Starting phenix.real_space_refine on Wed Mar 12 17:03:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvf_34292/03_2025/8gvf_34292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvf_34292/03_2025/8gvf_34292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvf_34292/03_2025/8gvf_34292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvf_34292/03_2025/8gvf_34292.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvf_34292/03_2025/8gvf_34292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvf_34292/03_2025/8gvf_34292.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.145 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 5370 2.51 5 N 1326 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8072 Number of models: 1 Model: "" Number of chains: 2 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 Time building chain proxies: 5.01, per 1000 atoms: 0.62 Number of scatterers: 8072 At special positions: 0 Unit cell: (84.7, 135.3, 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 1330 8.00 N 1326 7.00 C 5370 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: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 58 helices and 4 sheets defined 73.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.536A pdb=" N PHE A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.606A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.783A 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 removed outlier: 3.569A pdb=" N LEU A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 810 removed outlier: 4.175A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 797 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.758A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 818 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.529A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 843 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 844 " --> pdb=" O PHE A 840 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 845 " --> pdb=" O TYR A 841 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 921 removed outlier: 3.507A pdb=" N SER A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 924 No H-bonds generated for 'chain 'A' and resid 922 through 924' Processing helix chain 'A' and resid 928 through 938 Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.781A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.928A pdb=" N ARG A 976 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.694A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1020 removed outlier: 3.579A pdb=" N ALA A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1047 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: 3.691A pdb=" N ILE A1113 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 4.034A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A1120 " --> pdb=" O ALA A1116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1121 " --> pdb=" O VAL A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 removed outlier: 3.687A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.945A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.729A pdb=" N LYS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.522A pdb=" N MET A1181 " --> pdb=" O LEU A1177 " (cutoff:3.500A) 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: 3.562A pdb=" N LEU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1201 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 3.640A pdb=" N CYS A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.561A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.618A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 717 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 3.784A 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 removed outlier: 3.518A pdb=" N LEU B 772 " --> pdb=" O SER B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 4.139A pdb=" N GLY B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 818 removed outlier: 3.897A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.531A pdb=" N GLN B 824 " --> pdb=" O SER B 820 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 843 " --> pdb=" O THR B 839 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 844 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 845 " --> pdb=" O TYR B 841 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 921 removed outlier: 3.647A pdb=" N LEU B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 924 No H-bonds generated for 'chain 'B' and resid 922 through 924' Processing helix chain 'B' and resid 928 through 938 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.787A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 removed outlier: 3.890A pdb=" N ARG B 976 " --> pdb=" O PRO B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 997 removed outlier: 3.789A pdb=" N MET B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 removed outlier: 3.550A pdb=" N ALA B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1047 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: 3.650A pdb=" N ILE B1113 " --> pdb=" O LEU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 4.058A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B1120 " --> pdb=" O ALA B1116 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1141 removed outlier: 3.692A pdb=" N LEU B1141 " --> pdb=" O GLU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.758A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.814A 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: 4.018A pdb=" N LEU B1204 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.367A 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: 3.622A 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 removed outlier: 6.810A pdb=" N VAL A1070 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.593A 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: 6.773A pdb=" N VAL B1070 " --> pdb=" O GLN B1084 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1341 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: 2.25 Time building geometry restraints manager: 2.09 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: 2457 1.34 - 1.46: 1194 1.46 - 1.57: 4543 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8272 Sorted by residual: bond pdb=" CG1 ILE A 834 " pdb=" CD1 ILE A 834 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 bond pdb=" CA SER B1103 " pdb=" C SER B1103 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.80e-02 3.09e+03 1.35e+00 bond pdb=" CA VAL B 819 " pdb=" CB VAL B 819 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.24e+00 bond pdb=" CG LYS B1022 " pdb=" CD LYS B1022 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" N THR B1058 " pdb=" CA THR B1058 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.08e+00 ... (remaining 8267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10943 1.67 - 3.33: 228 3.33 - 5.00: 43 5.00 - 6.67: 9 6.67 - 8.33: 3 Bond angle restraints: 11226 Sorted by residual: angle pdb=" C ALA B1057 " pdb=" N THR B1058 " pdb=" CA THR B1058 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ALA B1074 " pdb=" N VAL B1075 " pdb=" CA VAL B1075 " ideal model delta sigma weight residual 121.97 127.85 -5.88 1.80e+00 3.09e-01 1.07e+01 angle pdb=" CB LYS A1022 " pdb=" CG LYS A1022 " pdb=" CD LYS A1022 " ideal model delta sigma weight residual 111.30 118.53 -7.23 2.30e+00 1.89e-01 9.88e+00 angle pdb=" CB LYS B1022 " pdb=" CG LYS B1022 " pdb=" CD LYS B1022 " ideal model delta sigma weight residual 111.30 118.44 -7.14 2.30e+00 1.89e-01 9.64e+00 angle pdb=" N LYS A1073 " pdb=" CA LYS A1073 " pdb=" C LYS A1073 " ideal model delta sigma weight residual 108.19 112.16 -3.97 1.29e+00 6.01e-01 9.47e+00 ... (remaining 11221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4411 17.95 - 35.89: 410 35.89 - 53.84: 56 53.84 - 71.78: 11 71.78 - 89.73: 6 Dihedral angle restraints: 4894 sinusoidal: 1950 harmonic: 2944 Sorted by residual: dihedral pdb=" CA SER B1072 " pdb=" C SER B1072 " pdb=" N LYS B1073 " pdb=" CA LYS B1073 " ideal model delta harmonic sigma weight residual 180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 784 " pdb=" C SER A 784 " pdb=" N ASN A 785 " pdb=" CA ASN A 785 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLY A1107 " pdb=" C GLY A1107 " pdb=" N ASP A1108 " pdb=" CA ASP A1108 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 726 0.030 - 0.060: 450 0.060 - 0.090: 84 0.090 - 0.120: 54 0.120 - 0.150: 16 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA ASN A1066 " pdb=" N ASN A1066 " pdb=" C ASN A1066 " pdb=" CB ASN A1066 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ASN B1066 " pdb=" N ASN B1066 " pdb=" C ASN B1066 " pdb=" CB ASN B1066 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA MET B 947 " pdb=" N MET B 947 " pdb=" C MET B 947 " pdb=" CB MET B 947 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1327 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 693 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 694 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 693 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO B 694 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 705 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 706 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 706 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 706 " 0.022 5.00e-02 4.00e+02 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2304 2.82 - 3.34: 7636 3.34 - 3.86: 12166 3.86 - 4.38: 13877 4.38 - 4.90: 25290 Nonbonded interactions: 61273 Sorted by model distance: nonbonded pdb=" N GLY A 684 " pdb=" OE2 GLU A 811 " model vdw 2.306 3.120 nonbonded pdb=" NE2 GLN B1089 " pdb=" OG1 THR B1092 " model vdw 2.314 3.120 nonbonded pdb=" N GLY B 684 " pdb=" OE2 GLU B 811 " model vdw 2.328 3.120 nonbonded pdb=" O ALA B1074 " pdb=" N ALA B1076 " model vdw 2.377 3.120 nonbonded pdb=" O GLY A 758 " pdb=" NH2 ARG A1090 " model vdw 2.432 3.120 ... (remaining 61268 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: 0.810 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: 0.090 Process input model: 20.940 Find NCS groups from input model: 0.250 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.005 0.046 8272 Z= 0.332 Angle : 0.637 8.332 11226 Z= 0.340 Chirality : 0.042 0.150 1330 Planarity : 0.005 0.063 1378 Dihedral : 14.001 89.730 2990 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.94 % Favored : 95.76 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1014 helix: 1.41 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.00 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.007 0.001 HIS A1149 PHE 0.009 0.002 PHE A1166 TYR 0.011 0.002 TYR B1124 ARG 0.002 0.000 ARG A 933 *********************** 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 145 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.958 Fit side-chains REVERT: A 688 ASP cc_start: 0.7135 (m-30) cc_final: 0.6919 (m-30) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.2453 time to fit residues: 46.2400 Evaluate side-chains 132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 ASN A1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102530 restraints weight = 8624.575| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.79 r_work: 0.2895 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8272 Z= 0.180 Angle : 0.531 8.753 11226 Z= 0.271 Chirality : 0.039 0.139 1330 Planarity : 0.005 0.068 1378 Dihedral : 4.299 49.426 1099 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.85 % Favored : 95.86 % Rotamer: Outliers : 1.48 % Allowed : 5.81 % Favored : 92.71 % 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: 1.29 (0.27), residues: 1014 helix: 1.81 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.004 0.001 HIS A1149 PHE 0.010 0.001 PHE A 774 TYR 0.010 0.001 TYR B1124 ARG 0.003 0.000 ARG B 690 *********************** 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 150 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 805 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7256 (mp) REVERT: B 688 ASP cc_start: 0.6485 (m-30) cc_final: 0.6263 (m-30) REVERT: B 738 ILE cc_start: 0.8250 (mt) cc_final: 0.8026 (mt) REVERT: B 805 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7348 (mp) outliers start: 13 outliers final: 7 residues processed: 141 average time/residue: 0.2365 time to fit residues: 43.7712 Evaluate side-chains 140 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain B residue 805 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 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 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 = 0.3562 r_free = 0.3562 target = 0.141999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102356 restraints weight = 8749.841| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.85 r_work: 0.2894 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8272 Z= 0.197 Angle : 0.513 8.722 11226 Z= 0.262 Chirality : 0.039 0.136 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.697 18.285 1096 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.94 % Favored : 95.76 % Rotamer: Outliers : 1.14 % Allowed : 8.20 % Favored : 90.66 % 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: 1.40 (0.27), residues: 1014 helix: 1.93 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.05 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.005 0.001 HIS A 786 PHE 0.010 0.001 PHE A 774 TYR 0.009 0.001 TYR A1124 ARG 0.006 0.000 ARG B 690 *********************** 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 144 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.826 Fit side-chains REVERT: A 805 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7277 (mp) REVERT: B 688 ASP cc_start: 0.6631 (m-30) cc_final: 0.6415 (m-30) REVERT: B 805 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7332 (mp) outliers start: 10 outliers final: 6 residues processed: 138 average time/residue: 0.2415 time to fit residues: 43.6591 Evaluate side-chains 139 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain B residue 805 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.145305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.107845 restraints weight = 8691.842| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.66 r_work: 0.2941 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8272 Z= 0.164 Angle : 0.482 8.636 11226 Z= 0.245 Chirality : 0.038 0.137 1330 Planarity : 0.005 0.067 1378 Dihedral : 3.567 17.255 1096 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.55 % Favored : 96.15 % Rotamer: Outliers : 1.37 % Allowed : 9.57 % Favored : 89.07 % 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: 1.55 (0.27), residues: 1014 helix: 2.06 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.00 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.003 0.001 HIS A1149 PHE 0.009 0.001 PHE A 774 TYR 0.009 0.001 TYR B1124 ARG 0.004 0.000 ARG B 690 *********************** 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 144 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.823 Fit side-chains REVERT: A 805 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7242 (mp) REVERT: B 688 ASP cc_start: 0.6655 (m-30) cc_final: 0.6419 (m-30) REVERT: B 805 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7268 (mp) outliers start: 12 outliers final: 8 residues processed: 138 average time/residue: 0.2290 time to fit residues: 41.6098 Evaluate side-chains 138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 947 MET Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.139085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100384 restraints weight = 8695.548| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.76 r_work: 0.2864 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8272 Z= 0.318 Angle : 0.565 8.597 11226 Z= 0.288 Chirality : 0.041 0.156 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.765 18.039 1096 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.04 % Favored : 95.76 % Rotamer: Outliers : 2.05 % Allowed : 10.48 % Favored : 87.47 % 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: 1.36 (0.27), residues: 1014 helix: 1.99 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.15 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 795 HIS 0.006 0.001 HIS A1149 PHE 0.009 0.001 PHE A1166 TYR 0.012 0.002 TYR B1124 ARG 0.002 0.000 ARG A1090 *********************** 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 150 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.945 Fit side-chains REVERT: A 805 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7317 (mp) REVERT: B 805 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7331 (mp) REVERT: B 1151 ASP cc_start: 0.7282 (t0) cc_final: 0.6783 (p0) outliers start: 18 outliers final: 10 residues processed: 139 average time/residue: 0.2304 time to fit residues: 42.1545 Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU 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 38 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.142658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102927 restraints weight = 8683.275| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.90 r_work: 0.2887 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8272 Z= 0.196 Angle : 0.505 8.545 11226 Z= 0.258 Chirality : 0.039 0.147 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.641 16.755 1096 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.75 % Favored : 96.06 % Rotamer: Outliers : 1.03 % Allowed : 11.96 % Favored : 87.02 % 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: 1.44 (0.27), residues: 1014 helix: 1.96 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -1.03 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 795 HIS 0.003 0.001 HIS A1149 PHE 0.010 0.001 PHE A 774 TYR 0.009 0.001 TYR A1124 ARG 0.002 0.000 ARG A1090 *********************** 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 146 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.909 Fit side-chains REVERT: A 805 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7333 (mp) REVERT: B 805 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7317 (mp) outliers start: 9 outliers final: 7 residues processed: 142 average time/residue: 0.2362 time to fit residues: 43.9966 Evaluate side-chains 143 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.141415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100980 restraints weight = 8644.605| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.99 r_work: 0.2874 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8272 Z= 0.198 Angle : 0.503 8.501 11226 Z= 0.256 Chirality : 0.039 0.149 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.599 16.266 1096 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 1.37 % Allowed : 11.96 % Favored : 86.67 % 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: 1.48 (0.27), residues: 1014 helix: 1.98 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 795 HIS 0.003 0.001 HIS A1149 PHE 0.010 0.001 PHE A 774 TYR 0.010 0.001 TYR A1124 ARG 0.002 0.000 ARG A1090 *********************** 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 148 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.852 Fit side-chains REVERT: A 805 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7305 (mp) REVERT: B 805 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7313 (mp) outliers start: 12 outliers final: 10 residues processed: 142 average time/residue: 0.2442 time to fit residues: 45.4448 Evaluate side-chains 148 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.0010 chunk 98 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8126 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.141813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102034 restraints weight = 8763.138| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.94 r_work: 0.2886 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8272 Z= 0.191 Angle : 0.500 8.442 11226 Z= 0.255 Chirality : 0.038 0.151 1330 Planarity : 0.005 0.068 1378 Dihedral : 3.554 15.516 1096 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.82 % Allowed : 11.73 % Favored : 86.45 % 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: 1.58 (0.27), residues: 1014 helix: 2.16 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.003 0.001 HIS A1149 PHE 0.010 0.001 PHE A 774 TYR 0.009 0.001 TYR B1124 ARG 0.009 0.000 ARG B 817 *********************** 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 154 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.985 Fit side-chains REVERT: A 805 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7319 (mp) REVERT: B 688 ASP cc_start: 0.6685 (m-30) cc_final: 0.6399 (m-30) REVERT: B 805 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7275 (mp) REVERT: B 818 PHE cc_start: 0.8722 (m-10) cc_final: 0.8465 (m-80) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.2236 time to fit residues: 43.1274 Evaluate side-chains 151 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102887 restraints weight = 8776.778| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.98 r_work: 0.2885 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8272 Z= 0.180 Angle : 0.493 8.391 11226 Z= 0.251 Chirality : 0.038 0.149 1330 Planarity : 0.005 0.068 1378 Dihedral : 3.513 14.996 1096 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 1.48 % Allowed : 12.30 % Favored : 86.22 % 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: 1.60 (0.27), residues: 1014 helix: 2.17 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.03 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.003 0.001 HIS B 850 PHE 0.010 0.001 PHE A 774 TYR 0.009 0.001 TYR B1124 ARG 0.007 0.000 ARG B 817 *********************** 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 147 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.894 Fit side-chains REVERT: A 805 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7248 (mp) REVERT: B 688 ASP cc_start: 0.6624 (m-30) cc_final: 0.6332 (m-30) REVERT: B 805 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7207 (mp) REVERT: B 818 PHE cc_start: 0.8710 (m-10) cc_final: 0.8463 (m-80) outliers start: 13 outliers final: 11 residues processed: 140 average time/residue: 0.2645 time to fit residues: 49.1906 Evaluate side-chains 147 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.140242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100339 restraints weight = 8638.248| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.94 r_work: 0.2857 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8272 Z= 0.245 Angle : 0.532 8.345 11226 Z= 0.271 Chirality : 0.040 0.160 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.612 15.478 1096 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 1.48 % Allowed : 12.53 % Favored : 85.99 % 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: 1.44 (0.27), residues: 1014 helix: 2.04 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.08 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.004 0.001 HIS A1149 PHE 0.010 0.001 PHE A 774 TYR 0.011 0.001 TYR A1124 ARG 0.007 0.000 ARG B 817 ********************** 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 148 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.841 Fit side-chains REVERT: A 688 ASP cc_start: 0.6466 (m-30) cc_final: 0.6236 (m-30) REVERT: A 690 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7758 (mtp85) REVERT: A 805 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7324 (mp) REVERT: B 805 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7278 (mp) outliers start: 13 outliers final: 11 residues processed: 141 average time/residue: 0.2295 time to fit residues: 42.7891 Evaluate side-chains 146 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1108 ASP Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1023 GLU Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1088 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102323 restraints weight = 8676.735| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.82 r_work: 0.2891 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8272 Z= 0.187 Angle : 0.505 8.297 11226 Z= 0.256 Chirality : 0.038 0.154 1330 Planarity : 0.005 0.069 1378 Dihedral : 3.536 14.629 1096 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.45 % Favored : 96.35 % Rotamer: Outliers : 1.48 % Allowed : 12.76 % 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: 1.54 (0.27), residues: 1014 helix: 2.11 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.01 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.003 0.001 HIS A1149 PHE 0.010 0.001 PHE A 774 TYR 0.009 0.001 TYR A1124 ARG 0.007 0.000 ARG B 817 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4988.75 seconds wall clock time: 87 minutes 54.83 seconds (5274.83 seconds total)