Starting phenix.real_space_refine on Wed Sep 17 10:32:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y86_39035/09_2025/8y86_39035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y86_39035/09_2025/8y86_39035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y86_39035/09_2025/8y86_39035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y86_39035/09_2025/8y86_39035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y86_39035/09_2025/8y86_39035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y86_39035/09_2025/8y86_39035.map" } resolution = 2.75 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= 0.001 sd= 0.138 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 34 5.16 5 C 5354 2.51 5 N 1330 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 8060 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4026 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 33, 'TRANS': 480} Chain breaks: 1 Chain: "B" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4026 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 33, 'TRANS': 480} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'BCT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.28 Number of scatterers: 8060 At special positions: 0 Unit cell: (115.5, 104.5, 83.6, 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 34 16.00 O 1342 8.00 N 1330 7.00 C 5354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 480.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 74.5% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 705 through 734 removed outlier: 4.150A pdb=" N VAL A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 739 through 758 removed outlier: 3.833A pdb=" N LEU A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 788 through 810 Processing helix chain 'A' and resid 811 through 819 removed outlier: 3.706A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.872A pdb=" N VAL A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 913 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 920 through 930 Processing helix chain 'A' and resid 930 through 946 removed outlier: 3.865A pdb=" N ILE A 946 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 989 Processing helix chain 'A' and resid 989 through 1012 removed outlier: 3.543A pdb=" N ALA A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.611A pdb=" N ARG A1017 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.688A pdb=" N GLY A1039 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1049 through 1060 removed outlier: 3.553A pdb=" N LEU A1060 " --> pdb=" O HIS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1106 through 1122 removed outlier: 4.148A pdb=" N LEU A1110 " --> pdb=" O PRO A1106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A1122 " --> pdb=" O GLY A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1133 removed outlier: 3.718A pdb=" N GLN A1129 " --> pdb=" O ILE A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.540A pdb=" N LYS A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1175 removed outlier: 3.749A pdb=" N LEU A1157 " --> pdb=" O TRP A1153 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A1158 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1179 No H-bonds generated for 'chain 'A' and resid 1177 through 1179' Processing helix chain 'A' and resid 1180 through 1187 Processing helix chain 'A' and resid 1187 through 1195 removed outlier: 3.809A pdb=" N LEU A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.575A pdb=" N LEU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1209 removed outlier: 3.633A pdb=" N ALA A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 695 through 702 Processing helix chain 'B' and resid 705 through 734 removed outlier: 4.154A pdb=" N VAL B 709 " --> pdb=" O HIS B 705 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER B 721 " --> pdb=" O PHE B 717 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 removed outlier: 3.835A pdb=" N LEU B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 788 through 810 Processing helix chain 'B' and resid 811 through 819 removed outlier: 3.681A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 Processing helix chain 'B' and resid 892 through 913 Processing helix chain 'B' and resid 914 through 916 No H-bonds generated for 'chain 'B' and resid 914 through 916' Processing helix chain 'B' and resid 920 through 930 Processing helix chain 'B' and resid 930 through 946 removed outlier: 3.645A pdb=" N ILE B 946 " --> pdb=" O VAL B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 989 Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.532A pdb=" N ALA B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 3.701A pdb=" N GLY B1039 " --> pdb=" O GLY B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1049 through 1060 removed outlier: 3.556A pdb=" N LEU B1060 " --> pdb=" O HIS B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1095 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1106 through 1122 removed outlier: 4.129A pdb=" N LEU B1110 " --> pdb=" O PRO B1106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B1122 " --> pdb=" O GLY B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1133 removed outlier: 3.713A pdb=" N GLN B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1149 Processing helix chain 'B' and resid 1151 through 1175 removed outlier: 3.555A pdb=" N HIS B1156 " --> pdb=" O THR B1152 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B1157 " --> pdb=" O TRP B1153 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B1158 " --> pdb=" O ARG B1154 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B1159 " --> pdb=" O MET B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1179 No H-bonds generated for 'chain 'B' and resid 1177 through 1179' Processing helix chain 'B' and resid 1180 through 1187 Processing helix chain 'B' and resid 1187 through 1195 removed outlier: 3.822A pdb=" N LEU B1191 " --> pdb=" O LEU B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1195 through 1200 removed outlier: 3.597A pdb=" N LEU B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1209 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 1061 through 1063 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 1061 through 1063 499 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2180 1.34 - 1.45: 1324 1.45 - 1.57: 4706 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 8266 Sorted by residual: bond pdb=" C BCT A1300 " pdb=" O3 BCT A1300 " ideal model delta sigma weight residual 1.389 1.436 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C BCT B1300 " pdb=" O3 BCT B1300 " ideal model delta sigma weight residual 1.389 1.435 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" CB GLU B1003 " pdb=" CG GLU B1003 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" C BCT A1300 " pdb=" O1 BCT A1300 " ideal model delta sigma weight residual 1.236 1.217 0.019 2.00e-02 2.50e+03 8.72e-01 bond pdb=" C BCT B1300 " pdb=" O1 BCT B1300 " ideal model delta sigma weight residual 1.236 1.218 0.018 2.00e-02 2.50e+03 7.72e-01 ... (remaining 8261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 10943 1.36 - 2.72: 235 2.72 - 4.08: 53 4.08 - 5.44: 17 5.44 - 6.81: 6 Bond angle restraints: 11254 Sorted by residual: angle pdb=" N ASP A 948 " pdb=" CA ASP A 948 " pdb=" C ASP A 948 " ideal model delta sigma weight residual 114.75 108.06 6.69 1.26e+00 6.30e-01 2.82e+01 angle pdb=" CB GLU B1003 " pdb=" CG GLU B1003 " pdb=" CD GLU B1003 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.70e+00 3.46e-01 1.38e+01 angle pdb=" N THR A 848 " pdb=" CA THR A 848 " pdb=" C THR A 848 " ideal model delta sigma weight residual 113.41 109.58 3.83 1.22e+00 6.72e-01 9.87e+00 angle pdb=" CA ASP A 948 " pdb=" C ASP A 948 " pdb=" N THR A 949 " ideal model delta sigma weight residual 119.80 115.62 4.18 1.34e+00 5.57e-01 9.75e+00 angle pdb=" CA GLY B1021 " pdb=" C GLY B1021 " pdb=" N SER B1022 " ideal model delta sigma weight residual 114.23 116.52 -2.29 8.80e-01 1.29e+00 6.75e+00 ... (remaining 11249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 4265 16.39 - 32.78: 453 32.78 - 49.17: 127 49.17 - 65.56: 21 65.56 - 81.95: 14 Dihedral angle restraints: 4880 sinusoidal: 1922 harmonic: 2958 Sorted by residual: dihedral pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" N ASP A 948 " pdb=" CA ASP A 948 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA THR B 947 " pdb=" C THR B 947 " pdb=" N ASP B 948 " pdb=" CA ASP B 948 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP A1071 " pdb=" CB ASP A1071 " pdb=" CG ASP A1071 " pdb=" OD1 ASP A1071 " ideal model delta sinusoidal sigma weight residual -30.00 -83.96 53.96 1 2.00e+01 2.50e-03 9.88e+00 ... (remaining 4877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 794 0.028 - 0.056: 357 0.056 - 0.085: 128 0.085 - 0.113: 52 0.113 - 0.141: 15 Chirality restraints: 1346 Sorted by residual: chirality pdb=" CA VAL A 956 " pdb=" N VAL A 956 " pdb=" C VAL A 956 " pdb=" CB VAL A 956 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ASP B1209 " pdb=" N ASP B1209 " pdb=" C ASP B1209 " pdb=" CB ASP B1209 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE B 972 " pdb=" N ILE B 972 " pdb=" C ILE B 972 " pdb=" CB ILE B 972 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1343 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A1300 " -0.046 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" O1 BCT A1300 " 0.017 2.00e-02 2.50e+03 pdb=" O2 BCT A1300 " 0.017 2.00e-02 2.50e+03 pdb=" O3 BCT A1300 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C BCT B1300 " -0.046 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" O1 BCT B1300 " 0.017 2.00e-02 2.50e+03 pdb=" O2 BCT B1300 " 0.017 2.00e-02 2.50e+03 pdb=" O3 BCT B1300 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B1003 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" CD GLU B1003 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU B1003 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B1003 " 0.010 2.00e-02 2.50e+03 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2135 2.81 - 3.33: 7447 3.33 - 3.86: 12492 3.86 - 4.38: 13787 4.38 - 4.90: 25830 Nonbonded interactions: 61691 Sorted by model distance: nonbonded pdb=" O ALA B1049 " pdb=" OG SER B1053 " model vdw 2.290 3.040 nonbonded pdb=" O ALA A1049 " pdb=" OG SER A1053 " model vdw 2.303 3.040 nonbonded pdb=" NE ARG A1192 " pdb=" OD2 ASP A1209 " model vdw 2.353 3.120 nonbonded pdb=" NH2 ARG A1130 " pdb=" OE1 GLN A1162 " model vdw 2.375 3.120 nonbonded pdb=" NH2 ARG A 793 " pdb=" O LEU A1043 " model vdw 2.377 3.120 ... (remaining 61686 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.520 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 0.047 8266 Z= 0.126 Angle : 0.537 6.806 11254 Z= 0.280 Chirality : 0.039 0.141 1346 Planarity : 0.005 0.042 1382 Dihedral : 15.013 81.952 2972 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.25 % Allowed : 11.62 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.26), residues: 1020 helix: 1.89 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.27 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1017 TYR 0.010 0.001 TYR B 789 PHE 0.016 0.001 PHE B 822 TRP 0.013 0.001 TRP A 795 HIS 0.001 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8266) covalent geometry : angle 0.53742 (11254) hydrogen bonds : bond 0.15780 ( 499) hydrogen bonds : angle 4.79165 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.305 Fit side-chains REVERT: A 1206 GLN cc_start: 0.7285 (tt0) cc_final: 0.6636 (tm-30) REVERT: B 1206 GLN cc_start: 0.7339 (tt0) cc_final: 0.6688 (tm-30) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.9278 time to fit residues: 84.9182 Evaluate side-chains 85 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 914 ARG Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 1172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1081 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114195 restraints weight = 9697.661| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.28 r_work: 0.3421 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8266 Z= 0.121 Angle : 0.493 5.940 11254 Z= 0.250 Chirality : 0.039 0.142 1346 Planarity : 0.005 0.039 1382 Dihedral : 4.253 37.288 1125 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 9.91 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.27), residues: 1020 helix: 2.02 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.05 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1017 TYR 0.007 0.001 TYR A 789 PHE 0.013 0.001 PHE B 822 TRP 0.011 0.001 TRP B 795 HIS 0.002 0.001 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8266) covalent geometry : angle 0.49292 (11254) hydrogen bonds : bond 0.05621 ( 499) hydrogen bonds : angle 3.87631 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.231 Fit side-chains REVERT: A 1206 GLN cc_start: 0.7220 (tt0) cc_final: 0.6544 (tm-30) REVERT: B 1206 GLN cc_start: 0.7173 (tt0) cc_final: 0.6605 (tm-30) outliers start: 22 outliers final: 9 residues processed: 92 average time/residue: 0.8291 time to fit residues: 79.5912 Evaluate side-chains 82 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 0.0000 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.144246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116538 restraints weight = 9556.917| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.26 r_work: 0.3428 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8266 Z= 0.103 Angle : 0.459 5.142 11254 Z= 0.230 Chirality : 0.038 0.137 1346 Planarity : 0.004 0.036 1382 Dihedral : 3.401 19.603 1110 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.96 % Allowed : 11.16 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.27), residues: 1020 helix: 2.26 (0.20), residues: 700 sheet: None (None), residues: 0 loop : 0.04 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1017 TYR 0.007 0.001 TYR B 789 PHE 0.014 0.001 PHE B 822 TRP 0.010 0.001 TRP B 795 HIS 0.002 0.000 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8266) covalent geometry : angle 0.45876 (11254) hydrogen bonds : bond 0.04700 ( 499) hydrogen bonds : angle 3.66364 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.337 Fit side-chains REVERT: A 1003 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: B 1003 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5116 (tm-30) REVERT: B 1080 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: B 1206 GLN cc_start: 0.7130 (tt0) cc_final: 0.6592 (tm-30) outliers start: 26 outliers final: 10 residues processed: 98 average time/residue: 0.7652 time to fit residues: 78.4523 Evaluate side-chains 92 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115991 restraints weight = 9770.126| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.27 r_work: 0.3443 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8266 Z= 0.109 Angle : 0.470 5.555 11254 Z= 0.234 Chirality : 0.039 0.136 1346 Planarity : 0.004 0.036 1382 Dihedral : 3.366 18.936 1110 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.30 % Allowed : 11.39 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.27), residues: 1020 helix: 2.24 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.03 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1017 TYR 0.008 0.001 TYR B 789 PHE 0.014 0.001 PHE B 822 TRP 0.010 0.001 TRP B 795 HIS 0.002 0.001 HIS B1025 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8266) covalent geometry : angle 0.46998 (11254) hydrogen bonds : bond 0.04843 ( 499) hydrogen bonds : angle 3.62366 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.315 Fit side-chains REVERT: A 1080 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: A 1199 LEU cc_start: 0.7892 (tp) cc_final: 0.7567 (tp) REVERT: B 1003 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5164 (tm-30) REVERT: B 1080 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 1206 GLN cc_start: 0.7189 (tt0) cc_final: 0.6558 (tm-30) outliers start: 29 outliers final: 10 residues processed: 94 average time/residue: 0.7727 time to fit residues: 76.0343 Evaluate side-chains 95 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN B1081 GLN B1201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109020 restraints weight = 9716.383| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.30 r_work: 0.3360 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8266 Z= 0.213 Angle : 0.581 7.235 11254 Z= 0.291 Chirality : 0.044 0.150 1346 Planarity : 0.005 0.043 1382 Dihedral : 3.676 18.577 1110 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.19 % Allowed : 12.87 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.27), residues: 1020 helix: 1.87 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.30 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1192 TYR 0.010 0.001 TYR B1146 PHE 0.032 0.002 PHE B 847 TRP 0.008 0.001 TRP B 795 HIS 0.003 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 8266) covalent geometry : angle 0.58116 (11254) hydrogen bonds : bond 0.07190 ( 499) hydrogen bonds : angle 3.88559 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.311 Fit side-chains REVERT: A 1003 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5615 (tm-30) REVERT: A 1199 LEU cc_start: 0.7734 (tp) cc_final: 0.7489 (tp) REVERT: B 1003 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5392 (tm-30) REVERT: B 1080 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: B 1206 GLN cc_start: 0.7195 (tt0) cc_final: 0.6518 (tm-30) outliers start: 28 outliers final: 15 residues processed: 91 average time/residue: 0.8617 time to fit residues: 81.8503 Evaluate side-chains 93 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1139 LYS Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1204 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 91 optimal weight: 0.0270 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1201 GLN B1081 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112989 restraints weight = 9576.905| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.32 r_work: 0.3409 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8266 Z= 0.118 Angle : 0.489 6.289 11254 Z= 0.245 Chirality : 0.039 0.140 1346 Planarity : 0.005 0.038 1382 Dihedral : 3.526 19.564 1110 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.73 % Allowed : 13.90 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.13 (0.27), residues: 1020 helix: 2.13 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.16 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1017 TYR 0.008 0.001 TYR B 789 PHE 0.014 0.001 PHE B 822 TRP 0.011 0.001 TRP B 795 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8266) covalent geometry : angle 0.48917 (11254) hydrogen bonds : bond 0.05343 ( 499) hydrogen bonds : angle 3.71944 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.356 Fit side-chains REVERT: A 1199 LEU cc_start: 0.7854 (tp) cc_final: 0.7535 (tp) REVERT: B 1003 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5269 (tm-30) REVERT: B 1206 GLN cc_start: 0.7136 (tt0) cc_final: 0.6472 (tm-30) outliers start: 24 outliers final: 12 residues processed: 85 average time/residue: 0.8601 time to fit residues: 76.2307 Evaluate side-chains 89 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1210 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1081 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113354 restraints weight = 9691.158| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.33 r_work: 0.3412 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8266 Z= 0.120 Angle : 0.486 5.898 11254 Z= 0.243 Chirality : 0.039 0.139 1346 Planarity : 0.005 0.038 1382 Dihedral : 3.467 18.317 1110 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.73 % Allowed : 14.81 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.27), residues: 1020 helix: 2.16 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1017 TYR 0.008 0.001 TYR A 789 PHE 0.016 0.001 PHE B 847 TRP 0.011 0.001 TRP B 795 HIS 0.002 0.001 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8266) covalent geometry : angle 0.48554 (11254) hydrogen bonds : bond 0.05244 ( 499) hydrogen bonds : angle 3.67028 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.336 Fit side-chains REVERT: A 1199 LEU cc_start: 0.7846 (tp) cc_final: 0.7526 (tp) REVERT: B 817 ARG cc_start: 0.7816 (ptm160) cc_final: 0.7087 (ptt180) REVERT: B 1003 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5276 (tm-30) REVERT: B 1206 GLN cc_start: 0.7082 (tt0) cc_final: 0.6482 (tm-30) outliers start: 24 outliers final: 12 residues processed: 88 average time/residue: 0.8801 time to fit residues: 80.8883 Evaluate side-chains 91 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1210 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 17 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1201 GLN B1081 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114924 restraints weight = 9625.348| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.33 r_work: 0.3434 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8266 Z= 0.109 Angle : 0.471 5.630 11254 Z= 0.235 Chirality : 0.039 0.135 1346 Planarity : 0.005 0.037 1382 Dihedral : 3.395 17.226 1110 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.16 % Allowed : 15.49 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.27), residues: 1020 helix: 2.16 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.02 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1017 TYR 0.007 0.001 TYR B 789 PHE 0.013 0.001 PHE B 822 TRP 0.011 0.001 TRP B 795 HIS 0.001 0.000 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8266) covalent geometry : angle 0.47073 (11254) hydrogen bonds : bond 0.04798 ( 499) hydrogen bonds : angle 3.60814 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.329 Fit side-chains REVERT: A 1199 LEU cc_start: 0.7804 (tp) cc_final: 0.7498 (tp) REVERT: B 817 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7070 (ptt180) REVERT: B 1003 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.5237 (tm-30) REVERT: B 1206 GLN cc_start: 0.7063 (tt0) cc_final: 0.6417 (tm-30) REVERT: B 1210 SER cc_start: 0.7329 (OUTLIER) cc_final: 0.6679 (p) outliers start: 19 outliers final: 9 residues processed: 88 average time/residue: 0.8936 time to fit residues: 81.9499 Evaluate side-chains 89 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1210 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1081 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117831 restraints weight = 9623.545| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.33 r_work: 0.3472 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8266 Z= 0.097 Angle : 0.453 5.816 11254 Z= 0.225 Chirality : 0.038 0.129 1346 Planarity : 0.004 0.035 1382 Dihedral : 3.275 16.009 1110 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.94 % Allowed : 16.17 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.27), residues: 1020 helix: 2.31 (0.20), residues: 712 sheet: None (None), residues: 0 loop : 0.08 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1017 TYR 0.007 0.001 TYR A 789 PHE 0.011 0.001 PHE B 822 TRP 0.011 0.001 TRP B 795 HIS 0.002 0.000 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8266) covalent geometry : angle 0.45281 (11254) hydrogen bonds : bond 0.04145 ( 499) hydrogen bonds : angle 3.51401 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.310 Fit side-chains REVERT: A 1003 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6631 (mm-30) REVERT: A 1199 LEU cc_start: 0.7857 (tp) cc_final: 0.7599 (tp) REVERT: A 1203 ARG cc_start: 0.7070 (ptm-80) cc_final: 0.6858 (ttt90) REVERT: B 817 ARG cc_start: 0.7757 (ptm160) cc_final: 0.7076 (ptt180) REVERT: B 1003 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5184 (tm-30) REVERT: B 1199 LEU cc_start: 0.7771 (tp) cc_final: 0.7442 (tp) REVERT: B 1206 GLN cc_start: 0.6968 (tt0) cc_final: 0.6351 (tm-30) REVERT: B 1210 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6643 (p) outliers start: 17 outliers final: 7 residues processed: 91 average time/residue: 0.8839 time to fit residues: 83.8327 Evaluate side-chains 91 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1201 GLN B1081 GLN B1201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113177 restraints weight = 9616.311| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.32 r_work: 0.3412 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8266 Z= 0.133 Angle : 0.489 5.564 11254 Z= 0.245 Chirality : 0.040 0.138 1346 Planarity : 0.005 0.037 1382 Dihedral : 3.406 15.621 1110 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 16.17 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.27), residues: 1020 helix: 2.10 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -0.02 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1017 TYR 0.007 0.001 TYR B1146 PHE 0.017 0.001 PHE B 822 TRP 0.009 0.001 TRP A 795 HIS 0.002 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8266) covalent geometry : angle 0.48941 (11254) hydrogen bonds : bond 0.05483 ( 499) hydrogen bonds : angle 3.64078 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.314 Fit side-chains REVERT: A 1199 LEU cc_start: 0.7690 (tp) cc_final: 0.7451 (tp) REVERT: A 1203 ARG cc_start: 0.7077 (ptm-80) cc_final: 0.6848 (ttt90) REVERT: B 817 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7065 (ptt180) REVERT: B 1003 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5254 (tm-30) REVERT: B 1199 LEU cc_start: 0.7811 (tp) cc_final: 0.7561 (tp) REVERT: B 1206 GLN cc_start: 0.7014 (tt0) cc_final: 0.6375 (tm-30) REVERT: B 1210 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.6773 (p) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.9227 time to fit residues: 79.7787 Evaluate side-chains 88 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 1003 GLU Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 3 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1201 GLN B1081 GLN B1201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114546 restraints weight = 9595.311| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.32 r_work: 0.3429 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8266 Z= 0.114 Angle : 0.473 6.578 11254 Z= 0.236 Chirality : 0.039 0.136 1346 Planarity : 0.005 0.037 1382 Dihedral : 3.381 15.997 1110 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.14 % Allowed : 16.63 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.33 (0.27), residues: 1020 helix: 2.19 (0.20), residues: 712 sheet: None (None), residues: 0 loop : 0.06 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1017 TYR 0.007 0.001 TYR A 789 PHE 0.014 0.001 PHE A 822 TRP 0.008 0.001 TRP A 795 HIS 0.002 0.001 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8266) covalent geometry : angle 0.47272 (11254) hydrogen bonds : bond 0.04993 ( 499) hydrogen bonds : angle 3.60366 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3345.37 seconds wall clock time: 57 minutes 32.21 seconds (3452.21 seconds total)