Starting phenix.real_space_refine on Thu Sep 18 07:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cph_45803/09_2025/9cph_45803_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cph_45803/09_2025/9cph_45803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cph_45803/09_2025/9cph_45803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cph_45803/09_2025/9cph_45803.map" model { file = "/net/cci-nas-00/data/ceres_data/9cph_45803/09_2025/9cph_45803_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cph_45803/09_2025/9cph_45803_trim.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 4772 2.51 5 N 1259 2.21 5 O 1466 1.98 5 H 7346 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14867 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7930 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 329 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "H" Number of atoms: 3358 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 3346 Classifications: {'peptide': 227} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 227, 3346 Classifications: {'peptide': 227} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3380 Chain: "L" Number of atoms: 3227 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 3203 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 214, 3203 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3209 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.93, per 1000 atoms: 0.26 Number of scatterers: 14867 At special positions: 0 Unit cell: (84.216, 79.86, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 1466 8.00 N 1259 7.00 C 4772 6.00 H 7346 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 213 " - pdb=" SG BCYS H 157 " distance=2.03 Simple disulfide: pdb=" SG CYS H 233 " - pdb=" SG CYS L 216 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG ACYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG BCYS L 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC C 1 " - " GLC C 2 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 641.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 39.6% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 820 through 836 Processing helix chain 'A' and resid 846 through 857 Proline residue: A 852 - end of helix removed outlier: 3.545A pdb=" N THR A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 878 removed outlier: 4.261A pdb=" N GLY A 872 " --> pdb=" O HIS A 868 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY A 873 " --> pdb=" O ASP A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 932 through 934 No H-bonds generated for 'chain 'A' and resid 932 through 934' Processing helix chain 'A' and resid 935 through 946 removed outlier: 3.677A pdb=" N LYS A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.865A pdb=" N THR A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Proline residue: A 963 - end of helix removed outlier: 4.610A pdb=" N ASP A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 969 " --> pdb=" O ILE A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1005 Processing helix chain 'A' and resid 1013 through 1024 Processing helix chain 'A' and resid 1032 through 1034 No H-bonds generated for 'chain 'A' and resid 1032 through 1034' Processing helix chain 'A' and resid 1035 through 1042 removed outlier: 3.508A pdb=" N SER A1042 " --> pdb=" O ASN A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1085 Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.611A pdb=" N VAL A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1117 removed outlier: 3.711A pdb=" N LYS A1117 " --> pdb=" O GLU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1131 removed outlier: 3.848A pdb=" N ALA A1122 " --> pdb=" O ASP A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1156 removed outlier: 4.220A pdb=" N ALA A1142 " --> pdb=" O PRO A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1183 removed outlier: 3.510A pdb=" N GLU A1173 " --> pdb=" O GLN A1169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A1176 " --> pdb=" O ILE A1172 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 Processing helix chain 'A' and resid 1204 through 1225 Processing helix chain 'A' and resid 1225 through 1236 Processing helix chain 'A' and resid 1239 through 1246 removed outlier: 3.712A pdb=" N VAL A1243 " --> pdb=" O ASN A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1255 removed outlier: 3.936A pdb=" N PHE A1254 " --> pdb=" O MET A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1281 removed outlier: 3.616A pdb=" N ILE A1264 " --> pdb=" O ASN A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1302 removed outlier: 3.603A pdb=" N LEU A1290 " --> pdb=" O ALA A1286 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A1291 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A1292 " --> pdb=" O GLU A1288 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1297 " --> pdb=" O SER A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1309 Processing helix chain 'A' and resid 1311 through 1319 removed outlier: 3.568A pdb=" N PHE A1315 " --> pdb=" O GLY A1311 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.526A pdb=" N SER H 35 " --> pdb=" O LEU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 171 through 175 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 184 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 839 through 842 removed outlier: 6.383A pdb=" N LEU A 811 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLU A 842 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 813 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 812 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE A 865 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP A 814 " --> pdb=" O PHE A 865 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ALA A 867 " --> pdb=" O TRP A 814 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY A1064 " --> pdb=" O VAL A 914 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 914 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A1066 " --> pdb=" O ILE A 912 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 839 through 842 removed outlier: 6.383A pdb=" N LEU A 811 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLU A 842 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 813 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 812 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE A 865 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP A 814 " --> pdb=" O PHE A 865 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ALA A 867 " --> pdb=" O TRP A 814 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 902 through 903 Processing sheet with id=AA4, first strand: chain 'A' and resid 949 through 951 removed outlier: 6.232A pdb=" N ALA A 950 " --> pdb=" O MET A1028 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE A1030 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A1027 " --> pdb=" O ASN A 922 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 974 through 976 removed outlier: 4.245A pdb=" N LYS A 974 " --> pdb=" O ASP A 981 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10 removed outlier: 5.294A pdb=" N GLY H 19 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.537A pdb=" N TYR H 97 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 137 through 141 removed outlier: 3.801A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 167 through 168 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 8 removed outlier: 4.204A pdb=" N GLN L 4 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.563A pdb=" N GLU L 107 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.563A pdb=" N GLU L 107 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.871A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 156 375 hydrogen bonds defined for protein. 1025 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: 3.87 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7346 1.03 - 1.23: 11 1.23 - 1.42: 3233 1.42 - 1.62: 4411 1.62 - 1.82: 36 Bond restraints: 15037 Sorted by residual: bond pdb=" C LEU A1174 " pdb=" O LEU A1174 " ideal model delta sigma weight residual 1.234 1.182 0.052 1.35e-02 5.49e+03 1.49e+01 bond pdb=" N ILE A1171 " pdb=" CA ILE A1171 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.69e+00 bond pdb=" N ILE A1172 " pdb=" CA ILE A1172 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.37e+00 bond pdb=" N LEU A1174 " pdb=" CA LEU A1174 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.51e+00 bond pdb=" N GLU A1173 " pdb=" CA GLU A1173 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.33e+00 ... (remaining 15032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 26954 2.10 - 4.20: 178 4.20 - 6.29: 12 6.29 - 8.39: 5 8.39 - 10.49: 1 Bond angle restraints: 27150 Sorted by residual: angle pdb=" C LEU A1174 " pdb=" N TYR A1175 " pdb=" CA TYR A1175 " ideal model delta sigma weight residual 120.44 127.73 -7.29 1.30e+00 5.92e-01 3.14e+01 angle pdb=" C ALA H 150 " pdb=" CA ALA H 150 " pdb=" CB ALA H 150 " ideal model delta sigma weight residual 115.79 110.65 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" N LEU A1174 " pdb=" CA LEU A1174 " pdb=" C LEU A1174 " ideal model delta sigma weight residual 112.68 107.39 5.29 1.33e+00 5.65e-01 1.58e+01 angle pdb=" C THR A1124 " pdb=" N MET A1125 " pdb=" CA MET A1125 " ideal model delta sigma weight residual 122.38 116.00 6.38 1.81e+00 3.05e-01 1.24e+01 angle pdb=" O1 GLC C 1 " pdb=" C1 GLC C 1 " pdb=" O5 GLC C 1 " ideal model delta sigma weight residual 112.95 102.46 10.49 3.00e+00 1.11e-01 1.22e+01 ... (remaining 27145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6265 17.61 - 35.23: 634 35.23 - 52.84: 209 52.84 - 70.45: 68 70.45 - 88.06: 22 Dihedral angle restraints: 7198 sinusoidal: 3874 harmonic: 3324 Sorted by residual: dihedral pdb=" CB ACYS H 157 " pdb=" SG ACYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 157.67 -64.67 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB BCYS H 157 " pdb=" SG BCYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 157.67 -64.67 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG ACYS L 196 " pdb=" CB ACYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -29.25 -56.75 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 7195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 954 0.046 - 0.092: 144 0.092 - 0.137: 69 0.137 - 0.183: 7 0.183 - 0.229: 2 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C1 GLC C 1 " pdb=" C2 GLC C 1 " pdb=" O1 GLC C 1 " pdb=" O5 GLC C 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.27 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C3 GLC C 2 " pdb=" C2 GLC C 2 " pdb=" C4 GLC C 2 " pdb=" O3 GLC C 2 " both_signs ideal model delta sigma weight residual False 2.34 2.54 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA ILE A1172 " pdb=" N ILE A1172 " pdb=" C ILE A1172 " pdb=" CB ILE A1172 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 1173 not shown) Planarity restraints: 2261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 68 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C SER L 68 " 0.040 2.00e-02 2.50e+03 pdb=" O SER L 68 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY L 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1125 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C MET A1125 " -0.028 2.00e-02 2.50e+03 pdb=" O MET A1125 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A1126 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1169 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C GLN A1169 " -0.027 2.00e-02 2.50e+03 pdb=" O GLN A1169 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A1170 " 0.009 2.00e-02 2.50e+03 ... (remaining 2258 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 917 2.17 - 2.78: 30226 2.78 - 3.39: 43398 3.39 - 3.99: 56445 3.99 - 4.60: 86232 Nonbonded interactions: 217218 Sorted by model distance: nonbonded pdb=" OE1 GLN L 102 " pdb=" H GLN L 102 " model vdw 1.567 2.450 nonbonded pdb="HH12 ARG L 62 " pdb=" OD2 ASP L 83 " model vdw 1.582 2.450 nonbonded pdb=" HE1 TRP H 50 " pdb=" OG SER H 53 " model vdw 1.588 2.450 nonbonded pdb=" O GLU H 9 " pdb=" HG1 THR H 124 " model vdw 1.605 2.450 nonbonded pdb=" O ASN A1071 " pdb=" HG SER A1074 " model vdw 1.616 2.450 ... (remaining 217213 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.28 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: 1.680 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.003 0.052 7699 Z= 0.166 Angle : 0.619 11.656 10470 Z= 0.326 Chirality : 0.043 0.229 1176 Planarity : 0.003 0.038 1336 Dihedral : 17.681 88.063 2802 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 0.99 % Allowed : 28.00 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.27), residues: 965 helix: -0.28 (0.28), residues: 325 sheet: 0.26 (0.35), residues: 230 loop : -0.35 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1184 TYR 0.014 0.001 TYR L 142 PHE 0.016 0.001 PHE A1062 TRP 0.010 0.001 TRP A1305 HIS 0.003 0.001 HIS A1252 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7691) covalent geometry : angle 0.60740 (10453) SS BOND : bond 0.00282 ( 7) SS BOND : angle 0.93338 ( 14) hydrogen bonds : bond 0.13561 ( 367) hydrogen bonds : angle 7.80740 ( 1025) link_ALPHA1-4 : bond 0.03108 ( 1) link_ALPHA1-4 : angle 6.80808 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 51 average time/residue: 0.1879 time to fit residues: 13.8909 Evaluate side-chains 42 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 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 = 0.3772 r_free = 0.3772 target = 0.100725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.075412 restraints weight = 72553.410| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.72 r_work: 0.3157 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7699 Z= 0.243 Angle : 0.608 8.312 10470 Z= 0.322 Chirality : 0.043 0.174 1176 Planarity : 0.004 0.038 1336 Dihedral : 4.524 24.462 1091 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.09 % Favored : 94.59 % Rotamer: Outliers : 2.73 % Allowed : 26.02 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.27), residues: 965 helix: -0.05 (0.28), residues: 326 sheet: 0.19 (0.36), residues: 226 loop : -0.38 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 25 TYR 0.015 0.002 TYR L 142 PHE 0.010 0.001 PHE A 889 TRP 0.006 0.001 TRP A1144 HIS 0.004 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 7691) covalent geometry : angle 0.60724 (10453) SS BOND : bond 0.00321 ( 7) SS BOND : angle 0.88583 ( 14) hydrogen bonds : bond 0.04993 ( 367) hydrogen bonds : angle 6.32499 ( 1025) link_ALPHA1-4 : bond 0.02105 ( 1) link_ALPHA1-4 : angle 1.92148 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1223 ASN cc_start: 0.8558 (m-40) cc_final: 0.8336 (m-40) REVERT: A 1293 SER cc_start: 0.9487 (t) cc_final: 0.9218 (p) REVERT: B 71 MET cc_start: 0.0322 (ttt) cc_final: -0.2136 (mpp) outliers start: 18 outliers final: 9 residues processed: 63 average time/residue: 0.1765 time to fit residues: 16.4653 Evaluate side-chains 52 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1076 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.101261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075681 restraints weight = 71947.287| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.76 r_work: 0.3162 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7699 Z= 0.170 Angle : 0.565 7.669 10470 Z= 0.295 Chirality : 0.041 0.167 1176 Planarity : 0.004 0.039 1336 Dihedral : 4.461 23.617 1091 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 1.49 % Allowed : 27.14 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.27), residues: 965 helix: 0.16 (0.28), residues: 326 sheet: 0.22 (0.36), residues: 226 loop : -0.39 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 25 TYR 0.015 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.007 0.001 TRP A1305 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7691) covalent geometry : angle 0.56302 (10453) SS BOND : bond 0.00254 ( 7) SS BOND : angle 1.28944 ( 14) hydrogen bonds : bond 0.04213 ( 367) hydrogen bonds : angle 5.98777 ( 1025) link_ALPHA1-4 : bond 0.01087 ( 1) link_ALPHA1-4 : angle 1.75946 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9466 (t) cc_final: 0.9203 (p) REVERT: H 221 ASN cc_start: 0.9363 (t0) cc_final: 0.9138 (t0) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1907 time to fit residues: 15.6729 Evaluate side-chains 54 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 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 = 0.3772 r_free = 0.3772 target = 0.100858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075575 restraints weight = 77108.439| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.86 r_work: 0.3152 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7699 Z= 0.168 Angle : 0.553 7.744 10470 Z= 0.288 Chirality : 0.041 0.163 1176 Planarity : 0.004 0.039 1336 Dihedral : 4.427 22.733 1091 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 1.61 % Allowed : 27.39 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.27), residues: 965 helix: 0.16 (0.28), residues: 331 sheet: 0.23 (0.36), residues: 226 loop : -0.39 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 25 TYR 0.014 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.007 0.001 TRP A1305 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7691) covalent geometry : angle 0.55033 (10453) SS BOND : bond 0.00339 ( 7) SS BOND : angle 1.41083 ( 14) hydrogen bonds : bond 0.03988 ( 367) hydrogen bonds : angle 5.82176 ( 1025) link_ALPHA1-4 : bond 0.01402 ( 1) link_ALPHA1-4 : angle 1.88266 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9470 (t) cc_final: 0.9204 (p) REVERT: H 221 ASN cc_start: 0.9369 (t0) cc_final: 0.9113 (t0) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1996 time to fit residues: 16.7497 Evaluate side-chains 55 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.101295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075691 restraints weight = 70629.867| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.75 r_work: 0.3164 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7699 Z= 0.153 Angle : 0.540 7.901 10470 Z= 0.281 Chirality : 0.041 0.155 1176 Planarity : 0.004 0.039 1336 Dihedral : 4.379 21.995 1091 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.68 % Favored : 95.11 % Rotamer: Outliers : 1.98 % Allowed : 26.27 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.27), residues: 965 helix: 0.21 (0.28), residues: 334 sheet: 0.24 (0.36), residues: 226 loop : -0.45 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.013 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.008 0.001 TRP A1305 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7691) covalent geometry : angle 0.53747 (10453) SS BOND : bond 0.00487 ( 7) SS BOND : angle 1.18495 ( 14) hydrogen bonds : bond 0.03840 ( 367) hydrogen bonds : angle 5.71617 ( 1025) link_ALPHA1-4 : bond 0.01003 ( 1) link_ALPHA1-4 : angle 1.78112 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9556 (t) cc_final: 0.9265 (p) REVERT: B 71 MET cc_start: 0.0330 (OUTLIER) cc_final: -0.1868 (mpp) REVERT: H 49 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 221 ASN cc_start: 0.9396 (t0) cc_final: 0.9080 (t0) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.1973 time to fit residues: 16.9906 Evaluate side-chains 56 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0470 chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.100562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075107 restraints weight = 67389.411| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.63 r_work: 0.3157 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7699 Z= 0.180 Angle : 0.553 7.890 10470 Z= 0.288 Chirality : 0.041 0.157 1176 Planarity : 0.004 0.039 1336 Dihedral : 4.405 21.447 1091 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 1.98 % Allowed : 26.27 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.27), residues: 965 helix: 0.20 (0.28), residues: 331 sheet: 0.12 (0.35), residues: 231 loop : -0.46 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.014 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.009 0.001 TRP A1305 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7691) covalent geometry : angle 0.55075 (10453) SS BOND : bond 0.00281 ( 7) SS BOND : angle 1.29920 ( 14) hydrogen bonds : bond 0.03902 ( 367) hydrogen bonds : angle 5.67977 ( 1025) link_ALPHA1-4 : bond 0.01450 ( 1) link_ALPHA1-4 : angle 1.81551 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1288 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: A 1293 SER cc_start: 0.9564 (t) cc_final: 0.9271 (p) REVERT: B 71 MET cc_start: 0.0253 (OUTLIER) cc_final: -0.2091 (mpp) REVERT: H 49 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8047 (tm-30) REVERT: H 221 ASN cc_start: 0.9432 (t0) cc_final: 0.9096 (t0) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 0.1936 time to fit residues: 16.7429 Evaluate side-chains 59 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1288 GLU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.098830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072888 restraints weight = 81129.732| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.99 r_work: 0.3105 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7699 Z= 0.244 Angle : 0.593 8.744 10470 Z= 0.313 Chirality : 0.042 0.158 1176 Planarity : 0.004 0.040 1336 Dihedral : 4.603 21.168 1091 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 2.35 % Allowed : 27.01 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.27), residues: 965 helix: 0.02 (0.27), residues: 331 sheet: -0.08 (0.34), residues: 236 loop : -0.64 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.017 0.002 TYR L 142 PHE 0.014 0.002 PHE A 831 TRP 0.009 0.002 TRP A1305 HIS 0.004 0.001 HIS H 217 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 7691) covalent geometry : angle 0.59041 (10453) SS BOND : bond 0.00261 ( 7) SS BOND : angle 1.34310 ( 14) hydrogen bonds : bond 0.04190 ( 367) hydrogen bonds : angle 5.80484 ( 1025) link_ALPHA1-4 : bond 0.01758 ( 1) link_ALPHA1-4 : angle 1.86354 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9553 (t) cc_final: 0.9343 (p) REVERT: B 71 MET cc_start: 0.0470 (OUTLIER) cc_final: -0.1853 (mpp) REVERT: H 49 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8125 (tm-30) REVERT: H 221 ASN cc_start: 0.9349 (t0) cc_final: 0.9003 (t0) REVERT: L 163 GLU cc_start: 0.8877 (pm20) cc_final: 0.8614 (pp20) outliers start: 17 outliers final: 13 residues processed: 62 average time/residue: 0.1883 time to fit residues: 16.8453 Evaluate side-chains 62 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1076 ASN Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1288 GLU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.100686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.075261 restraints weight = 66824.806| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.60 r_work: 0.3158 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7699 Z= 0.137 Angle : 0.541 7.006 10470 Z= 0.281 Chirality : 0.041 0.149 1176 Planarity : 0.004 0.040 1336 Dihedral : 4.437 21.752 1091 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.68 % Favored : 95.11 % Rotamer: Outliers : 1.86 % Allowed : 26.89 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.27), residues: 965 helix: 0.27 (0.28), residues: 331 sheet: -0.14 (0.34), residues: 236 loop : -0.45 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.014 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.009 0.001 TRP A1305 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7691) covalent geometry : angle 0.53918 (10453) SS BOND : bond 0.00357 ( 7) SS BOND : angle 1.23283 ( 14) hydrogen bonds : bond 0.03706 ( 367) hydrogen bonds : angle 5.57386 ( 1025) link_ALPHA1-4 : bond 0.00926 ( 1) link_ALPHA1-4 : angle 1.73566 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9558 (t) cc_final: 0.9348 (p) REVERT: B 71 MET cc_start: 0.0496 (OUTLIER) cc_final: -0.1686 (mpp) REVERT: H 49 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8053 (tm-30) REVERT: H 221 ASN cc_start: 0.9336 (t0) cc_final: 0.8974 (t0) REVERT: L 163 GLU cc_start: 0.8810 (pm20) cc_final: 0.8535 (pp20) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 0.1907 time to fit residues: 16.2484 Evaluate side-chains 60 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1288 GLU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.099632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074000 restraints weight = 79018.239| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.90 r_work: 0.3125 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7699 Z= 0.188 Angle : 0.556 7.725 10470 Z= 0.291 Chirality : 0.041 0.149 1176 Planarity : 0.004 0.041 1336 Dihedral : 4.465 21.180 1091 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.39 % Rotamer: Outliers : 2.11 % Allowed : 26.89 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.27), residues: 965 helix: 0.28 (0.28), residues: 331 sheet: -0.14 (0.34), residues: 231 loop : -0.55 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.017 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.007 0.001 TRP A1305 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7691) covalent geometry : angle 0.55333 (10453) SS BOND : bond 0.00224 ( 7) SS BOND : angle 1.38627 ( 14) hydrogen bonds : bond 0.03865 ( 367) hydrogen bonds : angle 5.59770 ( 1025) link_ALPHA1-4 : bond 0.01395 ( 1) link_ALPHA1-4 : angle 1.76033 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9559 (t) cc_final: 0.9358 (p) REVERT: B 71 MET cc_start: 0.0538 (OUTLIER) cc_final: -0.1667 (mpp) REVERT: H 221 ASN cc_start: 0.9343 (t0) cc_final: 0.8981 (t0) REVERT: L 163 GLU cc_start: 0.8841 (pm20) cc_final: 0.8556 (pp20) outliers start: 15 outliers final: 12 residues processed: 63 average time/residue: 0.1904 time to fit residues: 17.4046 Evaluate side-chains 62 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain A residue 1169 GLN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1288 GLU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 19 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.100948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075629 restraints weight = 67190.694| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.61 r_work: 0.3167 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7699 Z= 0.132 Angle : 0.532 6.691 10470 Z= 0.276 Chirality : 0.041 0.146 1176 Planarity : 0.004 0.039 1336 Dihedral : 4.351 21.351 1091 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.68 % Favored : 95.11 % Rotamer: Outliers : 1.36 % Allowed : 27.39 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.27), residues: 965 helix: 0.43 (0.28), residues: 331 sheet: -0.07 (0.35), residues: 231 loop : -0.43 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.013 0.001 TYR L 142 PHE 0.012 0.001 PHE A1062 TRP 0.010 0.001 TRP A1305 HIS 0.003 0.001 HIS A1007 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7691) covalent geometry : angle 0.52921 (10453) SS BOND : bond 0.00238 ( 7) SS BOND : angle 1.27969 ( 14) hydrogen bonds : bond 0.03595 ( 367) hydrogen bonds : angle 5.47354 ( 1025) link_ALPHA1-4 : bond 0.00833 ( 1) link_ALPHA1-4 : angle 1.69058 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1234 is missing expected H atoms. Skipping. Residue LYS 1238 is missing expected H atoms. Skipping. Residue LYS 1244 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1293 SER cc_start: 0.9548 (t) cc_final: 0.9346 (p) REVERT: B 71 MET cc_start: 0.0437 (OUTLIER) cc_final: -0.1685 (mpp) REVERT: H 49 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8046 (tm-30) REVERT: H 221 ASN cc_start: 0.9367 (t0) cc_final: 0.8995 (t0) REVERT: L 163 GLU cc_start: 0.8841 (pm20) cc_final: 0.8529 (pp20) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.2004 time to fit residues: 15.7113 Evaluate side-chains 57 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1288 GLU Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 189 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.101013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075474 restraints weight = 74658.657| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.84 r_work: 0.3158 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7699 Z= 0.138 Angle : 0.526 6.855 10470 Z= 0.274 Chirality : 0.040 0.142 1176 Planarity : 0.004 0.040 1336 Dihedral : 4.284 20.859 1091 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.68 % Favored : 95.11 % Rotamer: Outliers : 1.49 % Allowed : 27.39 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.28), residues: 965 helix: 0.52 (0.28), residues: 331 sheet: -0.17 (0.34), residues: 238 loop : -0.32 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1176 TYR 0.015 0.001 TYR L 142 PHE 0.011 0.001 PHE A1062 TRP 0.009 0.001 TRP A1305 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7691) covalent geometry : angle 0.52418 (10453) SS BOND : bond 0.00251 ( 7) SS BOND : angle 1.25473 ( 14) hydrogen bonds : bond 0.03572 ( 367) hydrogen bonds : angle 5.42038 ( 1025) link_ALPHA1-4 : bond 0.01002 ( 1) link_ALPHA1-4 : angle 1.59744 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4317.91 seconds wall clock time: 74 minutes 16.07 seconds (4456.07 seconds total)