Starting phenix.real_space_refine on Sat Jun 14 19:03:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x0x_6699/06_2025/5x0x_6699.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x0x_6699/06_2025/5x0x_6699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5x0x_6699/06_2025/5x0x_6699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x0x_6699/06_2025/5x0x_6699.map" model { file = "/net/cci-nas-00/data/ceres_data/5x0x_6699/06_2025/5x0x_6699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x0x_6699/06_2025/5x0x_6699.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 29 5.16 5 C 9647 2.51 5 N 3083 2.21 5 O 3697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16748 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4789 Classifications: {'peptide': 583} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 566} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 9.58, per 1000 atoms: 0.57 Number of scatterers: 16748 At special positions: 0 Unit cell: (139.92, 149.16, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 292 15.00 O 3697 8.00 N 3083 7.00 C 9647 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: 4.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 68.1% alpha, 4.1% beta 133 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 7.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.665A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.235A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.224A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.723A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.525A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.802A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.493A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.808A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.744A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.665A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.234A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.224A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.723A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.526A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.802A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.493A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.809A pdb=" N MET H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.744A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 689 removed outlier: 3.937A pdb=" N LEU O 683 " --> pdb=" O ILE O 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 744 through 749 Processing helix chain 'O' and resid 768 through 784 removed outlier: 3.580A pdb=" N PHE O 782 " --> pdb=" O MET O 778 " (cutoff:3.500A) Processing helix chain 'O' and resid 797 through 811 Processing helix chain 'O' and resid 824 through 838 removed outlier: 4.004A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 863 removed outlier: 3.726A pdb=" N GLU O 853 " --> pdb=" O GLY O 849 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG O 854 " --> pdb=" O SER O 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 856 " --> pdb=" O ASN O 852 " (cutoff:3.500A) Processing helix chain 'O' and resid 873 through 879 removed outlier: 3.645A pdb=" N ILE O 877 " --> pdb=" O PHE O 873 " (cutoff:3.500A) Processing helix chain 'O' and resid 879 through 886 Processing helix chain 'O' and resid 895 through 901 removed outlier: 4.377A pdb=" N ASN O 901 " --> pdb=" O ARG O 898 " (cutoff:3.500A) Processing helix chain 'O' and resid 904 through 913 removed outlier: 3.724A pdb=" N LEU O 908 " --> pdb=" O SER O 904 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN O 911 " --> pdb=" O SER O 907 " (cutoff:3.500A) Processing helix chain 'O' and resid 932 through 942 removed outlier: 3.525A pdb=" N LEU O 942 " --> pdb=" O LEU O 938 " (cutoff:3.500A) Processing helix chain 'O' and resid 942 through 948 Processing helix chain 'O' and resid 948 through 958 removed outlier: 4.842A pdb=" N TRP O 955 " --> pdb=" O SER O 951 " (cutoff:3.500A) Processing helix chain 'O' and resid 968 through 973 Processing helix chain 'O' and resid 975 through 988 removed outlier: 5.346A pdb=" N ARG O 981 " --> pdb=" O LEU O 977 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS O 984 " --> pdb=" O ILE O 980 " (cutoff:3.500A) Processing helix chain 'O' and resid 1016 through 1022 removed outlier: 4.613A pdb=" N MET O1022 " --> pdb=" O LEU O1018 " (cutoff:3.500A) Processing helix chain 'O' and resid 1025 through 1030 removed outlier: 3.596A pdb=" N TYR O1029 " --> pdb=" O GLN O1025 " (cutoff:3.500A) Processing helix chain 'O' and resid 1053 through 1058 removed outlier: 4.161A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE O1058 " --> pdb=" O GLN O1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1053 through 1058' Processing helix chain 'O' and resid 1066 through 1073 Processing helix chain 'O' and resid 1086 through 1103 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1114 through 1127 removed outlier: 4.332A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) Processing helix chain 'O' and resid 1138 through 1151 Processing helix chain 'O' and resid 1162 through 1167 Processing helix chain 'O' and resid 1187 through 1199 removed outlier: 4.065A pdb=" N ALA O1197 " --> pdb=" O ALA O1193 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG O1199 " --> pdb=" O ASP O1195 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1245 removed outlier: 3.947A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) Processing helix chain 'O' and resid 1247 through 1269 removed outlier: 3.898A pdb=" N GLU O1262 " --> pdb=" O LEU O1258 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU O1269 " --> pdb=" O ARG O1265 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1287 Processing helix chain 'O' and resid 1292 through 1307 removed outlier: 3.595A pdb=" N THR O1298 " --> pdb=" O MET O1294 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1349 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.928A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.619A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.846A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.678A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'O' and resid 789 through 790 removed outlier: 6.961A pdb=" N ILE O 789 " --> pdb=" O LEU O 992 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 844 through 845 removed outlier: 5.561A pdb=" N ILE O 845 " --> pdb=" O LEU O 870 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR O 872 " --> pdb=" O ILE O 845 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL O 889 " --> pdb=" O ALA O 916 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 1009 through 1011 removed outlier: 3.510A pdb=" N LYS O1009 " --> pdb=" O ILE O1208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG O1210 " --> pdb=" O LYS O1009 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU O1131 " --> pdb=" O ILE O1160 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 331 hydrogen bonds 618 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2532 1.32 - 1.44: 5857 1.44 - 1.57: 8606 1.57 - 1.69: 582 1.69 - 1.81: 53 Bond restraints: 17630 Sorted by residual: bond pdb=" C ARG C 99 " pdb=" N VAL C 100 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" C ARG G 99 " pdb=" N VAL G 100 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.60e+00 bond pdb=" CB LYS O 944 " pdb=" CG LYS O 944 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" CB ILE O 945 " pdb=" CG2 ILE O 945 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 bond pdb=" CB TYR H 39 " pdb=" CG TYR H 39 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.20e-02 2.07e+03 3.28e+00 ... (remaining 17625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 24653 2.85 - 5.70: 335 5.70 - 8.55: 49 8.55 - 11.41: 9 11.41 - 14.26: 1 Bond angle restraints: 25047 Sorted by residual: angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.51 110.40 -6.89 9.60e-01 1.09e+00 5.15e+01 angle pdb=" N CYS O1059 " pdb=" CA CYS O1059 " pdb=" C CYS O1059 " ideal model delta sigma weight residual 113.51 106.22 7.29 1.52e+00 4.33e-01 2.30e+01 angle pdb=" CA THR O 958 " pdb=" C THR O 958 " pdb=" N PRO O 959 " ideal model delta sigma weight residual 120.58 117.09 3.49 7.40e-01 1.83e+00 2.22e+01 angle pdb=" CA LEU O1253 " pdb=" CB LEU O1253 " pdb=" CG LEU O1253 " ideal model delta sigma weight residual 116.30 102.04 14.26 3.50e+00 8.16e-02 1.66e+01 angle pdb=" C LEU O 775 " pdb=" N GLN O 776 " pdb=" CA GLN O 776 " ideal model delta sigma weight residual 120.38 125.91 -5.53 1.37e+00 5.33e-01 1.63e+01 ... (remaining 25042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.91: 8224 29.91 - 59.81: 1612 59.81 - 89.72: 74 89.72 - 119.63: 2 119.63 - 149.54: 2 Dihedral angle restraints: 9914 sinusoidal: 5995 harmonic: 3919 Sorted by residual: dihedral pdb=" CA LEU O 931 " pdb=" C LEU O 931 " pdb=" N PRO O 932 " pdb=" CA PRO O 932 " ideal model delta harmonic sigma weight residual 180.00 136.27 43.73 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CA PRO O 926 " pdb=" C PRO O 926 " pdb=" N LEU O 927 " pdb=" CA LEU O 927 " ideal model delta harmonic sigma weight residual -180.00 -148.63 -31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA HIS O 915 " pdb=" C HIS O 915 " pdb=" N ALA O 916 " pdb=" CA ALA O 916 " ideal model delta harmonic sigma weight residual 180.00 149.64 30.36 0 5.00e+00 4.00e-02 3.69e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1927 0.048 - 0.096: 757 0.096 - 0.144: 158 0.144 - 0.191: 11 0.191 - 0.239: 1 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' DG I 85 " pdb=" O4' DG I 85 " pdb=" C2' DG I 85 " pdb=" N9 DG I 85 " both_signs ideal model delta sigma weight residual False 2.42 2.24 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 2851 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 946 " 0.025 2.00e-02 2.50e+03 2.21e-02 8.54e+00 pdb=" CG PHE O 946 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE O 946 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE O 946 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE O 946 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE O 946 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE O 946 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL O 823 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO O 824 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO O 824 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO O 824 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.030 2.00e-02 2.50e+03 1.46e-02 5.84e+00 pdb=" N9 DA I 39 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.023 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 246 2.57 - 3.15: 15870 3.15 - 3.73: 31100 3.73 - 4.32: 40947 4.32 - 4.90: 59006 Nonbonded interactions: 147169 Sorted by model distance: nonbonded pdb=" O ARG O 880 " pdb=" OG SER O 884 " model vdw 1.986 3.040 nonbonded pdb=" O GLU O1338 " pdb=" OG SER O1342 " model vdw 2.015 3.040 nonbonded pdb=" O2 DC I 11 " pdb=" N2 DG J 137 " model vdw 2.047 2.496 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.058 2.496 nonbonded pdb=" O2 DC I 110 " pdb=" N2 DG J 38 " model vdw 2.061 2.496 ... (remaining 147164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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 group one per residue 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: 1.650 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: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 47.460 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.011 0.060 17630 Z= 0.492 Angle : 0.955 14.257 25047 Z= 0.537 Chirality : 0.049 0.239 2854 Planarity : 0.005 0.067 2163 Dihedral : 24.667 149.536 7370 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.06 % Favored : 90.49 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.16 % 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: -5.29 (0.16), residues: 1314 helix: -3.93 (0.10), residues: 826 sheet: -3.72 (0.39), residues: 70 loop : -1.89 (0.24), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP O 831 HIS 0.014 0.003 HIS O 897 PHE 0.049 0.004 PHE O 946 TYR 0.033 0.004 TYR B 98 ARG 0.021 0.001 ARG O 982 Details of bonding type rmsd hydrogen bonds : bond 0.14482 ( 952) hydrogen bonds : angle 9.94739 ( 2442) covalent geometry : bond 0.01079 (17630) covalent geometry : angle 0.95528 (25047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7708 (m-80) cc_final: 0.7350 (m-80) REVERT: A 58 THR cc_start: 0.9183 (p) cc_final: 0.8935 (t) REVERT: A 87 SER cc_start: 0.9040 (p) cc_final: 0.8826 (t) REVERT: A 125 GLN cc_start: 0.9053 (mt0) cc_final: 0.8801 (mm-40) REVERT: B 53 GLU cc_start: 0.9020 (tp30) cc_final: 0.8735 (mm-30) REVERT: B 59 LYS cc_start: 0.8811 (tttt) cc_final: 0.8180 (tttm) REVERT: B 63 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8350 (mt-10) REVERT: C 38 ASN cc_start: 0.8458 (m-40) cc_final: 0.8133 (m-40) REVERT: D 37 TYR cc_start: 0.8769 (m-80) cc_final: 0.8548 (m-80) REVERT: D 56 MET cc_start: 0.8984 (tpp) cc_final: 0.8741 (tpp) REVERT: D 82 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8720 (mmtm) REVERT: D 102 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8444 (mm-30) REVERT: D 117 LYS cc_start: 0.8880 (tttp) cc_final: 0.8295 (ttmt) REVERT: E 56 LYS cc_start: 0.9284 (tttp) cc_final: 0.8978 (tppt) REVERT: E 73 GLU cc_start: 0.8587 (tt0) cc_final: 0.8002 (tt0) REVERT: E 93 GLN cc_start: 0.8592 (tt0) cc_final: 0.8213 (tt0) REVERT: E 120 MET cc_start: 0.9182 (mtp) cc_final: 0.8959 (mtp) REVERT: E 125 GLN cc_start: 0.8790 (mt0) cc_final: 0.8531 (mp10) REVERT: F 25 ASN cc_start: 0.8504 (m-40) cc_final: 0.7302 (m110) REVERT: F 52 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8727 (mm-30) REVERT: F 53 GLU cc_start: 0.8579 (tp30) cc_final: 0.7750 (tp30) REVERT: F 55 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8022 (mtm-85) REVERT: F 96 THR cc_start: 0.9362 (m) cc_final: 0.9106 (p) REVERT: H 37 TYR cc_start: 0.9246 (m-80) cc_final: 0.8884 (m-80) REVERT: H 59 MET cc_start: 0.8821 (mmm) cc_final: 0.8507 (mmm) REVERT: H 85 THR cc_start: 0.8960 (m) cc_final: 0.8759 (t) REVERT: O 888 TRP cc_start: 0.6233 (m100) cc_final: 0.5844 (m100) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.4270 time to fit residues: 243.2623 Evaluate side-chains 249 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 64 ASN G 94 ASN H 81 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 928 GLN ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1198 HIS O1347 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.059249 restraints weight = 60995.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060825 restraints weight = 32029.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061822 restraints weight = 21620.381| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17630 Z= 0.229 Angle : 0.723 14.718 25047 Z= 0.405 Chirality : 0.041 0.164 2854 Planarity : 0.006 0.062 2163 Dihedral : 29.571 149.679 4669 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 2.79 % Allowed : 12.58 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.78 (0.21), residues: 1314 helix: -0.84 (0.17), residues: 834 sheet: -2.82 (0.44), residues: 71 loop : -1.21 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP O 955 HIS 0.009 0.002 HIS O1198 PHE 0.049 0.003 PHE O 946 TYR 0.025 0.002 TYR B 98 ARG 0.009 0.001 ARG O 988 Details of bonding type rmsd hydrogen bonds : bond 0.07671 ( 952) hydrogen bonds : angle 5.57431 ( 2442) covalent geometry : bond 0.00503 (17630) covalent geometry : angle 0.72314 (25047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 327 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9182 (m-10) cc_final: 0.8834 (m-10) REVERT: A 58 THR cc_start: 0.9139 (p) cc_final: 0.8911 (t) REVERT: A 87 SER cc_start: 0.8929 (p) cc_final: 0.8725 (t) REVERT: A 105 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 59 LYS cc_start: 0.8763 (tttt) cc_final: 0.8166 (tttt) REVERT: B 63 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7877 (mt-10) REVERT: D 117 LYS cc_start: 0.8699 (tttp) cc_final: 0.8185 (ttpp) REVERT: E 56 LYS cc_start: 0.8773 (tttp) cc_final: 0.8300 (tppt) REVERT: E 64 LYS cc_start: 0.8374 (mmtp) cc_final: 0.8062 (mmtp) REVERT: E 90 MET cc_start: 0.8218 (mmm) cc_final: 0.7950 (mmm) REVERT: E 105 GLU cc_start: 0.7419 (tp30) cc_final: 0.7160 (tp30) REVERT: F 31 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8703 (tmtt) REVERT: F 53 GLU cc_start: 0.7974 (tp30) cc_final: 0.7661 (tp30) REVERT: F 88 TYR cc_start: 0.8199 (m-10) cc_final: 0.7950 (m-10) REVERT: F 92 ARG cc_start: 0.8432 (tpt90) cc_final: 0.8118 (tpt90) REVERT: F 93 GLN cc_start: 0.8832 (mt0) cc_final: 0.8526 (mt0) REVERT: G 84 GLN cc_start: 0.8991 (tp40) cc_final: 0.8287 (tm-30) REVERT: G 89 ASN cc_start: 0.8716 (t0) cc_final: 0.8477 (m110) REVERT: G 101 THR cc_start: 0.9117 (m) cc_final: 0.8825 (p) REVERT: H 85 THR cc_start: 0.9020 (m) cc_final: 0.8810 (t) REVERT: O 888 TRP cc_start: 0.7283 (m100) cc_final: 0.6800 (m100) REVERT: O 955 TRP cc_start: 0.5829 (m100) cc_final: 0.5577 (m100) REVERT: O 1116 MET cc_start: 0.7484 (mtm) cc_final: 0.7167 (mtt) REVERT: O 1158 CYS cc_start: 0.7596 (m) cc_final: 0.7075 (t) REVERT: O 1248 GLU cc_start: 0.8851 (tp30) cc_final: 0.7968 (pm20) REVERT: O 1262 GLU cc_start: 0.8892 (tp30) cc_final: 0.8485 (tp30) REVERT: O 1263 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: O 1294 MET cc_start: 0.7976 (mmm) cc_final: 0.7475 (mmp) outliers start: 32 outliers final: 16 residues processed: 339 average time/residue: 0.3606 time to fit residues: 178.2892 Evaluate side-chains 266 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 249 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1263 GLU Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 146 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 93 GLN G 38 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 947 ASN ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.083273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060588 restraints weight = 60435.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062211 restraints weight = 31274.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063238 restraints weight = 20958.990| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17630 Z= 0.176 Angle : 0.658 12.478 25047 Z= 0.370 Chirality : 0.039 0.163 2854 Planarity : 0.005 0.056 2163 Dihedral : 29.096 148.453 4669 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 3.14 % Allowed : 15.11 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.16 % 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: -0.38 (0.23), residues: 1314 helix: 0.35 (0.18), residues: 847 sheet: -2.07 (0.48), residues: 72 loop : -0.98 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 955 HIS 0.005 0.001 HIS O 984 PHE 0.044 0.003 PHE O 946 TYR 0.015 0.002 TYR H 37 ARG 0.004 0.001 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.07065 ( 952) hydrogen bonds : angle 4.90470 ( 2442) covalent geometry : bond 0.00381 (17630) covalent geometry : angle 0.65850 (25047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: A 105 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 125 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8572 (mm-40) REVERT: B 59 LYS cc_start: 0.8657 (tttt) cc_final: 0.8158 (tttt) REVERT: B 63 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 80 THR cc_start: 0.8836 (p) cc_final: 0.8557 (p) REVERT: D 83 ARG cc_start: 0.7848 (mpt180) cc_final: 0.7641 (mpt180) REVERT: D 117 LYS cc_start: 0.8650 (tttp) cc_final: 0.7946 (ttmt) REVERT: E 56 LYS cc_start: 0.8726 (tttp) cc_final: 0.8075 (tppt) REVERT: E 64 LYS cc_start: 0.8521 (mmtp) cc_final: 0.8275 (mmtp) REVERT: E 73 GLU cc_start: 0.7888 (tt0) cc_final: 0.6954 (mt-10) REVERT: E 79 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8237 (ttmm) REVERT: E 108 ASN cc_start: 0.9262 (t0) cc_final: 0.8987 (t0) REVERT: E 120 MET cc_start: 0.8478 (mtp) cc_final: 0.8181 (mtm) REVERT: F 25 ASN cc_start: 0.8150 (m-40) cc_final: 0.6887 (m110) REVERT: F 92 ARG cc_start: 0.8401 (tpt90) cc_final: 0.8074 (tpt90) REVERT: G 61 GLU cc_start: 0.7904 (tp30) cc_final: 0.7685 (tt0) REVERT: G 84 GLN cc_start: 0.8941 (tp40) cc_final: 0.8613 (tm-30) REVERT: G 89 ASN cc_start: 0.8664 (t0) cc_final: 0.8452 (m110) REVERT: G 90 ASP cc_start: 0.8701 (t70) cc_final: 0.8495 (t70) REVERT: G 101 THR cc_start: 0.9076 (m) cc_final: 0.8793 (p) REVERT: H 32 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8047 (tm-30) REVERT: H 56 MET cc_start: 0.9002 (tpp) cc_final: 0.8775 (tpp) REVERT: H 80 TYR cc_start: 0.7893 (m-10) cc_final: 0.7159 (m-10) REVERT: H 85 THR cc_start: 0.9042 (m) cc_final: 0.8682 (t) REVERT: O 828 LEU cc_start: 0.9010 (tt) cc_final: 0.8795 (tp) REVERT: O 888 TRP cc_start: 0.7014 (m100) cc_final: 0.6298 (m100) REVERT: O 935 TRP cc_start: 0.7956 (m-10) cc_final: 0.7423 (m100) REVERT: O 1053 MET cc_start: 0.9179 (mtt) cc_final: 0.8940 (mtt) REVERT: O 1119 MET cc_start: 0.8389 (ttp) cc_final: 0.8188 (ttp) REVERT: O 1158 CYS cc_start: 0.7738 (m) cc_final: 0.7035 (t) REVERT: O 1248 GLU cc_start: 0.8777 (tp30) cc_final: 0.8050 (pm20) REVERT: O 1249 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8440 (mt-10) REVERT: O 1262 GLU cc_start: 0.8988 (tp30) cc_final: 0.8564 (tp30) REVERT: O 1278 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7520 (pt) REVERT: O 1294 MET cc_start: 0.7891 (mmm) cc_final: 0.7529 (mmm) REVERT: O 1307 LYS cc_start: 0.7895 (tptt) cc_final: 0.7666 (tptt) outliers start: 36 outliers final: 24 residues processed: 314 average time/residue: 0.3829 time to fit residues: 176.5557 Evaluate side-chains 265 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain O residue 674 THR Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1263 GLU Chi-restraints excluded: chain O residue 1278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.061233 restraints weight = 60181.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062888 restraints weight = 31205.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063886 restraints weight = 20832.550| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17630 Z= 0.163 Angle : 0.627 9.208 25047 Z= 0.355 Chirality : 0.038 0.230 2854 Planarity : 0.004 0.052 2163 Dihedral : 28.818 147.082 4669 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 3.41 % Allowed : 17.21 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: 0.23 (0.23), residues: 1314 helix: 0.83 (0.18), residues: 845 sheet: -1.61 (0.53), residues: 78 loop : -0.77 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 831 HIS 0.004 0.001 HIS B 75 PHE 0.039 0.002 PHE O 946 TYR 0.020 0.002 TYR H 37 ARG 0.007 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.06860 ( 952) hydrogen bonds : angle 4.56643 ( 2442) covalent geometry : bond 0.00355 (17630) covalent geometry : angle 0.62705 (25047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8864 (ttpt) REVERT: A 76 GLN cc_start: 0.7582 (mp10) cc_final: 0.6875 (mp10) REVERT: A 105 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 59 LYS cc_start: 0.8696 (tttt) cc_final: 0.8033 (tttt) REVERT: B 63 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 80 THR cc_start: 0.8602 (p) cc_final: 0.8319 (p) REVERT: D 83 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7657 (mpt180) REVERT: E 56 LYS cc_start: 0.8530 (tttp) cc_final: 0.7953 (tppt) REVERT: E 64 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8338 (mmmm) REVERT: E 73 GLU cc_start: 0.7780 (tt0) cc_final: 0.6344 (mt-10) REVERT: E 79 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8368 (ttmm) REVERT: E 93 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7392 (tm-30) REVERT: E 106 ASP cc_start: 0.8527 (m-30) cc_final: 0.8311 (m-30) REVERT: G 61 GLU cc_start: 0.7882 (tp30) cc_final: 0.7661 (tt0) REVERT: G 84 GLN cc_start: 0.9074 (tp40) cc_final: 0.8593 (tm-30) REVERT: G 90 ASP cc_start: 0.8707 (t70) cc_final: 0.8427 (t0) REVERT: G 91 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8145 (pp20) REVERT: G 92 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: H 32 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7962 (tm-30) REVERT: H 80 TYR cc_start: 0.7859 (m-10) cc_final: 0.7477 (m-10) REVERT: O 888 TRP cc_start: 0.7011 (m100) cc_final: 0.6539 (m100) REVERT: O 1015 MET cc_start: 0.5561 (ttt) cc_final: 0.5267 (ttt) REVERT: O 1112 MET cc_start: 0.7595 (ttm) cc_final: 0.7343 (ttm) REVERT: O 1119 MET cc_start: 0.8361 (ttp) cc_final: 0.8157 (ttp) REVERT: O 1158 CYS cc_start: 0.7704 (m) cc_final: 0.6998 (t) REVERT: O 1248 GLU cc_start: 0.8709 (tp30) cc_final: 0.7931 (pm20) REVERT: O 1249 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8431 (mt-10) REVERT: O 1294 MET cc_start: 0.7945 (mmm) cc_final: 0.7523 (mmm) REVERT: O 1337 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7325 (mmp80) outliers start: 39 outliers final: 22 residues processed: 307 average time/residue: 0.4162 time to fit residues: 188.5987 Evaluate side-chains 266 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1263 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 114 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 123 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 89 ASN G 112 GLN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1073 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.085262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062551 restraints weight = 60481.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064210 restraints weight = 31220.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065256 restraints weight = 20779.881| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17630 Z= 0.151 Angle : 0.611 10.328 25047 Z= 0.346 Chirality : 0.037 0.150 2854 Planarity : 0.005 0.068 2163 Dihedral : 28.621 145.972 4669 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 2.97 % Allowed : 18.69 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: 0.67 (0.23), residues: 1314 helix: 1.17 (0.18), residues: 850 sheet: -1.26 (0.57), residues: 72 loop : -0.70 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP O 777 HIS 0.006 0.001 HIS B 75 PHE 0.037 0.002 PHE O 946 TYR 0.020 0.002 TYR H 37 ARG 0.006 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.06691 ( 952) hydrogen bonds : angle 4.35348 ( 2442) covalent geometry : bond 0.00322 (17630) covalent geometry : angle 0.61134 (25047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8908 (ttpt) REVERT: A 76 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: A 94 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 105 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 59 LYS cc_start: 0.8657 (tttt) cc_final: 0.8188 (tttt) REVERT: B 63 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 80 THR cc_start: 0.8574 (p) cc_final: 0.8283 (p) REVERT: C 84 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.8768 (tp40) REVERT: D 102 GLU cc_start: 0.7992 (pm20) cc_final: 0.7546 (pp20) REVERT: D 117 LYS cc_start: 0.8866 (tttp) cc_final: 0.8103 (ttmt) REVERT: E 41 TYR cc_start: 0.8038 (m-80) cc_final: 0.7836 (m-80) REVERT: E 64 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8345 (mmmm) REVERT: G 84 GLN cc_start: 0.9001 (tp40) cc_final: 0.8712 (tm-30) REVERT: G 90 ASP cc_start: 0.8503 (t70) cc_final: 0.8145 (t0) REVERT: G 92 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: H 32 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7930 (tm-30) REVERT: H 49 THR cc_start: 0.9252 (m) cc_final: 0.8880 (t) REVERT: H 59 MET cc_start: 0.8931 (mmm) cc_final: 0.8663 (mmm) REVERT: O 888 TRP cc_start: 0.6974 (m100) cc_final: 0.6654 (m100) REVERT: O 947 ASN cc_start: 0.5781 (m110) cc_final: 0.5486 (m110) REVERT: O 987 LEU cc_start: 0.8297 (mt) cc_final: 0.8071 (tp) REVERT: O 1053 MET cc_start: 0.9032 (mtt) cc_final: 0.8598 (mpp) REVERT: O 1112 MET cc_start: 0.7943 (ttm) cc_final: 0.7644 (ttm) REVERT: O 1158 CYS cc_start: 0.7608 (m) cc_final: 0.6857 (t) REVERT: O 1248 GLU cc_start: 0.8599 (tp30) cc_final: 0.7940 (pm20) REVERT: O 1249 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8386 (mt-10) REVERT: O 1294 MET cc_start: 0.7756 (mmm) cc_final: 0.7294 (mmp) outliers start: 34 outliers final: 22 residues processed: 297 average time/residue: 0.3381 time to fit residues: 148.5535 Evaluate side-chains 276 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1263 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 890 HIS ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062726 restraints weight = 60626.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064402 restraints weight = 31468.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065443 restraints weight = 20872.370| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17630 Z= 0.154 Angle : 0.620 14.935 25047 Z= 0.348 Chirality : 0.037 0.152 2854 Planarity : 0.004 0.065 2163 Dihedral : 28.513 144.924 4669 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 3.49 % Allowed : 19.39 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: 0.77 (0.23), residues: 1314 helix: 1.24 (0.18), residues: 853 sheet: -1.09 (0.58), residues: 72 loop : -0.67 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP O 777 HIS 0.004 0.001 HIS B 75 PHE 0.035 0.002 PHE O 946 TYR 0.026 0.002 TYR F 88 ARG 0.008 0.001 ARG O 919 Details of bonding type rmsd hydrogen bonds : bond 0.06666 ( 952) hydrogen bonds : angle 4.32213 ( 2442) covalent geometry : bond 0.00332 (17630) covalent geometry : angle 0.62014 (25047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8908 (ttpt) REVERT: A 76 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: B 47 SER cc_start: 0.8874 (t) cc_final: 0.8468 (m) REVERT: B 80 THR cc_start: 0.8634 (p) cc_final: 0.8369 (p) REVERT: C 84 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8789 (tp40) REVERT: D 102 GLU cc_start: 0.8033 (pm20) cc_final: 0.7559 (pp20) REVERT: D 117 LYS cc_start: 0.8851 (tttp) cc_final: 0.8117 (ttmt) REVERT: E 59 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: E 64 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8234 (mmmm) REVERT: E 100 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9520 (tp) REVERT: E 120 MET cc_start: 0.8402 (mtp) cc_final: 0.7962 (mtm) REVERT: F 88 TYR cc_start: 0.8190 (m-10) cc_final: 0.7244 (m-80) REVERT: F 92 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8312 (ttp80) REVERT: G 84 GLN cc_start: 0.9042 (tp40) cc_final: 0.8689 (tm-30) REVERT: G 90 ASP cc_start: 0.8536 (t70) cc_final: 0.8107 (t0) REVERT: G 91 GLU cc_start: 0.8255 (pp20) cc_final: 0.7216 (pp20) REVERT: H 49 THR cc_start: 0.9240 (m) cc_final: 0.8926 (t) REVERT: O 888 TRP cc_start: 0.7033 (m100) cc_final: 0.6563 (m100) REVERT: O 946 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7188 (p90) REVERT: O 1119 MET cc_start: 0.8258 (ttp) cc_final: 0.7859 (ptm) REVERT: O 1158 CYS cc_start: 0.7567 (m) cc_final: 0.6727 (t) REVERT: O 1248 GLU cc_start: 0.8593 (tp30) cc_final: 0.8088 (pm20) REVERT: O 1249 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8467 (mt-10) REVERT: O 1294 MET cc_start: 0.7691 (mmm) cc_final: 0.7412 (mmm) outliers start: 40 outliers final: 25 residues processed: 288 average time/residue: 0.3265 time to fit residues: 139.6841 Evaluate side-chains 277 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 908 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 946 PHE Chi-restraints excluded: chain O residue 1061 HIS Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1263 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/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-dev-5710/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-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/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-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-dev-5710/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-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2724 > 50: distance: 2 - 26: 21.149 distance: 22 - 26: 23.306 distance: 26 - 27: 10.310 distance: 27 - 28: 17.728 distance: 27 - 30: 26.831 distance: 28 - 29: 16.839 distance: 28 - 31: 16.159 distance: 31 - 32: 4.253 distance: 32 - 33: 5.139 distance: 33 - 34: 11.531 distance: 33 - 35: 12.502 distance: 35 - 36: 10.355 distance: 36 - 37: 20.185 distance: 36 - 39: 10.612 distance: 37 - 38: 18.269 distance: 37 - 43: 16.210 distance: 39 - 40: 17.111 distance: 40 - 41: 8.177 distance: 40 - 42: 15.791 distance: 43 - 44: 28.529 distance: 44 - 45: 66.425 distance: 44 - 47: 45.456 distance: 45 - 46: 16.478 distance: 45 - 52: 48.400 distance: 47 - 48: 21.519 distance: 48 - 49: 26.980 distance: 49 - 50: 8.250 distance: 49 - 51: 13.251 distance: 52 - 53: 24.837 distance: 53 - 54: 52.981 distance: 53 - 56: 36.763 distance: 54 - 55: 26.768 distance: 54 - 63: 33.651 distance: 56 - 57: 15.763 distance: 57 - 58: 29.563 distance: 57 - 59: 26.790 distance: 58 - 60: 18.029 distance: 59 - 61: 24.239 distance: 60 - 62: 13.701 distance: 61 - 62: 14.104 distance: 63 - 64: 34.992 distance: 63 - 69: 24.874 distance: 64 - 65: 22.531 distance: 64 - 67: 26.103 distance: 65 - 66: 16.804 distance: 65 - 70: 24.121 distance: 66 - 92: 15.907 distance: 67 - 68: 21.654 distance: 68 - 69: 19.275 distance: 70 - 71: 22.807 distance: 71 - 72: 8.057 distance: 71 - 74: 10.109 distance: 72 - 73: 12.799 distance: 72 - 77: 5.269 distance: 73 - 99: 14.725 distance: 74 - 75: 24.983 distance: 74 - 76: 27.311 distance: 77 - 78: 5.572 distance: 78 - 79: 5.722 distance: 79 - 80: 9.848 distance: 79 - 81: 8.830 distance: 80 - 105: 10.079 distance: 81 - 82: 3.560 distance: 82 - 83: 14.622 distance: 82 - 85: 7.538 distance: 83 - 84: 7.699 distance: 83 - 92: 22.575 distance: 84 - 113: 13.603 distance: 85 - 86: 5.027 distance: 86 - 87: 14.393 distance: 87 - 88: 3.901 distance: 88 - 89: 3.010 distance: 89 - 90: 3.158 distance: 89 - 91: 3.452 distance: 92 - 93: 8.077 distance: 93 - 94: 10.822 distance: 93 - 96: 8.544 distance: 94 - 95: 8.147 distance: 94 - 99: 8.298 distance: 95 - 121: 8.857 distance: 96 - 97: 9.874 distance: 96 - 98: 11.697