.6427 (m-80) REVERT: B 749 MET cc_start: 0.6131 (mpp) cc_final: 0.5892 (mpp) REVERT: B 957 MET cc_start: 0.8655 (mmp) cc_final: 0.8239 (mmm) REVERT: B 990 PHE cc_start: 0.7038 (m-80) cc_final: 0.6446 (m-80) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.1439 time to fit residues: 17.5852 Evaluate side-chains 77 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 1078 HIS 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: 4.9990 chunk 70 optimal weight: 0.0040 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.4549 r_free = 0.4549 target = 0.119553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.103110 restraints weight = 35243.456| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 5.79 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.3134 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= 0.143 Angle : 0.537 8.458 10874 Z= 0.266 Chirality : 0.041 0.161 1160 Planarity : 0.003 0.035 1388 Dihedral : 3.872 21.348 1072 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.18 % Allowed : 13.03 % Favored : 85.78 % 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: 0.42 (0.27), residues: 950 helix: 1.68 (0.27), residues: 390 sheet: 0.24 (0.58), residues: 78 loop : -0.91 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.004 0.001 HIS B1099 PHE 0.018 0.001 PHE B 906 TYR 0.022 0.001 TYR B 769 ARG 0.001 0.000 ARG B 736 *********************** 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 : 0.896 Fit side-chains REVERT: A 749 MET cc_start: 0.6094 (mpp) cc_final: 0.5573 (mpp) REVERT: A 957 MET cc_start: 0.8723 (mmp) cc_final: 0.8455 (mmm) REVERT: A 959 PHE cc_start: 0.8213 (m-80) cc_final: 0.7936 (m-80) REVERT: A 990 PHE cc_start: 0.7179 (m-80) cc_final: 0.6556 (m-80) REVERT: A 1097 LEU cc_start: 0.2846 (OUTLIER) cc_final: 0.2231 (mt) REVERT: B 749 MET cc_start: 0.6158 (mpp) cc_final: 0.5667 (mpp) REVERT: B 957 MET cc_start: 0.8750 (mmp) cc_final: 0.8312 (mmm) REVERT: B 959 PHE cc_start: 0.8261 (m-80) cc_final: 0.7987 (m-80) REVERT: B 990 PHE cc_start: 0.6944 (m-80) cc_final: 0.6368 (m-80) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1424 time to fit residues: 17.1355 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 : 0.948 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.116712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.100211 restraints weight = 35677.544| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 5.70 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8044 Z= 0.197 Angle : 0.589 8.940 10874 Z= 0.294 Chirality : 0.042 0.152 1160 Planarity : 0.004 0.036 1388 Dihedral : 4.264 22.607 1072 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.01 % Allowed : 12.68 % Favored : 85.31 % 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: 0.26 (0.27), residues: 950 helix: 1.51 (0.27), residues: 388 sheet: 0.41 (0.56), residues: 88 loop : -1.03 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 861 HIS 0.005 0.001 HIS B1099 PHE 0.016 0.001 PHE A 906 TYR 0.023 0.002 TYR B1029 ARG 0.003 0.000 ARG A1131 *********************** 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 84 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.902 Fit side-chains REVERT: A 749 MET cc_start: 0.6675 (mpp) cc_final: 0.6355 (mpp) REVERT: A 957 MET cc_start: 0.8837 (mmp) cc_final: 0.8536 (mmm) REVERT: A 959 PHE cc_start: 0.8226 (m-80) cc_final: 0.7934 (m-80) REVERT: A 990 PHE cc_start: 0.7088 (m-80) cc_final: 0.6486 (m-80) REVERT: A 1097 LEU cc_start: 0.2797 (OUTLIER) cc_final: 0.2063 (mt) REVERT: B 749 MET cc_start: 0.6639 (mpp) cc_final: 0.6329 (mpp) REVERT: B 957 MET cc_start: 0.8821 (mmp) cc_final: 0.8297 (mmm) REVERT: B 959 PHE cc_start: 0.8119 (m-80) cc_final: 0.7789 (m-80) REVERT: B 990 PHE cc_start: 0.7076 (m-80) cc_final: 0.6449 (m-80) REVERT: B 1097 LEU cc_start: 0.2766 (OUTLIER) cc_final: 0.2117 (mt) outliers start: 17 outliers final: 11 residues processed: 79 average time/residue: 0.1386 time to fit residues: 17.1765 Evaluate side-chains 73 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 30 optimal weight: 0.0670 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.117820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.101703 restraints weight = 35192.638| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 5.64 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8044 Z= 0.143 Angle : 0.548 9.145 10874 Z= 0.272 Chirality : 0.041 0.153 1160 Planarity : 0.003 0.038 1388 Dihedral : 4.003 22.445 1072 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.54 % Allowed : 14.34 % 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: 0.36 (0.27), residues: 950 helix: 1.65 (0.27), residues: 388 sheet: 0.37 (0.55), residues: 88 loop : -1.02 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 861 HIS 0.003 0.001 HIS B1099 PHE 0.014 0.001 PHE A 906 TYR 0.024 0.001 TYR B 769 ARG 0.001 0.000 ARG B 985 *********************** 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 79 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.947 Fit side-chains REVERT: A 749 MET cc_start: 0.6592 (mpp) cc_final: 0.6314 (mpp) REVERT: A 957 MET cc_start: 0.8719 (mmp) cc_final: 0.8447 (mmm) REVERT: A 959 PHE cc_start: 0.8171 (m-80) cc_final: 0.7850 (m-80) REVERT: A 990 PHE cc_start: 0.7015 (m-80) cc_final: 0.6423 (m-80) REVERT: A 1097 LEU cc_start: 0.2718 (OUTLIER) cc_final: 0.2441 (pp) REVERT: B 749 MET cc_start: 0.6456 (mpp) cc_final: 0.6219 (mpp) REVERT: B 957 MET cc_start: 0.8744 (mmp) cc_final: 0.8220 (mmm) REVERT: B 959 PHE cc_start: 0.8027 (m-80) cc_final: 0.7693 (m-80) REVERT: B 990 PHE cc_start: 0.7031 (m-80) cc_final: 0.6411 (m-80) REVERT: B 1097 LEU cc_start: 0.2743 (OUTLIER) cc_final: 0.2109 (mt) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.1432 time to fit residues: 17.0367 Evaluate side-chains 75 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.118796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.103027 restraints weight = 37260.328| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 5.61 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8044 Z= 0.150 Angle : 0.560 9.858 10874 Z= 0.276 Chirality : 0.041 0.151 1160 Planarity : 0.003 0.038 1388 Dihedral : 3.980 22.009 1072 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.42 % Allowed : 14.81 % Favored : 83.77 % 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: 1.68 (0.27), residues: 388 sheet: 0.41 (0.55), residues: 88 loop : -1.00 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 861 HIS 0.004 0.001 HIS A1099 PHE 0.014 0.001 PHE A 906 TYR 0.020 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 78 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.959 Fit side-chains REVERT: A 957 MET cc_start: 0.8670 (mmp) cc_final: 0.8402 (mmm) REVERT: A 959 PHE cc_start: 0.8118 (m-80) cc_final: 0.7810 (m-80) REVERT: A 990 PHE cc_start: 0.7094 (m-80) cc_final: 0.6512 (m-80) REVERT: A 1097 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.2191 (mt) REVERT: B 957 MET cc_start: 0.8644 (mmp) cc_final: 0.8158 (mmm) REVERT: B 959 PHE cc_start: 0.7978 (m-80) cc_final: 0.7624 (m-80) REVERT: B 990 PHE cc_start: 0.7075 (m-80) cc_final: 0.6434 (m-80) REVERT: B 1097 LEU cc_start: 0.2841 (OUTLIER) cc_final: 0.2085 (mt) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.1386 time to fit residues: 16.3969 Evaluate side-chains 76 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 52 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1014 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.115380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.099101 restraints weight = 31671.666| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 5.04 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8044 Z= 0.240 Angle : 0.639 10.215 10874 Z= 0.317 Chirality : 0.044 0.157 1160 Planarity : 0.004 0.041 1388 Dihedral : 4.569 23.274 1072 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.42 % Allowed : 15.05 % Favored : 83.53 % 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: 0.07 (0.27), residues: 950 helix: 1.34 (0.27), residues: 388 sheet: 0.30 (0.55), residues: 88 loop : -1.14 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 861 HIS 0.004 0.001 HIS B1099 PHE 0.016 0.001 PHE A 906 TYR 0.028 0.002 TYR B 769 ARG 0.003 0.001 ARG B 873 ********************** 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 78 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.869 Fit side-chains REVERT: A 957 MET cc_start: 0.8879 (mmp) cc_final: 0.8568 (mmm) REVERT: A 959 PHE cc_start: 0.8218 (m-80) cc_final: 0.7894 (m-80) REVERT: A 990 PHE cc_start: 0.7064 (m-80) cc_final: 0.6542 (m-80) REVERT: B 957 MET cc_start: 0.8878 (mmp) cc_final: 0.8288 (mmm) REVERT: B 959 PHE cc_start: 0.8046 (m-80) cc_final: 0.7830 (m-80) REVERT: B 990 PHE cc_start: 0.7191 (m-80) cc_final: 0.6497 (m-80) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.1385 time to fit residues: 16.2242 Evaluate side-chains 72 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1053 VAL Chi-restraints excluded: chain B residue 1078 HIS 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: 0.9980 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 60 optimal weight: 0.0010 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.3002 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.117653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.101761 restraints weight = 36253.937| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 5.66 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8044 Z= 0.142 Angle : 0.578 10.562 10874 Z= 0.285 Chirality : 0.042 0.166 1160 Planarity : 0.003 0.038 1388 Dihedral : 4.135 23.520 1072 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.07 % Allowed : 15.76 % Favored : 83.18 % 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: 0.31 (0.27), residues: 950 helix: 1.66 (0.27), residues: 388 sheet: 0.33 (0.55), residues: 88 loop : -1.09 (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 B1099 PHE 0.013 0.001 PHE A 906 TYR 0.022 0.001 TYR A 888 ARG 0.003 0.000 ARG B 985 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3618.54 seconds wall clock time: 65 minutes 12.70 seconds (3912.70 seconds total)