Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 13:38:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/07_2023/8gvc_34290_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/07_2023/8gvc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/07_2023/8gvc_34290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/07_2023/8gvc_34290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/07_2023/8gvc_34290_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvc_34290/07_2023/8gvc_34290_trim_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A ASP 736": "OD1" <-> "OD2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 937": "OD1" <-> "OD2" Residue "A PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 699": "OD1" <-> "OD2" Residue "B PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 937": "OD1" <-> "OD2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 4.28, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 3.07 Conformation dependent library (CDL) restraints added in 1.1 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... running ksdssp... Secondary structure from input PDB file: 46 helices and 0 sheets defined 66.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 683 through 695 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 697 through 703 removed outlier: 4.271A pdb=" N ALA A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 733 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 741 through 757 Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.781A pdb=" N ASN A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 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 812 through 818 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 821 through 849 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 901 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 929 through 953 removed outlier: 3.583A pdb=" N PHE A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Proline residue: A 941 - end of helix Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 991 through 1020 removed outlier: 3.713A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1034 through 1049 removed outlier: 3.570A pdb=" N ALA A1047 " --> pdb=" O GLY A1043 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1048 " --> pdb=" O GLY A1044 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A1049 " --> pdb=" O ILE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1065 Processing helix chain 'A' and resid 1092 through 1101 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1115 through 1130 removed outlier: 3.525A pdb=" N ILE A1121 " --> pdb=" O VAL A1117 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A1130 " --> pdb=" O GLY A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1142 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) removed outlier: 3.827A pdb=" N LEU A1142 " --> pdb=" O ARG A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1153 through 1156 No H-bonds generated for 'chain 'A' and resid 1153 through 1156' Processing helix chain 'A' and resid 1160 through 1182 Processing helix chain 'A' and resid 1186 through 1207 removed outlier: 3.696A pdb=" N PHE A1189 " --> pdb=" O SER A1186 " (cutoff:3.500A) Proline residue: A1190 - end of helix Proline residue: A1198 - end of helix removed outlier: 4.628A pdb=" N VAL A1203 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A1204 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A1205 " --> pdb=" O VAL A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1216 Processing helix chain 'B' and resid 683 through 695 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 697 through 703 removed outlier: 4.350A pdb=" N ALA B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 733 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 741 through 757 Processing helix chain 'B' and resid 769 through 785 Processing helix chain 'B' and resid 789 through 809 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 812 through 818 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 821 through 849 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 901 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 929 through 953 removed outlier: 3.530A pdb=" N PHE B 938 " --> pdb=" O VAL B 934 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 939 " --> pdb=" O ILE B 935 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 940 " --> pdb=" O GLY B 936 " (cutoff:3.500A) Proline residue: B 941 - end of helix Processing helix chain 'B' and resid 973 through 975 No H-bonds generated for 'chain 'B' and resid 973 through 975' Processing helix chain 'B' and resid 992 through 1020 removed outlier: 5.491A pdb=" N LEU B 998 " --> pdb=" O MET B 994 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Proline residue: B1000 - end of helix Processing helix chain 'B' and resid 1034 through 1049 removed outlier: 3.534A pdb=" N ALA B1047 " --> pdb=" O GLY B1043 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU B1048 " --> pdb=" O GLY B1044 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE B1049 " --> pdb=" O ILE B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1065 Processing helix chain 'B' and resid 1092 through 1101 Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1115 through 1130 removed outlier: 3.524A pdb=" N ILE B1121 " --> pdb=" O VAL B1117 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B1130 " --> pdb=" O GLY B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1142 removed outlier: 3.726A pdb=" N LEU B1141 " --> pdb=" O GLU B1137 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B1142 " --> pdb=" O ARG B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1148 No H-bonds generated for 'chain 'B' and resid 1146 through 1148' Processing helix chain 'B' and resid 1153 through 1156 No H-bonds generated for 'chain 'B' and resid 1153 through 1156' Processing helix chain 'B' and resid 1160 through 1182 Processing helix chain 'B' and resid 1186 through 1207 removed outlier: 3.681A pdb=" N PHE B1189 " --> pdb=" O SER B1186 " (cutoff:3.500A) Proline residue: B1190 - end of helix Proline residue: B1198 - end of helix removed outlier: 4.594A pdb=" N VAL B1203 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B1204 " --> pdb=" O MET B1201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B1205 " --> pdb=" O VAL B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1216 403 hydrogen bonds defined for protein. 1143 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: 2.03 Time building geometry restraints manager: 3.32 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: 100.59 - 107.27: 311 107.27 - 113.94: 4779 113.94 - 120.62: 3420 120.62 - 127.29: 2631 127.29 - 133.97: 91 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: 3988 2.96 - 3.61: 11290 3.61 - 4.25: 17063 4.25 - 4.90: 30000 Nonbonded interactions: 62351 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 2.520 nonbonded pdb=" O ALA B1057 " pdb=" OG1 THR B1058 " model vdw 2.031 2.440 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 2.520 ... (remaining 62346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.130 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: 4.340 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.950 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- 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= 0.160 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 % 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.895 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 1.3218 time to fit residues: 184.7428 Evaluate side-chains 125 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0740 time to fit residues: 1.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8278 Z= 0.175 Angle : 0.504 8.977 11232 Z= 0.251 Chirality : 0.038 0.136 1330 Planarity : 0.004 0.053 1380 Dihedral : 3.344 15.859 1096 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer Outliers : 2.39 % 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: 2.02 (0.28), residues: 1014 helix: 2.32 (0.21), residues: 652 sheet: None (None), residues: 0 loop : -0.53 (0.32), residues: 362 *********************** 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 142 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.983 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 1.3151 time to fit residues: 183.7928 Evaluate side-chains 124 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 6 average time/residue: 0.1144 time to fit residues: 2.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0963 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= 0.182 Angle : 0.494 8.724 11232 Z= 0.249 Chirality : 0.038 0.130 1330 Planarity : 0.004 0.054 1380 Dihedral : 3.396 16.059 1096 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.17 % Favored : 97.63 % Rotamer Outliers : 1.82 % 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: 1.91 (0.27), residues: 1014 helix: 2.30 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -0.59 (0.32), residues: 376 *********************** 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 fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.831 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 122 average time/residue: 1.3495 time to fit residues: 174.0880 Evaluate side-chains 123 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 7 average time/residue: 0.3665 time to fit residues: 4.2549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.002 0.024 8278 Z= 0.162 Angle : 0.474 8.706 11232 Z= 0.237 Chirality : 0.038 0.128 1330 Planarity : 0.004 0.054 1380 Dihedral : 3.357 16.105 1096 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.37 % Favored : 97.44 % Rotamer Outliers : 2.39 % 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: 1.90 (0.27), residues: 1014 helix: 2.29 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -0.60 (0.32), residues: 374 *********************** 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 140 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.888 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 130 average time/residue: 1.2954 time to fit residues: 178.5156 Evaluate side-chains 124 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 5 average time/residue: 0.1113 time to fit residues: 2.1668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 0.0170 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8278 Z= 0.212 Angle : 0.509 8.664 11232 Z= 0.254 Chirality : 0.039 0.132 1330 Planarity : 0.005 0.055 1380 Dihedral : 3.474 16.319 1096 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.56 % Favored : 97.24 % Rotamer Outliers : 2.62 % 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: 1.76 (0.27), residues: 1014 helix: 2.16 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -0.61 (0.31), residues: 374 *********************** 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 137 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.924 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 127 average time/residue: 1.3103 time to fit residues: 176.1109 Evaluate side-chains 123 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 6 average time/residue: 0.1051 time to fit residues: 2.2756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8278 Z= 0.204 Angle : 0.507 8.650 11232 Z= 0.252 Chirality : 0.038 0.132 1330 Planarity : 0.005 0.056 1380 Dihedral : 3.489 16.580 1096 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer Outliers : 2.05 % 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: 1.74 (0.27), residues: 1014 helix: 2.16 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -0.62 (0.31), residues: 376 *********************** 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 136 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.985 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 129 average time/residue: 1.2794 time to fit residues: 175.1115 Evaluate side-chains 126 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.4870 time to fit residues: 4.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1245 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= 0.202 Angle : 0.514 8.644 11232 Z= 0.255 Chirality : 0.038 0.128 1330 Planarity : 0.005 0.057 1380 Dihedral : 3.494 16.716 1096 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.47 % Favored : 97.34 % Rotamer Outliers : 1.71 % 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: 1.73 (0.27), residues: 1014 helix: 2.16 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.64 (0.31), residues: 378 *********************** 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 129 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.888 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 1.3061 time to fit residues: 174.3026 Evaluate side-chains 122 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.1154 time to fit residues: 1.6139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.0070 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8278 Z= 0.163 Angle : 0.488 8.608 11232 Z= 0.241 Chirality : 0.037 0.130 1330 Planarity : 0.005 0.057 1380 Dihedral : 3.396 16.581 1096 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.47 % Favored : 97.34 % Rotamer Outliers : 1.82 % 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: 1.82 (0.27), residues: 1014 helix: 2.28 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -0.67 (0.31), residues: 380 *********************** 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 127 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.933 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 122 average time/residue: 1.3117 time to fit residues: 169.9831 Evaluate side-chains 118 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.1090 time to fit residues: 1.7414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0418 > 50: distance: 50 - 67: 14.315 distance: 54 - 75: 15.609 distance: 59 - 82: 18.676 distance: 62 - 67: 14.524 distance: 67 - 68: 17.990 distance: 68 - 69: 27.755 distance: 68 - 71: 18.359 distance: 69 - 70: 25.293 distance: 69 - 75: 13.297 distance: 71 - 72: 28.164 distance: 72 - 73: 26.271 distance: 72 - 74: 24.084 distance: 75 - 76: 18.514 distance: 76 - 77: 10.366 distance: 76 - 79: 17.190 distance: 77 - 78: 25.460 distance: 77 - 82: 25.679 distance: 79 - 80: 17.817 distance: 79 - 81: 12.159 distance: 82 - 83: 32.676 distance: 83 - 84: 19.570 distance: 84 - 85: 39.219 distance: 84 - 86: 32.715 distance: 86 - 87: 24.994 distance: 87 - 88: 20.768 distance: 87 - 90: 22.044 distance: 88 - 89: 15.104 distance: 88 - 94: 33.001 distance: 90 - 91: 10.150 distance: 91 - 92: 11.314 distance: 91 - 93: 6.466 distance: 94 - 95: 14.340 distance: 95 - 96: 39.220 distance: 95 - 98: 25.786 distance: 96 - 97: 46.450 distance: 96 - 100: 41.029 distance: 98 - 99: 42.345 distance: 100 - 101: 25.022 distance: 101 - 102: 28.502 distance: 101 - 104: 24.304 distance: 102 - 103: 23.859 distance: 102 - 108: 29.623 distance: 104 - 105: 49.232 distance: 104 - 106: 24.385 distance: 105 - 107: 33.617 distance: 108 - 109: 14.827 distance: 109 - 110: 40.959 distance: 109 - 112: 20.320 distance: 110 - 111: 20.775 distance: 110 - 115: 42.247 distance: 112 - 113: 36.781 distance: 112 - 114: 28.759 distance: 115 - 116: 13.032 distance: 116 - 117: 17.845 distance: 116 - 119: 17.968 distance: 117 - 118: 5.357 distance: 117 - 123: 21.923 distance: 119 - 120: 31.865 distance: 119 - 121: 31.675 distance: 120 - 122: 24.607 distance: 123 - 124: 17.770 distance: 124 - 125: 8.854 distance: 125 - 126: 11.896 distance: 125 - 127: 24.387 distance: 127 - 128: 19.816 distance: 128 - 129: 22.342 distance: 128 - 131: 13.684 distance: 129 - 130: 16.636 distance: 129 - 135: 16.627 distance: 131 - 132: 9.618 distance: 132 - 133: 34.769 distance: 132 - 134: 12.795