Starting phenix.real_space_refine on Mon Mar 11 09:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j88_36063/03_2024/8j88_36063.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j88_36063/03_2024/8j88_36063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j88_36063/03_2024/8j88_36063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j88_36063/03_2024/8j88_36063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j88_36063/03_2024/8j88_36063.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j88_36063/03_2024/8j88_36063.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 5058 2.51 5 N 1346 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A ASP 818": "OD1" <-> "OD2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B ASP 818": "OD1" <-> "OD2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.39, per 1000 atoms: 0.56 Number of scatterers: 7846 At special positions: 0 Unit cell: (148.57, 77.19, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1420 8.00 N 1346 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 47.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.720A pdb=" N LYS A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 725 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 806 through 814 removed outlier: 3.668A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.594A pdb=" N LEU A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 891 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.695A pdb=" N TYR A 946 " --> pdb=" O PRO A 942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 removed outlier: 3.572A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 981 No H-bonds generated for 'chain 'A' and resid 979 through 981' Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.381A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1028 through 1070 Proline residue: A1037 - end of helix removed outlier: 3.771A pdb=" N GLN A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1056 " --> pdb=" O ALA A1052 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 3.604A pdb=" N LEU A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.502A pdb=" N ASN A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A1115 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.805A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1158 removed outlier: 3.674A pdb=" N ILE A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1187 removed outlier: 3.518A pdb=" N LEU A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 729 removed outlier: 3.673A pdb=" N GLY B 724 " --> pdb=" O LYS B 720 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 725 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 754 through 766 Processing helix chain 'B' and resid 806 through 814 removed outlier: 3.669A pdb=" N THR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.594A pdb=" N LEU B 886 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 891 " --> pdb=" O HIS B 887 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 892 " --> pdb=" O TYR B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.695A pdb=" N TYR B 946 " --> pdb=" O PRO B 942 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 947 " --> pdb=" O THR B 943 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 948 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 951 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 960 removed outlier: 3.572A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 981 No H-bonds generated for 'chain 'B' and resid 979 through 981' Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.381A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 Processing helix chain 'B' and resid 1028 through 1070 Proline residue: B1037 - end of helix removed outlier: 3.771A pdb=" N GLN B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B1056 " --> pdb=" O ALA B1052 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B1069 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1089 removed outlier: 3.603A pdb=" N LEU B1089 " --> pdb=" O ALA B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1119 removed outlier: 3.502A pdb=" N ASN B1114 " --> pdb=" O ILE B1110 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B1115 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.805A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1158 removed outlier: 3.673A pdb=" N ILE B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B1146 " --> pdb=" O VAL B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.519A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.951A pdb=" N GLN A 804 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.689A pdb=" N PHE A 913 " --> pdb=" O TYR A 916 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 919 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A1007 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 926 removed outlier: 6.120A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 926 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 931 " --> pdb=" O SER A 926 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 934 " --> pdb=" O ILE A 974 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 974 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1015 through 1016 Processing sheet with id=AA6, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.951A pdb=" N GLN B 804 " --> pdb=" O ILE B 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.689A pdb=" N PHE B 913 " --> pdb=" O TYR B 916 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 919 " --> pdb=" O ASN B1007 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B1007 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 922 through 926 removed outlier: 6.121A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 926 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 931 " --> pdb=" O SER B 926 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 934 " --> pdb=" O ILE B 974 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 974 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1015 through 1016 288 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2524 1.35 - 1.46: 1928 1.46 - 1.58: 3554 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8044 Sorted by residual: bond pdb=" C SER B1162 " pdb=" N PRO B1163 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.69e+00 bond pdb=" C SER A1162 " pdb=" N PRO A1163 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.59e+00 bond pdb=" C ARG A 900 " pdb=" N PRO A 901 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.25e-02 6.40e+03 9.81e-01 bond pdb=" C ARG B 900 " pdb=" N PRO B 901 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.25e-02 6.40e+03 9.29e-01 bond pdb=" C LEU A 937 " pdb=" N PRO A 938 " ideal model delta sigma weight residual 1.331 1.343 -0.011 1.21e-02 6.83e+03 8.76e-01 ... (remaining 8039 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.86: 236 106.86 - 113.64: 4296 113.64 - 120.42: 3107 120.42 - 127.20: 3143 127.20 - 133.98: 92 Bond angle restraints: 10874 Sorted by residual: angle pdb=" CB MET B 957 " pdb=" CG MET B 957 " pdb=" SD MET B 957 " ideal model delta sigma weight residual 112.70 121.96 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" CB MET A 957 " pdb=" CG MET A 957 " pdb=" SD MET A 957 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.48e+00 angle pdb=" CA LEU B1159 " pdb=" CB LEU B1159 " pdb=" CG LEU B1159 " ideal model delta sigma weight residual 116.30 125.37 -9.07 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU A1159 " pdb=" CB LEU A1159 " pdb=" CG LEU A1159 " ideal model delta sigma weight residual 116.30 125.34 -9.04 3.50e+00 8.16e-02 6.68e+00 angle pdb=" CA LEU B1126 " pdb=" CB LEU B1126 " pdb=" CG LEU B1126 " ideal model delta sigma weight residual 116.30 125.00 -8.70 3.50e+00 8.16e-02 6.18e+00 ... (remaining 10869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 4413 15.66 - 31.31: 353 31.31 - 46.97: 74 46.97 - 62.62: 4 62.62 - 78.28: 6 Dihedral angle restraints: 4850 sinusoidal: 2026 harmonic: 2824 Sorted by residual: dihedral pdb=" CA THR A1123 " pdb=" C THR A1123 " pdb=" N TYR A1124 " pdb=" CA TYR A1124 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR B1123 " pdb=" C THR B1123 " pdb=" N TYR B1124 " pdb=" CA TYR B1124 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO B 938 " pdb=" C PRO B 938 " pdb=" N LEU B 939 " pdb=" CA LEU B 939 " ideal model delta harmonic sigma weight residual -180.00 -164.90 -15.10 0 5.00e+00 4.00e-02 9.12e+00 ... (remaining 4847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 676 0.028 - 0.056: 314 0.056 - 0.084: 103 0.084 - 0.112: 50 0.112 - 0.141: 17 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CB VAL A 838 " pdb=" CA VAL A 838 " pdb=" CG1 VAL A 838 " pdb=" CG2 VAL A 838 " both_signs ideal model delta sigma weight residual False -2.63 -2.77 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CB VAL B 838 " pdb=" CA VAL B 838 " pdb=" CG1 VAL B 838 " pdb=" CG2 VAL B 838 " both_signs ideal model delta sigma weight residual False -2.63 -2.77 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA SER B1162 " pdb=" N SER B1162 " pdb=" C SER B1162 " pdb=" CB SER B1162 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1157 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 938 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 938 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 900 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 901 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 901 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 901 " -0.022 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 662 2.74 - 3.28: 7950 3.28 - 3.82: 12752 3.82 - 4.36: 14599 4.36 - 4.90: 24565 Nonbonded interactions: 60528 Sorted by model distance: nonbonded pdb=" OG SER B1071 " pdb=" OE1 GLU B1073 " model vdw 2.205 2.440 nonbonded pdb=" OG SER A1071 " pdb=" OE1 GLU A1073 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.272 2.440 nonbonded pdb=" O THR A1100 " pdb=" OG SER A1104 " model vdw 2.285 2.440 ... (remaining 60523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 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: 14.190 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.800 Find NCS groups from input model: 0.400 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8044 Z= 0.129 Angle : 0.562 9.258 10874 Z= 0.290 Chirality : 0.040 0.141 1160 Planarity : 0.004 0.047 1388 Dihedral : 11.869 78.275 3038 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 950 helix: -0.25 (0.27), residues: 374 sheet: -0.36 (0.53), residues: 124 loop : -0.94 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1189 HIS 0.002 0.001 HIS A1078 PHE 0.017 0.001 PHE B 913 TYR 0.019 0.001 TYR B1079 ARG 0.004 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.951 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1964 time to fit residues: 19.9634 Evaluate side-chains 51 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1014 ASN B1012 HIS B1014 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.2185 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= 0.219 Angle : 0.598 8.254 10874 Z= 0.306 Chirality : 0.042 0.150 1160 Planarity : 0.004 0.043 1388 Dihedral : 4.150 19.711 1072 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.59 % Allowed : 6.75 % Favored : 92.65 % 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: -0.47 (0.28), residues: 950 helix: 0.65 (0.27), residues: 390 sheet: -0.33 (0.53), residues: 122 loop : -1.16 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 856 HIS 0.007 0.001 HIS A1051 PHE 0.015 0.001 PHE B 913 TYR 0.018 0.002 TYR B1043 ARG 0.008 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.841 Fit side-chains REVERT: B 894 ILE cc_start: 0.8898 (pt) cc_final: 0.8331 (mm) REVERT: B 903 ASN cc_start: 0.8176 (m-40) cc_final: 0.7733 (t0) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.1743 time to fit residues: 15.8158 Evaluate side-chains 54 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain B residue 750 PHE Chi-restraints excluded: chain B residue 756 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN A1012 HIS A1014 ASN B 753 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.2714 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= 0.153 Angle : 0.520 8.523 10874 Z= 0.262 Chirality : 0.041 0.128 1160 Planarity : 0.004 0.040 1388 Dihedral : 3.977 21.129 1072 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.71 % Allowed : 10.07 % 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: -0.26 (0.28), residues: 950 helix: 1.12 (0.28), residues: 392 sheet: -0.47 (0.51), residues: 122 loop : -1.28 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 856 HIS 0.005 0.001 HIS A1051 PHE 0.018 0.001 PHE B 913 TYR 0.021 0.001 TYR A 888 ARG 0.008 0.000 ARG B1039 *********************** 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 58 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: B 903 ASN cc_start: 0.8257 (m-40) cc_final: 0.7799 (t0) REVERT: B 957 MET cc_start: 0.6538 (tpt) cc_final: 0.5992 (mmm) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.1498 time to fit residues: 13.0213 Evaluate side-chains 48 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 958 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8044 Z= 0.155 Angle : 0.514 7.773 10874 Z= 0.260 Chirality : 0.041 0.150 1160 Planarity : 0.004 0.042 1388 Dihedral : 3.983 22.638 1072 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.42 % Allowed : 11.02 % Favored : 87.56 % 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: -0.17 (0.28), residues: 950 helix: 1.17 (0.28), residues: 398 sheet: -0.65 (0.48), residues: 132 loop : -1.16 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 856 HIS 0.005 0.001 HIS A1051 PHE 0.026 0.001 PHE A1164 TYR 0.010 0.001 TYR B 769 ARG 0.002 0.000 ARG B1087 *********************** 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 69 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 1076 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6813 (pp) REVERT: B 903 ASN cc_start: 0.8237 (m-40) cc_final: 0.7732 (t0) REVERT: B 1029 TYR cc_start: 0.6623 (m-80) cc_final: 0.6222 (m-80) REVERT: B 1076 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6784 (pp) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 0.1569 time to fit residues: 16.1732 Evaluate side-chains 55 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.4067 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= 0.177 Angle : 0.546 10.490 10874 Z= 0.276 Chirality : 0.042 0.153 1160 Planarity : 0.004 0.042 1388 Dihedral : 4.115 24.452 1072 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.78 % Allowed : 11.37 % Favored : 86.85 % 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: -0.29 (0.28), residues: 950 helix: 1.06 (0.28), residues: 386 sheet: -0.37 (0.48), residues: 136 loop : -1.29 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.005 0.001 HIS A1051 PHE 0.021 0.001 PHE B 913 TYR 0.016 0.002 TYR A 888 ARG 0.002 0.000 ARG B 912 *********************** 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 70 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 1076 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6865 (pp) REVERT: B 894 ILE cc_start: 0.8996 (pt) cc_final: 0.8489 (mm) REVERT: B 903 ASN cc_start: 0.8343 (m-40) cc_final: 0.7980 (t0) REVERT: B 1076 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6837 (pp) outliers start: 15 outliers final: 7 residues processed: 67 average time/residue: 0.1561 time to fit residues: 16.2445 Evaluate side-chains 59 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8044 Z= 0.135 Angle : 0.515 8.419 10874 Z= 0.257 Chirality : 0.041 0.157 1160 Planarity : 0.004 0.042 1388 Dihedral : 3.911 21.904 1072 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.07 % Allowed : 12.80 % Favored : 86.14 % 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: -0.16 (0.28), residues: 950 helix: 1.25 (0.29), residues: 384 sheet: -0.35 (0.48), residues: 136 loop : -1.28 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1189 HIS 0.005 0.001 HIS B1051 PHE 0.022 0.001 PHE A 913 TYR 0.017 0.001 TYR A 888 ARG 0.002 0.000 ARG B 912 *********************** 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 63 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 775 LEU cc_start: 0.6367 (mp) cc_final: 0.5791 (tp) REVERT: A 978 LEU cc_start: 0.7407 (tp) cc_final: 0.7191 (tp) REVERT: A 1076 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6848 (pp) REVERT: B 894 ILE cc_start: 0.8986 (pt) cc_final: 0.8468 (mm) REVERT: B 903 ASN cc_start: 0.8342 (m-40) cc_final: 0.7953 (t0) REVERT: B 1076 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6868 (pp) outliers start: 9 outliers final: 3 residues processed: 62 average time/residue: 0.1565 time to fit residues: 15.4236 Evaluate side-chains 57 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.4464 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= 0.137 Angle : 0.513 8.022 10874 Z= 0.255 Chirality : 0.041 0.162 1160 Planarity : 0.004 0.044 1388 Dihedral : 3.858 22.539 1072 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.83 % Allowed : 13.86 % 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: -0.02 (0.29), residues: 950 helix: 1.36 (0.29), residues: 384 sheet: -0.08 (0.53), residues: 116 loop : -1.24 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.005 0.001 HIS B1051 PHE 0.023 0.001 PHE B 913 TYR 0.017 0.001 TYR A 888 ARG 0.002 0.000 ARG B 912 *********************** 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 61 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 978 LEU cc_start: 0.7449 (tp) cc_final: 0.7228 (tp) REVERT: A 1076 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6900 (pp) REVERT: B 775 LEU cc_start: 0.5956 (mp) cc_final: 0.5725 (tp) REVERT: B 894 ILE cc_start: 0.9021 (pt) cc_final: 0.8522 (mm) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1530 time to fit residues: 14.3153 Evaluate side-chains 59 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 838 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8044 Z= 0.138 Angle : 0.530 13.322 10874 Z= 0.259 Chirality : 0.041 0.142 1160 Planarity : 0.004 0.044 1388 Dihedral : 3.809 21.320 1072 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.95 % Allowed : 13.98 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.29), residues: 950 helix: 1.43 (0.29), residues: 384 sheet: -0.06 (0.53), residues: 116 loop : -1.21 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1189 HIS 0.004 0.001 HIS A1051 PHE 0.024 0.001 PHE B 913 TYR 0.017 0.001 TYR A 888 ARG 0.002 0.000 ARG A1039 *********************** 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 62 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 775 LEU cc_start: 0.6069 (mp) cc_final: 0.5697 (tp) REVERT: A 978 LEU cc_start: 0.7495 (tp) cc_final: 0.7244 (tp) REVERT: A 1076 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6907 (pp) REVERT: B 775 LEU cc_start: 0.6142 (mp) cc_final: 0.5663 (tp) REVERT: B 894 ILE cc_start: 0.9049 (pt) cc_final: 0.8555 (mm) REVERT: B 1076 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6862 (pp) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.1554 time to fit residues: 14.8156 Evaluate side-chains 59 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.0010 chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8044 Z= 0.125 Angle : 0.519 12.444 10874 Z= 0.251 Chirality : 0.041 0.134 1160 Planarity : 0.004 0.044 1388 Dihedral : 3.692 19.808 1072 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.83 % Allowed : 13.74 % 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: 0.17 (0.29), residues: 950 helix: 1.51 (0.29), residues: 384 sheet: 0.04 (0.53), residues: 116 loop : -1.13 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1170 HIS 0.004 0.001 HIS B1051 PHE 0.017 0.001 PHE A 913 TYR 0.017 0.001 TYR A 888 ARG 0.002 0.000 ARG A1039 *********************** 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 59 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 775 LEU cc_start: 0.6049 (mp) cc_final: 0.5652 (tp) REVERT: A 978 LEU cc_start: 0.7521 (tp) cc_final: 0.7261 (tp) REVERT: A 1076 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6914 (pp) REVERT: B 775 LEU cc_start: 0.5873 (mp) cc_final: 0.5610 (tp) REVERT: B 894 ILE cc_start: 0.9002 (pt) cc_final: 0.8574 (mm) REVERT: B 1076 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6842 (pp) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 0.1609 time to fit residues: 14.2969 Evaluate side-chains 58 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 86 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8044 Z= 0.140 Angle : 0.529 11.869 10874 Z= 0.259 Chirality : 0.041 0.144 1160 Planarity : 0.004 0.045 1388 Dihedral : 3.785 19.456 1072 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.83 % Allowed : 13.86 % 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: 0.15 (0.29), residues: 950 helix: 1.50 (0.29), residues: 384 sheet: 0.04 (0.53), residues: 116 loop : -1.14 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1189 HIS 0.004 0.001 HIS B1051 PHE 0.011 0.001 PHE B 750 TYR 0.018 0.001 TYR A 888 ARG 0.002 0.000 ARG A1039 ********************** 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 62 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 775 LEU cc_start: 0.6208 (mp) cc_final: 0.5690 (tp) REVERT: A 978 LEU cc_start: 0.7498 (tp) cc_final: 0.7232 (tp) REVERT: A 1076 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.7011 (pp) REVERT: B 775 LEU cc_start: 0.6124 (mp) cc_final: 0.5599 (tp) REVERT: B 962 GLU cc_start: 0.7580 (tp30) cc_final: 0.7049 (tp30) REVERT: B 1076 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6866 (pp) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.1494 time to fit residues: 13.9007 Evaluate side-chains 59 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain B residue 1076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 overall best weight: 0.3032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1014 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.122487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.106110 restraints weight = 40278.947| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 6.88 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.5159 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= 0.119 Angle : 0.514 11.244 10874 Z= 0.250 Chirality : 0.041 0.131 1160 Planarity : 0.004 0.043 1388 Dihedral : 3.637 18.465 1072 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.59 % Allowed : 14.34 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 950 helix: 1.54 (0.29), residues: 384 sheet: 0.41 (0.56), residues: 106 loop : -1.08 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1170 HIS 0.004 0.001 HIS B1051 PHE 0.018 0.001 PHE A 913 TYR 0.035 0.001 TYR B 769 ARG 0.002 0.000 ARG A1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.16 seconds wall clock time: 35 minutes 11.25 seconds (2111.25 seconds total)