Starting phenix.real_space_refine on Wed Feb 12 20:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gv8_34287/02_2025/8gv8_34287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gv8_34287/02_2025/8gv8_34287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gv8_34287/02_2025/8gv8_34287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gv8_34287/02_2025/8gv8_34287.map" model { file = "/net/cci-nas-00/data/ceres_data/8gv8_34287/02_2025/8gv8_34287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gv8_34287/02_2025/8gv8_34287.cif" } resolution = 3.08 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= 0.002 sd= 0.179 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 54 5.16 5 C 5422 2.51 5 N 1334 2.21 5 O 1351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8161 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4057 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4048 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 28, 'TRANS': 484} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'4KU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'4KU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.67 Number of scatterers: 8161 At special positions: 0 Unit cell: (86.9, 133.1, 79.2, 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 54 16.00 O 1351 8.00 N 1334 7.00 C 5422 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 999.4 milliseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 67.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 696 through 703 removed outlier: 3.892A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.983A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.678A pdb=" N VAL A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 removed outlier: 4.050A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 847 removed outlier: 4.190A pdb=" N GLU A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 923 removed outlier: 3.518A pdb=" N LEU A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 938 Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.550A pdb=" N ILE A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.816A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1020 removed outlier: 3.642A pdb=" N ALA A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1047 removed outlier: 3.502A pdb=" N GLY A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A1044 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A1047 " --> pdb=" O GLY A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.061A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A1120 " --> pdb=" O ALA A1116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A1121 " --> pdb=" O VAL A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1144 removed outlier: 3.719A pdb=" N GLU A1137 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1142 " --> pdb=" O ARG A1138 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A1144 " --> pdb=" O HIS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.926A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.652A pdb=" N LYS A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.537A pdb=" N HIS A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 4.289A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A1207 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 696 through 703 removed outlier: 3.884A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.983A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 removed outlier: 3.849A pdb=" N LEU B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 749 " --> pdb=" O MET B 745 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.677A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 796 " --> pdb=" O GLY B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 819 removed outlier: 3.739A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 834 removed outlier: 3.578A pdb=" N ILE B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 923 removed outlier: 3.518A pdb=" N LEU B 903 " --> pdb=" O ASN B 899 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 916 " --> pdb=" O PHE B 912 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 917 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 920 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.550A pdb=" N ILE B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 997 removed outlier: 3.821A pdb=" N MET B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 removed outlier: 3.637A pdb=" N ALA B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1047 removed outlier: 3.679A pdb=" N ILE B1039 " --> pdb=" O ASP B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1067 Processing helix chain 'B' and resid 1091 through 1102 Processing helix chain 'B' and resid 1103 through 1105 No H-bonds generated for 'chain 'B' and resid 1103 through 1105' Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.633A pdb=" N ILE B1113 " --> pdb=" O LEU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 4.023A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B1120 " --> pdb=" O ALA B1116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1144 removed outlier: 3.719A pdb=" N GLU B1137 " --> pdb=" O ILE B1133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B1142 " --> pdb=" O ARG B1138 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B1143 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B1144 " --> pdb=" O HIS B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.935A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.542A pdb=" N LYS B1156 " --> pdb=" O VAL B1152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B1157 " --> pdb=" O THR B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1152 through 1157' Processing helix chain 'B' and resid 1159 through 1183 removed outlier: 3.549A pdb=" N HIS B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B1166 " --> pdb=" O ARG B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1195 Processing helix chain 'B' and resid 1195 through 1208 removed outlier: 4.287A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B1206 " --> pdb=" O VAL B1202 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B1207 " --> pdb=" O VAL B1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1217 Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA2, first strand: chain 'A' and resid 1070 through 1071 removed outlier: 6.827A pdb=" N VAL A1070 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AA4, first strand: chain 'B' and resid 1070 through 1071 removed outlier: 6.842A pdb=" N VAL B1070 " --> pdb=" O GLN B1084 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1188 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: 2.26 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.17: 93 1.17 - 1.33: 1783 1.33 - 1.50: 3074 1.50 - 1.67: 3329 1.67 - 1.83: 86 Bond restraints: 8365 Sorted by residual: bond pdb=" C ILE B 836 " pdb=" O ILE B 836 " ideal model delta sigma weight residual 1.241 1.015 0.226 1.03e-02 9.43e+03 4.80e+02 bond pdb=" C LEU B 843 " pdb=" O LEU B 843 " ideal model delta sigma weight residual 1.234 1.000 0.235 1.17e-02 7.31e+03 4.03e+02 bond pdb=" C ILE B 834 " pdb=" O ILE B 834 " ideal model delta sigma weight residual 1.238 1.024 0.214 1.18e-02 7.18e+03 3.30e+02 bond pdb=" C ILE A 836 " pdb=" O ILE A 836 " ideal model delta sigma weight residual 1.241 1.054 0.187 1.03e-02 9.43e+03 3.29e+02 bond pdb=" C TYR B 837 " pdb=" O TYR B 837 " ideal model delta sigma weight residual 1.236 1.035 0.201 1.22e-02 6.72e+03 2.72e+02 ... (remaining 8360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.16: 11227 8.16 - 16.33: 120 16.33 - 24.49: 10 24.49 - 32.65: 2 32.65 - 40.81: 1 Bond angle restraints: 11360 Sorted by residual: angle pdb=" C ASP A1217 " pdb=" CA ASP A1217 " pdb=" CB ASP A1217 " ideal model delta sigma weight residual 111.31 70.50 40.81 1.68e+00 3.54e-01 5.90e+02 angle pdb=" O ILE B 914 " pdb=" C ILE B 914 " pdb=" N ALA B 915 " ideal model delta sigma weight residual 122.57 102.86 19.71 1.25e+00 6.40e-01 2.49e+02 angle pdb=" C PHE B 840 " pdb=" CA PHE B 840 " pdb=" CB PHE B 840 " ideal model delta sigma weight residual 110.42 81.24 29.18 1.99e+00 2.53e-01 2.15e+02 angle pdb=" C GLN A 824 " pdb=" CA GLN A 824 " pdb=" CB GLN A 824 " ideal model delta sigma weight residual 109.75 85.11 24.64 1.72e+00 3.38e-01 2.05e+02 angle pdb=" N LEU A1037 " pdb=" CA LEU A1037 " pdb=" C LEU A1037 " ideal model delta sigma weight residual 114.31 97.28 17.03 1.29e+00 6.01e-01 1.74e+02 ... (remaining 11355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4405 17.71 - 35.42: 403 35.42 - 53.13: 94 53.13 - 70.84: 21 70.84 - 88.55: 8 Dihedral angle restraints: 4931 sinusoidal: 1972 harmonic: 2959 Sorted by residual: dihedral pdb=" C ASP A1217 " pdb=" N ASP A1217 " pdb=" CA ASP A1217 " pdb=" CB ASP A1217 " ideal model delta harmonic sigma weight residual -122.60 -76.87 -45.73 0 2.50e+00 1.60e-01 3.35e+02 dihedral pdb=" C PHE B 840 " pdb=" N PHE B 840 " pdb=" CA PHE B 840 " pdb=" CB PHE B 840 " ideal model delta harmonic sigma weight residual -122.60 -88.67 -33.93 0 2.50e+00 1.60e-01 1.84e+02 dihedral pdb=" C GLN A 824 " pdb=" N GLN A 824 " pdb=" CA GLN A 824 " pdb=" CB GLN A 824 " ideal model delta harmonic sigma weight residual -122.60 -92.85 -29.75 0 2.50e+00 1.60e-01 1.42e+02 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1231 0.145 - 0.290: 68 0.290 - 0.434: 23 0.434 - 0.579: 9 0.579 - 0.724: 4 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 752 " pdb=" CA VAL A 752 " pdb=" CG1 VAL A 752 " pdb=" CG2 VAL A 752 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR A 841 " pdb=" N TYR A 841 " pdb=" C TYR A 841 " pdb=" CB TYR A 841 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA GLU A 838 " pdb=" N GLU A 838 " pdb=" C GLU A 838 " pdb=" CB GLU A 838 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 1332 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 914 " 0.046 2.00e-02 2.50e+03 7.85e-02 6.16e+01 pdb=" C ILE B 914 " -0.136 2.00e-02 2.50e+03 pdb=" O ILE B 914 " 0.043 2.00e-02 2.50e+03 pdb=" N ALA B 915 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 838 " 0.034 2.00e-02 2.50e+03 7.12e-02 5.07e+01 pdb=" C GLU B 838 " -0.123 2.00e-02 2.50e+03 pdb=" O GLU B 838 " 0.046 2.00e-02 2.50e+03 pdb=" N THR B 839 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 825 " 0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C GLU A 825 " -0.111 2.00e-02 2.50e+03 pdb=" O GLU A 825 " 0.040 2.00e-02 2.50e+03 pdb=" N ILE A 826 " 0.039 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.93: 3346 2.93 - 3.59: 11005 3.59 - 4.24: 16892 4.24 - 4.90: 30620 Nonbonded interactions: 61872 Sorted by model distance: nonbonded pdb=" O PHE B 840 " pdb=" CB PHE B 840 " model vdw 1.614 2.752 nonbonded pdb=" O ASP A1217 " pdb=" CB ASP A1217 " model vdw 1.635 2.752 nonbonded pdb=" O GLN A 824 " pdb=" CB GLN A 824 " model vdw 2.077 2.752 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.191 3.040 nonbonded pdb=" O GLN B 824 " pdb=" CB GLN B 824 " model vdw 2.238 2.752 ... (remaining 61867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 673 through 855 or resid 894 through 1223 or resid 1501)) 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: 0.910 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.080 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.019 0.235 8365 Z= 1.180 Angle : 1.928 40.813 11360 Z= 1.269 Chirality : 0.094 0.724 1335 Planarity : 0.010 0.098 1390 Dihedral : 14.992 88.551 3017 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.59 % Favored : 93.72 % Rotamer: Outliers : 3.97 % Allowed : 3.63 % Favored : 92.40 % Cbeta Deviations : 5.33 % 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: -0.32 (0.28), residues: 1019 helix: 0.62 (0.23), residues: 636 sheet: None (None), residues: 0 loop : -1.63 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 795 HIS 0.016 0.001 HIS A 850 PHE 0.040 0.003 PHE B 912 TYR 0.028 0.002 TYR B 837 ARG 0.004 0.000 ARG B1200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8841 (t) REVERT: A 838 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: A 842 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (mttp) REVERT: A 935 ILE cc_start: 0.8158 (mt) cc_final: 0.7885 (mm) REVERT: A 947 MET cc_start: 0.8339 (mmt) cc_final: 0.7884 (mmt) REVERT: A 993 MET cc_start: 0.7368 (tpt) cc_final: 0.6611 (tpt) REVERT: A 1080 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7376 (mptt) REVERT: A 1082 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7357 (ptmm) REVERT: B 817 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (ttp-170) REVERT: B 916 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 925 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7288 (mtm180) REVERT: B 935 ILE cc_start: 0.8159 (mt) cc_final: 0.7884 (mm) REVERT: B 993 MET cc_start: 0.7265 (tpt) cc_final: 0.6521 (tpt) REVERT: B 1075 VAL cc_start: 0.5532 (OUTLIER) cc_final: 0.5223 (t) REVERT: B 1080 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7488 (mppt) REVERT: B 1082 LYS cc_start: 0.7573 (mmtm) cc_final: 0.7236 (ptmm) REVERT: B 1109 LEU cc_start: 0.7477 (mp) cc_final: 0.7065 (tp) REVERT: B 1220 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7101 (pt0) outliers start: 35 outliers final: 16 residues processed: 212 average time/residue: 0.2406 time to fit residues: 65.9760 Evaluate side-chains 154 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 838 GLU Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 842 LYS Chi-restraints excluded: chain B residue 916 PHE Chi-restraints excluded: chain B residue 1075 VAL Chi-restraints excluded: chain B residue 1080 LYS Chi-restraints excluded: chain B residue 1220 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** 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 = 0.3570 r_free = 0.3570 target = 0.144854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108010 restraints weight = 8613.661| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.87 r_work: 0.2984 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8365 Z= 0.174 Angle : 0.605 7.868 11360 Z= 0.310 Chirality : 0.039 0.146 1335 Planarity : 0.006 0.079 1390 Dihedral : 9.501 76.379 1172 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.93 % Allowed : 8.74 % Favored : 89.33 % 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: 0.08 (0.27), residues: 1019 helix: 0.86 (0.22), residues: 659 sheet: None (None), residues: 0 loop : -1.42 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.003 0.000 HIS A 850 PHE 0.010 0.001 PHE A 822 TYR 0.009 0.001 TYR B 841 ARG 0.004 0.000 ARG B 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.896 Fit side-chains REVERT: A 745 MET cc_start: 0.8405 (mtp) cc_final: 0.8097 (mtt) REVERT: A 842 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7726 (mttt) REVERT: A 935 ILE cc_start: 0.7986 (mt) cc_final: 0.7723 (mm) REVERT: A 947 MET cc_start: 0.8688 (mmt) cc_final: 0.8362 (mmt) REVERT: A 993 MET cc_start: 0.7063 (tpt) cc_final: 0.6613 (tpt) REVERT: A 1035 ASP cc_start: 0.8358 (m-30) cc_final: 0.8134 (m-30) REVERT: A 1045 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7894 (tp) REVERT: A 1080 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6813 (mptt) REVERT: B 745 MET cc_start: 0.8038 (mtp) cc_final: 0.7744 (mtt) REVERT: B 925 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7317 (mtm180) REVERT: B 935 ILE cc_start: 0.7992 (mt) cc_final: 0.7744 (mm) REVERT: B 1220 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6736 (pt0) outliers start: 17 outliers final: 6 residues processed: 134 average time/residue: 0.2158 time to fit residues: 39.5945 Evaluate side-chains 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1220 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 0.0040 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.146383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110280 restraints weight = 8610.600| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.77 r_work: 0.3011 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8365 Z= 0.222 Angle : 0.573 8.507 11360 Z= 0.289 Chirality : 0.040 0.159 1335 Planarity : 0.006 0.084 1390 Dihedral : 7.553 72.675 1131 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 2.50 % Allowed : 8.63 % Favored : 88.88 % 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: 0.27 (0.27), residues: 1019 helix: 0.95 (0.22), residues: 659 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 795 HIS 0.003 0.001 HIS B 853 PHE 0.018 0.001 PHE A1135 TYR 0.009 0.001 TYR A 789 ARG 0.005 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.876 Fit side-chains REVERT: A 745 MET cc_start: 0.8502 (mtp) cc_final: 0.8256 (mtt) REVERT: A 842 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8114 (mttt) REVERT: A 916 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7828 (t80) REVERT: A 935 ILE cc_start: 0.8243 (mt) cc_final: 0.8017 (mm) REVERT: A 1045 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7850 (tp) REVERT: A 1080 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6622 (mptt) REVERT: B 745 MET cc_start: 0.8275 (mtp) cc_final: 0.8005 (mtt) REVERT: B 925 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7757 (mtm180) REVERT: B 935 ILE cc_start: 0.8252 (mt) cc_final: 0.8032 (mm) REVERT: B 1210 ASP cc_start: 0.7329 (m-30) cc_final: 0.7081 (t0) REVERT: B 1220 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6737 (pt0) outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 0.2115 time to fit residues: 37.9158 Evaluate side-chains 128 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1144 MET Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1220 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102959 restraints weight = 8645.569| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.84 r_work: 0.2912 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8365 Z= 0.161 Angle : 0.512 8.034 11360 Z= 0.256 Chirality : 0.038 0.133 1335 Planarity : 0.006 0.072 1390 Dihedral : 7.082 68.533 1131 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.55 % Rotamer: Outliers : 1.93 % Allowed : 9.76 % Favored : 88.31 % 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: 0.53 (0.27), residues: 1019 helix: 1.18 (0.22), residues: 653 sheet: None (None), residues: 0 loop : -1.15 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.002 0.000 HIS B1149 PHE 0.010 0.001 PHE A1135 TYR 0.010 0.001 TYR A 789 ARG 0.004 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.892 Fit side-chains REVERT: A 702 ASP cc_start: 0.7329 (t0) cc_final: 0.6992 (t0) REVERT: A 745 MET cc_start: 0.8360 (mtp) cc_final: 0.8071 (mtt) REVERT: A 842 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7705 (mttt) REVERT: A 916 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7499 (t80) REVERT: A 935 ILE cc_start: 0.7908 (mt) cc_final: 0.7679 (mm) REVERT: A 1073 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7568 (ttmm) REVERT: A 1080 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6409 (mmmt) REVERT: B 745 MET cc_start: 0.8034 (mtp) cc_final: 0.7736 (mtt) REVERT: B 925 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7449 (mtm180) REVERT: B 931 ILE cc_start: 0.7984 (mp) cc_final: 0.7755 (mm) REVERT: B 935 ILE cc_start: 0.7903 (mt) cc_final: 0.7670 (mm) REVERT: B 1210 ASP cc_start: 0.7075 (m-30) cc_final: 0.6823 (t0) REVERT: B 1220 GLU cc_start: 0.7065 (tt0) cc_final: 0.6436 (pt0) outliers start: 17 outliers final: 12 residues processed: 131 average time/residue: 0.2061 time to fit residues: 37.1964 Evaluate side-chains 138 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1144 MET Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.138508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100729 restraints weight = 8615.937| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.84 r_work: 0.2881 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8365 Z= 0.189 Angle : 0.527 8.374 11360 Z= 0.262 Chirality : 0.039 0.135 1335 Planarity : 0.006 0.069 1390 Dihedral : 6.557 65.032 1126 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.93 % Allowed : 10.44 % Favored : 87.63 % 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: 0.60 (0.27), residues: 1019 helix: 1.22 (0.22), residues: 652 sheet: None (None), residues: 0 loop : -1.08 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 795 HIS 0.002 0.001 HIS B1149 PHE 0.012 0.001 PHE A1135 TYR 0.010 0.001 TYR A 789 ARG 0.006 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.795 Fit side-chains REVERT: A 745 MET cc_start: 0.8331 (mtp) cc_final: 0.8057 (mtt) REVERT: A 842 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7823 (mttt) REVERT: A 916 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 931 ILE cc_start: 0.8040 (mp) cc_final: 0.7834 (mm) REVERT: A 1011 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6784 (tt0) REVERT: A 1073 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7183 (ttmm) REVERT: B 702 ASP cc_start: 0.7384 (t0) cc_final: 0.7070 (t0) REVERT: B 745 MET cc_start: 0.8049 (mtp) cc_final: 0.7820 (mtt) REVERT: B 925 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7496 (mtm180) REVERT: B 931 ILE cc_start: 0.8050 (mp) cc_final: 0.7843 (mm) REVERT: B 1210 ASP cc_start: 0.7129 (m-30) cc_final: 0.6885 (t0) REVERT: B 1220 GLU cc_start: 0.7159 (tt0) cc_final: 0.6321 (pt0) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.2027 time to fit residues: 38.3428 Evaluate side-chains 129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.138560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100559 restraints weight = 8588.023| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.83 r_work: 0.2885 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8365 Z= 0.180 Angle : 0.511 8.685 11360 Z= 0.256 Chirality : 0.038 0.137 1335 Planarity : 0.006 0.067 1390 Dihedral : 6.194 61.462 1122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 2.16 % Allowed : 10.44 % Favored : 87.40 % 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: 0.74 (0.27), residues: 1019 helix: 1.33 (0.22), residues: 651 sheet: None (None), residues: 0 loop : -1.01 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.002 0.000 HIS A1149 PHE 0.009 0.001 PHE B 822 TYR 0.011 0.001 TYR A 789 ARG 0.005 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.007 Fit side-chains REVERT: A 702 ASP cc_start: 0.7420 (t0) cc_final: 0.7059 (t0) REVERT: A 745 MET cc_start: 0.8345 (mtp) cc_final: 0.8070 (mtt) REVERT: A 842 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7835 (mttt) REVERT: A 916 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 1011 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6799 (tt0) REVERT: B 702 ASP cc_start: 0.7420 (t0) cc_final: 0.7048 (t0) REVERT: B 745 MET cc_start: 0.8049 (mtp) cc_final: 0.7776 (mtt) REVERT: B 925 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7522 (mtm180) REVERT: B 1210 ASP cc_start: 0.7201 (m-30) cc_final: 0.6844 (t0) REVERT: B 1220 GLU cc_start: 0.7192 (tt0) cc_final: 0.6287 (pt0) outliers start: 19 outliers final: 14 residues processed: 133 average time/residue: 0.1939 time to fit residues: 36.0979 Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 842 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.138550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100479 restraints weight = 8694.843| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.85 r_work: 0.2880 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8365 Z= 0.172 Angle : 0.506 8.173 11360 Z= 0.251 Chirality : 0.038 0.141 1335 Planarity : 0.005 0.067 1390 Dihedral : 6.028 57.971 1122 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Rotamer: Outliers : 1.70 % Allowed : 10.67 % Favored : 87.63 % 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: 0.87 (0.27), residues: 1019 helix: 1.42 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -0.93 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 795 HIS 0.002 0.000 HIS B1064 PHE 0.008 0.001 PHE B1135 TYR 0.010 0.001 TYR A 789 ARG 0.008 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.865 Fit side-chains REVERT: A 702 ASP cc_start: 0.7414 (t0) cc_final: 0.7023 (t0) REVERT: A 745 MET cc_start: 0.8316 (mtp) cc_final: 0.8039 (mtt) REVERT: A 916 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (t80) REVERT: A 1011 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6792 (tt0) REVERT: A 1210 ASP cc_start: 0.7200 (m-30) cc_final: 0.6994 (t0) REVERT: B 702 ASP cc_start: 0.7439 (t0) cc_final: 0.7043 (t0) REVERT: B 745 MET cc_start: 0.8044 (mtp) cc_final: 0.7775 (mtt) REVERT: B 925 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7587 (mtm180) REVERT: B 1210 ASP cc_start: 0.7108 (m-30) cc_final: 0.6758 (t0) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.1831 time to fit residues: 33.9346 Evaluate side-chains 134 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.138140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099582 restraints weight = 8737.476| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.89 r_work: 0.2861 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8365 Z= 0.179 Angle : 0.522 8.327 11360 Z= 0.254 Chirality : 0.038 0.136 1335 Planarity : 0.005 0.067 1390 Dihedral : 5.706 55.864 1118 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.36 % Favored : 97.55 % Rotamer: Outliers : 2.16 % Allowed : 10.44 % Favored : 87.40 % 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: 0.92 (0.27), residues: 1019 helix: 1.44 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -0.89 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 795 HIS 0.002 0.000 HIS A1149 PHE 0.008 0.001 PHE B1135 TYR 0.011 0.001 TYR B 789 ARG 0.008 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.918 Fit side-chains REVERT: A 702 ASP cc_start: 0.7474 (t0) cc_final: 0.7053 (t0) REVERT: A 745 MET cc_start: 0.8305 (mtp) cc_final: 0.8034 (mtt) REVERT: A 916 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7742 (t80) REVERT: A 1011 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6764 (tt0) REVERT: A 1075 VAL cc_start: 0.4543 (OUTLIER) cc_final: 0.4097 (t) REVERT: A 1210 ASP cc_start: 0.7185 (m-30) cc_final: 0.6978 (t0) REVERT: B 735 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7620 (mm-40) REVERT: B 745 MET cc_start: 0.8051 (mtp) cc_final: 0.7786 (mtt) REVERT: B 925 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7610 (mtm180) REVERT: B 1210 ASP cc_start: 0.7072 (m-30) cc_final: 0.6700 (t0) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.2032 time to fit residues: 37.9517 Evaluate side-chains 141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 845 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.138428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.099926 restraints weight = 8845.153| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.90 r_work: 0.2866 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8365 Z= 0.175 Angle : 0.517 8.372 11360 Z= 0.253 Chirality : 0.038 0.142 1335 Planarity : 0.005 0.067 1390 Dihedral : 5.640 54.698 1118 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 10.67 % Favored : 87.40 % 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: 0.98 (0.27), residues: 1019 helix: 1.49 (0.21), residues: 651 sheet: None (None), residues: 0 loop : -0.86 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.002 0.000 HIS B1149 PHE 0.008 0.001 PHE B 822 TYR 0.011 0.001 TYR B 789 ARG 0.009 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.853 Fit side-chains REVERT: A 745 MET cc_start: 0.8276 (mtp) cc_final: 0.7991 (mtt) REVERT: A 916 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 1011 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6755 (tt0) REVERT: A 1075 VAL cc_start: 0.4600 (OUTLIER) cc_final: 0.4142 (t) REVERT: A 1210 ASP cc_start: 0.7174 (m-30) cc_final: 0.6967 (t0) REVERT: B 735 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7601 (mm-40) REVERT: B 745 MET cc_start: 0.8031 (mtp) cc_final: 0.7771 (mtt) REVERT: B 925 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7624 (mtm180) REVERT: B 1084 GLN cc_start: 0.7829 (tt0) cc_final: 0.7585 (tt0) REVERT: B 1210 ASP cc_start: 0.7072 (m-30) cc_final: 0.6677 (t0) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1752 time to fit residues: 33.4599 Evaluate side-chains 135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 845 LYS Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 48 optimal weight: 0.0050 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.139773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101292 restraints weight = 8577.550| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.88 r_work: 0.2887 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8365 Z= 0.150 Angle : 0.501 8.380 11360 Z= 0.244 Chirality : 0.038 0.138 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.539 55.398 1118 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.70 % Allowed : 11.01 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1019 helix: 1.61 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -0.79 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.001 0.000 HIS B1149 PHE 0.007 0.001 PHE B 822 TYR 0.010 0.001 TYR A 789 ARG 0.008 0.000 ARG A 701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.914 Fit side-chains REVERT: A 745 MET cc_start: 0.8241 (mtp) cc_final: 0.7945 (mtt) REVERT: A 916 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7699 (t80) REVERT: A 1011 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6745 (tt0) REVERT: A 1075 VAL cc_start: 0.4575 (OUTLIER) cc_final: 0.4102 (t) REVERT: A 1210 ASP cc_start: 0.7167 (m-30) cc_final: 0.6954 (t0) REVERT: B 702 ASP cc_start: 0.7328 (t0) cc_final: 0.7124 (t0) REVERT: B 745 MET cc_start: 0.8026 (mtp) cc_final: 0.7770 (mtt) REVERT: B 925 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7607 (mtm180) REVERT: B 1084 GLN cc_start: 0.7898 (tt0) cc_final: 0.7645 (tt0) outliers start: 15 outliers final: 12 residues processed: 129 average time/residue: 0.2042 time to fit residues: 36.0999 Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1153 THR Chi-restraints excluded: chain B residue 1180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 chunk 53 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101714 restraints weight = 8721.521| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.90 r_work: 0.2905 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8365 Z= 0.147 Angle : 0.497 8.158 11360 Z= 0.242 Chirality : 0.038 0.136 1335 Planarity : 0.005 0.066 1390 Dihedral : 5.460 55.552 1118 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.59 % Allowed : 11.12 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.27), residues: 1019 helix: 1.65 (0.21), residues: 653 sheet: None (None), residues: 0 loop : -0.74 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.001 0.000 HIS A1149 PHE 0.007 0.001 PHE A 822 TYR 0.010 0.001 TYR A 789 ARG 0.009 0.000 ARG B 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4371.11 seconds wall clock time: 77 minutes 53.87 seconds (4673.87 seconds total)