Starting phenix.real_space_refine on Wed Feb 12 16:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y86_39035/02_2025/8y86_39035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y86_39035/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y86_39035/02_2025/8y86_39035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y86_39035/02_2025/8y86_39035.map" model { file = "/net/cci-nas-00/data/ceres_data/8y86_39035/02_2025/8y86_39035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y86_39035/02_2025/8y86_39035.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.15, per 1000 atoms: 0.64 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: 2.14 Conformation dependent library (CDL) restraints added in 997.8 milliseconds 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: 0.89 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: 2.32 Time building geometry restraints manager: 2.47 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- 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= 0.181 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (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 TRP 0.013 0.001 TRP A 795 HIS 0.001 0.001 HIS B 695 PHE 0.016 0.001 PHE B 822 TYR 0.010 0.001 TYR B 789 ARG 0.005 0.000 ARG A1017 *********************** 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 : 0.856 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: 1.9064 time to fit residues: 175.4487 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 : 1.097 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113882 restraints weight = 9586.878| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.26 r_work: 0.3373 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8266 Z= 0.186 Angle : 0.496 5.997 11254 Z= 0.251 Chirality : 0.040 0.143 1346 Planarity : 0.005 0.040 1382 Dihedral : 4.236 37.570 1125 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 10.14 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.27), residues: 1020 helix: 1.99 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.05 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.002 0.001 HIS A1025 PHE 0.015 0.001 PHE B 822 TYR 0.009 0.001 TYR A 789 ARG 0.003 0.000 ARG A1017 *********************** 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 106 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.855 Fit side-chains REVERT: A 1003 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: A 1206 GLN cc_start: 0.7356 (tt0) cc_final: 0.6659 (tm-30) REVERT: B 1206 GLN cc_start: 0.7454 (tt0) cc_final: 0.6876 (tm-30) outliers start: 22 outliers final: 9 residues processed: 95 average time/residue: 1.7305 time to fit residues: 172.1444 Evaluate side-chains 89 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.138586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110091 restraints weight = 9757.098| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.34 r_work: 0.3372 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8266 Z= 0.275 Angle : 0.533 5.533 11254 Z= 0.269 Chirality : 0.041 0.149 1346 Planarity : 0.005 0.040 1382 Dihedral : 3.659 20.713 1110 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.85 % Allowed : 11.39 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.27), residues: 1020 helix: 1.85 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.24 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.003 0.001 HIS A1025 PHE 0.026 0.002 PHE B 847 TYR 0.009 0.001 TYR B 789 ARG 0.003 0.000 ARG B1192 *********************** 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 106 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.857 Fit side-chains REVERT: A 1003 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5652 (tm-30) REVERT: A 1080 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: B 1003 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5273 (tm-30) REVERT: B 1080 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 1206 GLN cc_start: 0.7234 (tt0) cc_final: 0.6645 (tm-30) outliers start: 25 outliers final: 12 residues processed: 89 average time/residue: 1.7432 time to fit residues: 162.2994 Evaluate side-chains 92 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 1080 GLU Chi-restraints excluded: chain A residue 1155 MET Chi-restraints excluded: chain A residue 1199 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 1199 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 73 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115020 restraints weight = 9614.351| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.29 r_work: 0.3433 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.0832 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= 0.151 Angle : 0.472 5.533 11254 Z= 0.236 Chirality : 0.039 0.139 1346 Planarity : 0.005 0.036 1382 Dihedral : 3.486 20.482 1110 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.08 % Allowed : 12.19 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.27), residues: 1020 helix: 2.18 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.10 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 795 HIS 0.002 0.000 HIS A1025 PHE 0.014 0.001 PHE B 847 TYR 0.007 0.001 TYR B 789 ARG 0.004 0.000 ARG B1017 *********************** 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 111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.940 Fit side-chains REVERT: B 1003 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5139 (tm-30) REVERT: B 1206 GLN cc_start: 0.7174 (tt0) cc_final: 0.6535 (tm-30) outliers start: 27 outliers final: 11 residues processed: 94 average time/residue: 1.6860 time to fit residues: 165.9046 Evaluate side-chains 90 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 1199 LEU Chi-restraints excluded: chain B residue 1210 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 73 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1081 GLN B1201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116668 restraints weight = 9534.202| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.27 r_work: 0.3453 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8266 Z= 0.145 Angle : 0.460 5.083 11254 Z= 0.229 Chirality : 0.038 0.133 1346 Planarity : 0.004 0.036 1382 Dihedral : 3.359 18.268 1110 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.62 % Allowed : 13.67 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 1020 helix: 2.32 (0.20), residues: 702 sheet: None (None), residues: 0 loop : 0.04 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 795 HIS 0.002 0.000 HIS A1025 PHE 0.012 0.001 PHE B 822 TYR 0.007 0.001 TYR B 789 ARG 0.004 0.000 ARG B1017 *********************** 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 112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.926 Fit side-chains REVERT: A 1003 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: B 1003 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5140 (tm-30) REVERT: B 1206 GLN cc_start: 0.7110 (tt0) cc_final: 0.6476 (tm-30) outliers start: 23 outliers final: 7 residues processed: 98 average time/residue: 1.6429 time to fit residues: 168.6862 Evaluate side-chains 88 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 1003 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1081 GLN B1201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113605 restraints weight = 9544.212| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.31 r_work: 0.3418 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.003 0.032 8266 Z= 0.206 Angle : 0.489 5.127 11254 Z= 0.245 Chirality : 0.040 0.139 1346 Planarity : 0.005 0.037 1382 Dihedral : 3.419 17.816 1110 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.73 % Allowed : 14.12 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 1020 helix: 2.17 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.09 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.002 0.001 HIS A1156 PHE 0.017 0.001 PHE B 847 TYR 0.007 0.001 TYR B 789 ARG 0.003 0.000 ARG B1017 *********************** 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 105 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.893 Fit side-chains REVERT: A 738 MET cc_start: 0.8590 (mtm) cc_final: 0.8349 (mtm) REVERT: A 1199 LEU cc_start: 0.7885 (tp) cc_final: 0.7566 (tp) REVERT: B 1003 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5265 (tm-30) REVERT: B 1206 GLN cc_start: 0.7078 (tt0) cc_final: 0.6480 (tm-30) REVERT: B 1210 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6426 (p) outliers start: 24 outliers final: 11 residues processed: 88 average time/residue: 1.8688 time to fit residues: 171.7328 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 : 0.923 ------------------------------------------------------------------------------- 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 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 1019 LEU Chi-restraints excluded: chain B residue 1186 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 33 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.144680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116554 restraints weight = 9637.077| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.33 r_work: 0.3459 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1100 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= 0.152 Angle : 0.457 5.111 11254 Z= 0.229 Chirality : 0.038 0.132 1346 Planarity : 0.004 0.035 1382 Dihedral : 3.326 17.444 1110 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.96 % Allowed : 14.46 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.27), residues: 1020 helix: 2.38 (0.20), residues: 700 sheet: None (None), residues: 0 loop : 0.03 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.002 0.000 HIS A1025 PHE 0.012 0.001 PHE B 822 TYR 0.006 0.001 TYR B 789 ARG 0.005 0.000 ARG B1017 *********************** 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 110 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.882 Fit side-chains REVERT: A 1199 LEU cc_start: 0.7837 (tp) cc_final: 0.7513 (tp) REVERT: B 838 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 1003 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5137 (tm-30) REVERT: B 1206 GLN cc_start: 0.7065 (tt0) cc_final: 0.6438 (tm-30) REVERT: B 1210 SER cc_start: 0.7309 (OUTLIER) cc_final: 0.6674 (p) outliers start: 26 outliers final: 8 residues processed: 93 average time/residue: 1.7339 time to fit residues: 168.8230 Evaluate side-chains 91 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 1019 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 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN B1081 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100715 restraints weight = 9787.457| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.44 r_work: 0.3043 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8266 Z= 0.338 Angle : 0.558 5.661 11254 Z= 0.281 Chirality : 0.043 0.149 1346 Planarity : 0.005 0.042 1382 Dihedral : 3.628 16.617 1110 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.73 % Allowed : 14.69 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.27), residues: 1020 helix: 1.91 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.21 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 795 HIS 0.003 0.001 HIS A 850 PHE 0.023 0.002 PHE B 847 TYR 0.010 0.001 TYR B1146 ARG 0.008 0.001 ARG A1203 *********************** 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 109 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.871 Fit side-chains REVERT: A 738 MET cc_start: 0.8414 (mtm) cc_final: 0.8159 (mtm) REVERT: A 1199 LEU cc_start: 0.7397 (tp) cc_final: 0.7106 (tp) REVERT: B 817 ARG cc_start: 0.7469 (ptm160) cc_final: 0.6721 (ptt180) REVERT: B 838 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 1003 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5055 (tm-30) REVERT: B 1206 GLN cc_start: 0.6677 (tt0) cc_final: 0.6092 (tm-30) outliers start: 24 outliers final: 12 residues processed: 93 average time/residue: 1.7271 time to fit residues: 167.7825 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 : 0.933 ------------------------------------------------------------------------------- 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 1019 LEU Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN B1081 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104024 restraints weight = 9746.484| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.46 r_work: 0.3090 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1060 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= 0.198 Angle : 0.495 6.405 11254 Z= 0.248 Chirality : 0.040 0.139 1346 Planarity : 0.005 0.038 1382 Dihedral : 3.525 17.933 1110 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.39 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.27), residues: 1020 helix: 2.14 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.13 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.002 0.001 HIS A1156 PHE 0.015 0.001 PHE B 822 TYR 0.007 0.001 TYR B 789 ARG 0.007 0.000 ARG B1017 *********************** 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 98 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.959 Fit side-chains REVERT: A 738 MET cc_start: 0.8373 (mtm) cc_final: 0.8116 (mtm) REVERT: A 1199 LEU cc_start: 0.7474 (tp) cc_final: 0.7222 (tp) REVERT: B 817 ARG cc_start: 0.7401 (ptm160) cc_final: 0.6658 (ptt180) REVERT: B 838 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6722 (mm-30) REVERT: B 1003 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.4920 (tm-30) REVERT: B 1206 GLN cc_start: 0.6601 (tt0) cc_final: 0.6021 (tm-30) REVERT: B 1210 SER cc_start: 0.7145 (OUTLIER) cc_final: 0.6520 (p) outliers start: 21 outliers final: 11 residues processed: 83 average time/residue: 1.7936 time to fit residues: 155.7854 Evaluate side-chains 90 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN B1081 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101077 restraints weight = 9670.677| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.44 r_work: 0.3046 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8266 Z= 0.293 Angle : 0.553 8.243 11254 Z= 0.276 Chirality : 0.042 0.146 1346 Planarity : 0.005 0.041 1382 Dihedral : 3.664 17.233 1110 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.82 % Allowed : 16.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 1020 helix: 1.91 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.003 0.001 HIS A 850 PHE 0.021 0.002 PHE B 847 TYR 0.009 0.001 TYR B1146 ARG 0.007 0.000 ARG B1017 ********************** 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 97 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.948 Fit side-chains REVERT: A 738 MET cc_start: 0.8428 (mtm) cc_final: 0.8168 (mtm) REVERT: A 785 GLN cc_start: 0.7185 (tp40) cc_final: 0.6983 (tp40) REVERT: A 1199 LEU cc_start: 0.7430 (tp) cc_final: 0.7200 (tp) REVERT: B 817 ARG cc_start: 0.7435 (ptm160) cc_final: 0.6695 (ptt180) REVERT: B 838 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6720 (mm-30) REVERT: B 1003 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5021 (tm-30) REVERT: B 1199 LEU cc_start: 0.7364 (tp) cc_final: 0.7161 (tp) REVERT: B 1206 GLN cc_start: 0.6603 (tt0) cc_final: 0.5997 (tm-30) REVERT: B 1210 SER cc_start: 0.7283 (OUTLIER) cc_final: 0.6576 (p) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 1.7315 time to fit residues: 155.8538 Evaluate side-chains 88 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 70 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN B1081 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114358 restraints weight = 9643.508| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.33 r_work: 0.3424 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8266 Z= 0.173 Angle : 0.477 4.964 11254 Z= 0.240 Chirality : 0.039 0.138 1346 Planarity : 0.005 0.037 1382 Dihedral : 3.498 18.020 1110 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.82 % Allowed : 16.17 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1020 helix: 2.22 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.14 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.002 0.001 HIS A1025 PHE 0.013 0.001 PHE B 847 TYR 0.008 0.001 TYR A 789 ARG 0.007 0.000 ARG B1017 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6396.73 seconds wall clock time: 113 minutes 7.69 seconds (6787.69 seconds total)