Starting phenix.real_space_refine on Sat Dec 28 08:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvc_34290/12_2024/8gvc_34290_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvc_34290/12_2024/8gvc_34290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvc_34290/12_2024/8gvc_34290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvc_34290/12_2024/8gvc_34290.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvc_34290/12_2024/8gvc_34290_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvc_34290/12_2024/8gvc_34290_trim.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.165 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 46 5.16 5 C 5372 2.51 5 N 1326 2.21 5 O 1336 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-5532/modules/chem_data/mon_lib" Total number of atoms: 8080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4036 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 27, 'TRANS': 483} Chain breaks: 1 Chain: "B" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4036 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 27, 'TRANS': 483} 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: 5.04, per 1000 atoms: 0.62 Number of scatterers: 8080 At special positions: 0 Unit cell: (89.1, 129.8, 81.4, 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 46 16.00 O 1336 8.00 N 1326 7.00 C 5372 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: 2.01 Conformation dependent library (CDL) restraints added in 931.8 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 73.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.801A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.626A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 740 through 758 Processing helix chain 'A' and resid 768 through 784 Processing helix chain 'A' and resid 791 through 810 removed outlier: 4.196A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 797 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 removed outlier: 3.857A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 4.107A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 845 " --> pdb=" O TYR A 841 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 923 removed outlier: 3.646A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.684A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.708A pdb=" N ARG A 976 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 997 removed outlier: 3.713A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1020 Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 3.570A pdb=" N ALA A1047 " --> pdb=" O GLY A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1057 through 1066 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1109 through 1113 removed outlier: 3.659A pdb=" N ILE A1113 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 3.883A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A1121 " --> pdb=" O VAL A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 removed outlier: 3.660A pdb=" N HIS A1140 " --> pdb=" O TYR A1136 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.762A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.567A pdb=" N LYS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1152 through 1157' Processing helix chain 'A' and resid 1159 through 1183 Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 3.996A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.816A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.637A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 718 " --> pdb=" O PHE B 714 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 740 through 758 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.877A pdb=" N GLY B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 819 removed outlier: 3.971A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 removed outlier: 4.099A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 843 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 844 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS B 845 " --> pdb=" O TYR B 841 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 923 removed outlier: 3.517A pdb=" N LEU B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.661A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 removed outlier: 3.700A pdb=" N ARG B 976 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 997 removed outlier: 3.837A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1019 Processing helix chain 'B' and resid 1033 through 1047 removed outlier: 3.534A pdb=" N ALA B1047 " --> pdb=" O GLY B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1058 through 1066 Processing helix chain 'B' and resid 1091 through 1102 Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.637A pdb=" N ILE B1113 " --> pdb=" O LEU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 3.883A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1141 removed outlier: 3.726A pdb=" N LEU B1141 " --> pdb=" O GLU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.589A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.612A pdb=" N LYS B1156 " --> pdb=" O VAL B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1183 Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1188 through 1195 Processing helix chain 'B' and resid 1195 through 1208 removed outlier: 3.933A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B1205 " --> pdb=" O MET B1201 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1217 Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766 removed outlier: 3.527A pdb=" N ALA A1055 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.618A pdb=" N ALA B1055 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1070 through 1071 removed outlier: 3.507A pdb=" N GLU B1085 " --> pdb=" O VAL B1070 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1368 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: 2.15 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2224 1.33 - 1.45: 1259 1.45 - 1.57: 4717 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8278 Sorted by residual: bond pdb=" C BCT B1301 " pdb=" O3 BCT B1301 " ideal model delta sigma weight residual 1.389 1.311 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C BCT A1301 " pdb=" O3 BCT A1301 " ideal model delta sigma weight residual 1.389 1.311 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CA SER B 768 " pdb=" C SER B 768 " ideal model delta sigma weight residual 1.521 1.506 0.015 1.20e-02 6.94e+03 1.64e+00 bond pdb=" C BCT A1301 " pdb=" O2 BCT A1301 " ideal model delta sigma weight residual 1.241 1.217 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" CA SER A 768 " pdb=" C SER A 768 " ideal model delta sigma weight residual 1.521 1.507 0.014 1.20e-02 6.94e+03 1.44e+00 ... (remaining 8273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 11152 2.42 - 4.84: 70 4.84 - 7.26: 7 7.26 - 9.68: 1 9.68 - 12.10: 2 Bond angle restraints: 11232 Sorted by residual: angle pdb=" N VAL B 948 " pdb=" CA VAL B 948 " pdb=" C VAL B 948 " ideal model delta sigma weight residual 110.72 104.86 5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" N VAL A 948 " pdb=" CA VAL A 948 " pdb=" C VAL A 948 " ideal model delta sigma weight residual 110.72 104.87 5.85 1.01e+00 9.80e-01 3.36e+01 angle pdb=" N ILE A 946 " pdb=" CA ILE A 946 " pdb=" C ILE A 946 " ideal model delta sigma weight residual 110.42 114.55 -4.13 9.60e-01 1.09e+00 1.85e+01 angle pdb=" N ILE B 946 " pdb=" CA ILE B 946 " pdb=" C ILE B 946 " ideal model delta sigma weight residual 110.42 114.52 -4.10 9.60e-01 1.09e+00 1.82e+01 angle pdb=" O1 BCT B1301 " pdb=" C BCT B1301 " pdb=" O2 BCT B1301 " ideal model delta sigma weight residual 129.92 117.82 12.10 3.00e+00 1.11e-01 1.63e+01 ... (remaining 11227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4266 16.11 - 32.22: 482 32.22 - 48.33: 115 48.33 - 64.45: 24 64.45 - 80.56: 7 Dihedral angle restraints: 4894 sinusoidal: 1950 harmonic: 2944 Sorted by residual: dihedral pdb=" CG ARG B 691 " pdb=" CD ARG B 691 " pdb=" NE ARG B 691 " pdb=" CZ ARG B 691 " ideal model delta sinusoidal sigma weight residual 180.00 137.33 42.67 2 1.50e+01 4.44e-03 9.80e+00 dihedral pdb=" CG ARG A 691 " pdb=" CD ARG A 691 " pdb=" NE ARG A 691 " pdb=" CZ ARG A 691 " ideal model delta sinusoidal sigma weight residual 180.00 137.42 42.58 2 1.50e+01 4.44e-03 9.77e+00 dihedral pdb=" CB MET B 745 " pdb=" CG MET B 745 " pdb=" SD MET B 745 " pdb=" CE MET B 745 " ideal model delta sinusoidal sigma weight residual -180.00 -120.30 -59.70 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1006 0.039 - 0.077: 252 0.077 - 0.116: 62 0.116 - 0.154: 9 0.154 - 0.193: 1 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA GLU A 955 " pdb=" N GLU A 955 " pdb=" C GLU A 955 " pdb=" CB GLU A 955 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA VAL B 964 " pdb=" N VAL B 964 " pdb=" C VAL B 964 " pdb=" CB VAL B 964 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE A 946 " pdb=" N ILE A 946 " pdb=" C ILE A 946 " pdb=" CB ILE A 946 " both_signs ideal model delta sigma weight residual False 2.43 2.31 0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1327 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT B1301 " 0.064 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" O1 BCT B1301 " -0.021 2.00e-02 2.50e+03 pdb=" O2 BCT B1301 " -0.022 2.00e-02 2.50e+03 pdb=" O3 BCT B1301 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C BCT A1301 " 0.033 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" O1 BCT A1301 " -0.012 2.00e-02 2.50e+03 pdb=" O2 BCT A1301 " -0.011 2.00e-02 2.50e+03 pdb=" O3 BCT A1301 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 693 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.72e+00 pdb=" N PRO B 694 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " -0.023 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 10 2.32 - 2.96: 3948 2.96 - 3.61: 11248 3.61 - 4.25: 16924 4.25 - 4.90: 29953 Nonbonded interactions: 62083 Sorted by model distance: nonbonded pdb=" OG SER A 820 " pdb=" CZ ARG A1200 " model vdw 1.670 3.270 nonbonded pdb=" OG SER A 820 " pdb=" NE ARG A1200 " model vdw 1.925 3.120 nonbonded pdb=" O ALA B1057 " pdb=" OG1 THR B1058 " model vdw 2.031 3.040 nonbonded pdb=" O ASP A 956 " pdb=" OD1 ASP A 956 " model vdw 2.059 3.040 nonbonded pdb=" OD1 ASP A1151 " pdb=" NZ LYS A1156 " model vdw 2.148 3.120 ... (remaining 62078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.170 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.490 Find NCS groups from input model: 0.210 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 8278 Z= 0.173 Angle : 0.481 12.101 11232 Z= 0.267 Chirality : 0.036 0.193 1330 Planarity : 0.003 0.041 1380 Dihedral : 14.663 80.557 2990 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.97 % Favored : 97.83 % Rotamer: Outliers : 1.14 % Allowed : 13.10 % 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: 2.06 (0.28), residues: 1014 helix: 2.37 (0.22), residues: 652 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 795 HIS 0.002 0.001 HIS A1149 PHE 0.008 0.001 PHE B 938 TYR 0.007 0.001 TYR B1124 ARG 0.009 0.000 ARG B1206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.893 Fit side-chains REVERT: A 687 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6906 (mtp180) REVERT: A 1163 MET cc_start: 0.7431 (ttp) cc_final: 0.6840 (ttp) REVERT: B 1205 THR cc_start: 0.8454 (m) cc_final: 0.8070 (p) REVERT: B 1206 ARG cc_start: 0.7333 (mtm110) cc_final: 0.6710 (ttp-170) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 1.3653 time to fit residues: 190.1515 Evaluate side-chains 125 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1183 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8278 Z= 0.195 Angle : 0.534 8.626 11232 Z= 0.271 Chirality : 0.039 0.138 1330 Planarity : 0.005 0.055 1380 Dihedral : 3.926 24.207 1105 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.76 % Favored : 97.04 % Rotamer: Outliers : 1.82 % Allowed : 13.55 % Favored : 84.62 % 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: 1.98 (0.28), residues: 1014 helix: 2.29 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 795 HIS 0.005 0.001 HIS B 850 PHE 0.012 0.001 PHE B 774 TYR 0.009 0.001 TYR A1124 ARG 0.006 0.000 ARG B1206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.842 Fit side-chains REVERT: A 687 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6880 (mtm110) REVERT: A 701 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6767 (mtt-85) REVERT: A 1023 GLU cc_start: 0.6754 (mp0) cc_final: 0.6391 (mp0) REVERT: B 1206 ARG cc_start: 0.7283 (mtm110) cc_final: 0.6872 (ttp-170) outliers start: 16 outliers final: 9 residues processed: 128 average time/residue: 1.4285 time to fit residues: 192.7330 Evaluate side-chains 118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8278 Z= 0.249 Angle : 0.545 8.676 11232 Z= 0.279 Chirality : 0.040 0.151 1330 Planarity : 0.005 0.058 1380 Dihedral : 3.712 22.351 1097 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer: Outliers : 2.05 % Allowed : 14.12 % Favored : 83.83 % 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 (0.27), residues: 1014 helix: 2.13 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 795 HIS 0.006 0.001 HIS B 850 PHE 0.011 0.001 PHE B 774 TYR 0.014 0.001 TYR B1124 ARG 0.003 0.000 ARG B 933 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.921 Fit side-chains REVERT: A 687 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6987 (mtm110) REVERT: A 701 ARG cc_start: 0.7084 (mtt-85) cc_final: 0.6859 (mtt-85) REVERT: A 1023 GLU cc_start: 0.6889 (mp0) cc_final: 0.6339 (mp0) REVERT: B 1023 GLU cc_start: 0.7228 (mp0) cc_final: 0.6852 (mp0) REVERT: B 1071 MET cc_start: 0.8256 (mmm) cc_final: 0.7953 (mmt) REVERT: B 1206 ARG cc_start: 0.7166 (mtm110) cc_final: 0.6897 (ttp-170) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 1.4085 time to fit residues: 177.1071 Evaluate side-chains 117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 0.0060 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8278 Z= 0.144 Angle : 0.468 8.436 11232 Z= 0.238 Chirality : 0.037 0.135 1330 Planarity : 0.004 0.056 1380 Dihedral : 3.512 17.905 1097 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.37 % Favored : 97.44 % Rotamer: Outliers : 1.71 % Allowed : 15.15 % 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: 1.95 (0.27), residues: 1014 helix: 2.26 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 795 HIS 0.005 0.001 HIS B 850 PHE 0.009 0.001 PHE B 774 TYR 0.006 0.001 TYR A1154 ARG 0.005 0.000 ARG A 933 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.908 Fit side-chains REVERT: A 687 ARG cc_start: 0.7351 (mtm110) cc_final: 0.7029 (mtm110) REVERT: A 701 ARG cc_start: 0.7063 (mtt-85) cc_final: 0.6800 (mtt-85) REVERT: A 1023 GLU cc_start: 0.6914 (mp0) cc_final: 0.6460 (mp0) REVERT: B 1023 GLU cc_start: 0.7285 (mp0) cc_final: 0.6867 (mp0) REVERT: B 1206 ARG cc_start: 0.7205 (mtm110) cc_final: 0.6995 (ttp-170) outliers start: 15 outliers final: 9 residues processed: 133 average time/residue: 1.3631 time to fit residues: 191.6559 Evaluate side-chains 115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8278 Z= 0.373 Angle : 0.625 11.457 11232 Z= 0.314 Chirality : 0.043 0.176 1330 Planarity : 0.005 0.058 1380 Dihedral : 3.895 20.573 1097 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 2.62 % Allowed : 15.95 % Favored : 81.44 % 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: 1.49 (0.27), residues: 1014 helix: 1.92 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.82 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 795 HIS 0.005 0.001 HIS B 850 PHE 0.012 0.002 PHE A 835 TYR 0.017 0.002 TYR B1124 ARG 0.003 0.000 ARG A 933 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.846 Fit side-chains REVERT: A 687 ARG cc_start: 0.7354 (mtm110) cc_final: 0.6984 (mtm110) REVERT: A 1023 GLU cc_start: 0.7129 (mp0) cc_final: 0.6536 (mp0) REVERT: B 925 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: B 1023 GLU cc_start: 0.7357 (mp0) cc_final: 0.6766 (mp0) REVERT: B 1206 ARG cc_start: 0.7260 (mtm110) cc_final: 0.6967 (ttp-170) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 1.5367 time to fit residues: 191.1295 Evaluate side-chains 116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1183 THR Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 925 ARG Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8278 Z= 0.288 Angle : 0.568 9.614 11232 Z= 0.287 Chirality : 0.041 0.159 1330 Planarity : 0.005 0.058 1380 Dihedral : 3.892 21.639 1097 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.94 % Rotamer: Outliers : 2.39 % Allowed : 16.29 % Favored : 81.32 % 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: 1.42 (0.27), residues: 1014 helix: 1.88 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.88 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 795 HIS 0.005 0.001 HIS B 850 PHE 0.011 0.001 PHE A 835 TYR 0.013 0.001 TYR B1124 ARG 0.003 0.000 ARG A 933 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.942 Fit side-chains REVERT: A 687 ARG cc_start: 0.7314 (mtm110) cc_final: 0.6949 (mtm110) REVERT: A 1023 GLU cc_start: 0.7097 (mp0) cc_final: 0.6666 (mp0) REVERT: A 1082 LYS cc_start: 0.6921 (pttm) cc_final: 0.6668 (ptmm) REVERT: B 1023 GLU cc_start: 0.7398 (mp0) cc_final: 0.6822 (mp0) REVERT: B 1071 MET cc_start: 0.8278 (mmm) cc_final: 0.8001 (mmt) REVERT: B 1206 ARG cc_start: 0.7300 (mtm110) cc_final: 0.7095 (ttp-170) outliers start: 21 outliers final: 17 residues processed: 117 average time/residue: 1.4320 time to fit residues: 176.9598 Evaluate side-chains 115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1045 ILE Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8278 Z= 0.180 Angle : 0.505 8.601 11232 Z= 0.254 Chirality : 0.038 0.138 1330 Planarity : 0.005 0.059 1380 Dihedral : 3.697 18.716 1097 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.96 % Favored : 96.84 % Rotamer: Outliers : 1.94 % Allowed : 17.20 % Favored : 80.87 % 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: 1.65 (0.27), residues: 1014 helix: 2.06 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.78 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 795 HIS 0.005 0.001 HIS B 850 PHE 0.010 0.001 PHE B 774 TYR 0.008 0.001 TYR A1124 ARG 0.003 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.896 Fit side-chains REVERT: A 687 ARG cc_start: 0.7341 (mtm110) cc_final: 0.6997 (mtm110) REVERT: A 1023 GLU cc_start: 0.7005 (mp0) cc_final: 0.6487 (mp0) REVERT: A 1082 LYS cc_start: 0.6903 (pttm) cc_final: 0.6658 (ptmm) REVERT: B 895 ARG cc_start: 0.7115 (mpt-90) cc_final: 0.6907 (ttm110) REVERT: B 1023 GLU cc_start: 0.7283 (mp0) cc_final: 0.6725 (mp0) REVERT: B 1071 MET cc_start: 0.8296 (mmm) cc_final: 0.8013 (mmt) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 1.4335 time to fit residues: 186.0590 Evaluate side-chains 119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1194 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8278 Z= 0.187 Angle : 0.511 8.115 11232 Z= 0.255 Chirality : 0.038 0.143 1330 Planarity : 0.005 0.059 1380 Dihedral : 3.658 17.355 1097 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 18.11 % Favored : 80.75 % 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: 1.72 (0.27), residues: 1014 helix: 2.11 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.75 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 795 HIS 0.006 0.001 HIS B 850 PHE 0.010 0.001 PHE B 774 TYR 0.011 0.001 TYR B1124 ARG 0.008 0.000 ARG B 933 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.036 Fit side-chains REVERT: A 687 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6990 (mtm110) REVERT: A 1023 GLU cc_start: 0.7016 (mp0) cc_final: 0.6546 (mp0) REVERT: A 1082 LYS cc_start: 0.6909 (pttm) cc_final: 0.6660 (ptmm) REVERT: B 1023 GLU cc_start: 0.7289 (mp0) cc_final: 0.6724 (mp0) REVERT: B 1071 MET cc_start: 0.8289 (mmm) cc_final: 0.8003 (mmt) outliers start: 10 outliers final: 9 residues processed: 116 average time/residue: 1.4797 time to fit residues: 180.9106 Evaluate side-chains 111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1194 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 60 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8278 Z= 0.141 Angle : 0.475 9.913 11232 Z= 0.236 Chirality : 0.037 0.133 1330 Planarity : 0.004 0.058 1380 Dihedral : 3.476 16.929 1096 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer: Outliers : 1.14 % Allowed : 18.56 % Favored : 80.30 % 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: 1.97 (0.27), residues: 1014 helix: 2.30 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.64 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 795 HIS 0.005 0.001 HIS B 850 PHE 0.009 0.001 PHE B 774 TYR 0.006 0.001 TYR A1154 ARG 0.008 0.000 ARG B 933 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.824 Fit side-chains REVERT: A 687 ARG cc_start: 0.7335 (mtm110) cc_final: 0.7029 (mtm110) REVERT: A 1023 GLU cc_start: 0.6867 (mp0) cc_final: 0.6304 (mp0) REVERT: A 1082 LYS cc_start: 0.6885 (pttm) cc_final: 0.6636 (ptmm) REVERT: A 1200 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7131 (tmt-80) REVERT: B 752 VAL cc_start: 0.8428 (t) cc_final: 0.8222 (t) REVERT: B 1023 GLU cc_start: 0.7228 (mp0) cc_final: 0.6805 (mp0) REVERT: B 1200 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7198 (tmt-80) outliers start: 10 outliers final: 7 residues processed: 120 average time/residue: 1.4611 time to fit residues: 184.6765 Evaluate side-chains 117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1194 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8278 Z= 0.197 Angle : 0.528 10.610 11232 Z= 0.258 Chirality : 0.039 0.145 1330 Planarity : 0.005 0.058 1380 Dihedral : 3.569 17.002 1096 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.75 % Rotamer: Outliers : 0.80 % Allowed : 18.56 % Favored : 80.64 % 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: 1.92 (0.27), residues: 1014 helix: 2.27 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.70 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 795 HIS 0.006 0.001 HIS B 850 PHE 0.009 0.001 PHE B 774 TYR 0.012 0.001 TYR A1124 ARG 0.007 0.000 ARG B 933 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.927 Fit side-chains REVERT: A 687 ARG cc_start: 0.7322 (mtm110) cc_final: 0.7010 (mtm110) REVERT: A 1023 GLU cc_start: 0.7033 (mp0) cc_final: 0.6464 (mp0) REVERT: A 1200 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7166 (tmt-80) REVERT: A 1214 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7605 (mmmt) REVERT: B 895 ARG cc_start: 0.7108 (mpt-90) cc_final: 0.6832 (ttm110) REVERT: B 1023 GLU cc_start: 0.7301 (mp0) cc_final: 0.6838 (mp0) REVERT: B 1200 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7280 (tmt-80) outliers start: 7 outliers final: 7 residues processed: 113 average time/residue: 1.5509 time to fit residues: 184.1272 Evaluate side-chains 114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1194 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.157857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116959 restraints weight = 8407.140| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.92 r_work: 0.3334 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8278 Z= 0.201 Angle : 0.535 10.247 11232 Z= 0.261 Chirality : 0.039 0.145 1330 Planarity : 0.005 0.058 1380 Dihedral : 3.609 17.276 1096 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 1.37 % Allowed : 18.34 % Favored : 80.30 % 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: 1014 helix: 2.25 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.70 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.006 0.001 HIS B 850 PHE 0.009 0.001 PHE B 774 TYR 0.010 0.001 TYR A1124 ARG 0.008 0.000 ARG B 817 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.91 seconds wall clock time: 59 minutes 21.33 seconds (3561.33 seconds total)