Starting phenix.real_space_refine on Fri Feb 16 22:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0x_6699/02_2024/5x0x_6699.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0x_6699/02_2024/5x0x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0x_6699/02_2024/5x0x_6699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0x_6699/02_2024/5x0x_6699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0x_6699/02_2024/5x0x_6699.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0x_6699/02_2024/5x0x_6699.pdb" } 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 Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1349": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.07, per 1000 atoms: 0.54 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 - 3.50 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: 9.93 Conformation dependent library (CDL) restraints added in 2.2 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: 7.34 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: 9.08 Time building geometry restraints manager: 10.18 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: 97.35 - 104.69: 1293 104.69 - 112.03: 9714 112.03 - 119.37: 5469 119.37 - 126.71: 7712 126.71 - 134.05: 859 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 2.440 nonbonded pdb=" O GLU O1338 " pdb=" OG SER O1342 " model vdw 2.015 2.440 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 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: 0.800 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: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 56.210 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.460 ------------------------------------------------------------------------------- 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= 0.634 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 1.545 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: 0.4354 time to fit residues: 248.5233 Evaluate side-chains 249 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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: 0.8980 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1198 HIS ** O1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17630 Z= 0.245 Angle : 0.692 13.573 25047 Z= 0.390 Chirality : 0.040 0.166 2854 Planarity : 0.005 0.063 2163 Dihedral : 29.440 150.033 4669 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 2.97 % Allowed : 12.75 % Favored : 84.28 % 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: -1.56 (0.21), residues: 1314 helix: -0.66 (0.17), residues: 832 sheet: -2.67 (0.42), residues: 72 loop : -1.14 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP O 955 HIS 0.011 0.002 HIS O1198 PHE 0.049 0.003 PHE O 946 TYR 0.027 0.002 TYR B 98 ARG 0.006 0.001 ARG O 982 *********************** 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 366 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 332 time to evaluate : 1.443 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: A 105 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8459 (tm-30) REVERT: A 125 GLN cc_start: 0.9115 (mt0) cc_final: 0.8837 (mm-40) REVERT: B 27 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8704 (mp10) REVERT: B 31 LYS cc_start: 0.9308 (ttpt) cc_final: 0.9063 (tttm) REVERT: B 59 LYS cc_start: 0.8961 (tttt) cc_final: 0.8332 (tttt) REVERT: B 63 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 30 ARG cc_start: 0.7945 (ptt90) cc_final: 0.7729 (ptt90) REVERT: D 56 MET cc_start: 0.8805 (tpp) cc_final: 0.8520 (tpp) REVERT: D 82 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8747 (mmtm) REVERT: D 117 LYS cc_start: 0.8751 (tttp) cc_final: 0.8248 (ttpp) REVERT: E 56 LYS cc_start: 0.9125 (tttp) cc_final: 0.8647 (tppt) REVERT: E 73 GLU cc_start: 0.8330 (tt0) cc_final: 0.8033 (tt0) REVERT: F 29 ILE cc_start: 0.9196 (mm) cc_final: 0.8764 (tp) REVERT: F 31 LYS cc_start: 0.9262 (tmtt) cc_final: 0.9053 (tmtt) REVERT: F 52 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8574 (mm-30) REVERT: F 53 GLU cc_start: 0.8259 (tp30) cc_final: 0.8015 (tp30) REVERT: F 55 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8001 (mtm-85) REVERT: F 88 TYR cc_start: 0.8555 (m-10) cc_final: 0.8341 (m-10) REVERT: G 38 ASN cc_start: 0.8665 (t0) cc_final: 0.8421 (p0) REVERT: G 84 GLN cc_start: 0.9012 (tp40) cc_final: 0.8343 (tm-30) REVERT: G 89 ASN cc_start: 0.8777 (t0) cc_final: 0.8543 (m110) REVERT: G 101 THR cc_start: 0.9133 (m) cc_final: 0.8889 (p) REVERT: H 59 MET cc_start: 0.8925 (mmm) cc_final: 0.8722 (mmp) REVERT: H 85 THR cc_start: 0.8960 (m) cc_final: 0.8709 (t) REVERT: O 1116 MET cc_start: 0.6216 (mtm) cc_final: 0.5967 (mtm) outliers start: 34 outliers final: 17 residues processed: 343 average time/residue: 0.3658 time to fit residues: 180.5765 Evaluate side-chains 266 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 249 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 77 ASP 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 48 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 81 ASP 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 1229 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 143 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- 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 A 113 HIS ** 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 93 GLN G 94 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 947 ASN O1050 ASN ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17630 Z= 0.217 Angle : 0.644 11.782 25047 Z= 0.364 Chirality : 0.038 0.191 2854 Planarity : 0.005 0.055 2163 Dihedral : 29.016 148.349 4669 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 3.58 % Allowed : 15.81 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.08 % 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: -0.29 (0.23), residues: 1314 helix: 0.41 (0.18), residues: 848 sheet: -1.87 (0.47), residues: 72 loop : -0.98 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 955 HIS 0.005 0.001 HIS O1188 PHE 0.042 0.003 PHE O 946 TYR 0.014 0.002 TYR H 37 ARG 0.004 0.001 ARG O1299 *********************** 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 324 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 1.513 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 76 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: A 79 LYS cc_start: 0.9167 (tttt) cc_final: 0.8939 (tptm) REVERT: A 105 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 125 GLN cc_start: 0.9167 (mt0) cc_final: 0.8881 (mm-40) REVERT: B 27 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8734 (mp10) REVERT: B 31 LYS cc_start: 0.9346 (ttpt) cc_final: 0.9063 (tttp) REVERT: B 59 LYS cc_start: 0.9019 (tttt) cc_final: 0.8490 (tttt) REVERT: B 63 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 80 THR cc_start: 0.8796 (p) cc_final: 0.8512 (p) REVERT: C 41 GLU cc_start: 0.8792 (tt0) cc_final: 0.8560 (pt0) REVERT: D 56 MET cc_start: 0.8942 (tpp) cc_final: 0.8614 (tpp) REVERT: D 82 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8913 (mmtp) REVERT: D 83 ARG cc_start: 0.8723 (mpt180) cc_final: 0.8507 (mpt180) REVERT: D 117 LYS cc_start: 0.8756 (tttp) cc_final: 0.8053 (ttmt) REVERT: E 56 LYS cc_start: 0.9002 (tttp) cc_final: 0.8430 (tppt) REVERT: E 79 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8571 (ttmm) REVERT: E 93 GLN cc_start: 0.8183 (tt0) cc_final: 0.7815 (tt0) REVERT: E 105 GLU cc_start: 0.8231 (tp30) cc_final: 0.8010 (tp30) REVERT: E 108 ASN cc_start: 0.9415 (t0) cc_final: 0.9166 (t0) REVERT: E 120 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8820 (mtm) REVERT: F 29 ILE cc_start: 0.9235 (mm) cc_final: 0.8883 (tp) REVERT: F 55 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8159 (mtm-85) REVERT: G 38 ASN cc_start: 0.8760 (t0) cc_final: 0.8458 (p0) REVERT: G 84 GLN cc_start: 0.9085 (tp40) cc_final: 0.8591 (tm-30) REVERT: G 92 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8852 (mp0) REVERT: H 85 THR cc_start: 0.9010 (m) cc_final: 0.8695 (t) outliers start: 41 outliers final: 26 residues processed: 301 average time/residue: 0.3168 time to fit residues: 138.2220 Evaluate side-chains 282 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 253 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 77 ASP 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 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL 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 92 GLU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 928 GLN ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1188 HIS ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17630 Z= 0.326 Angle : 0.688 11.621 25047 Z= 0.384 Chirality : 0.040 0.167 2854 Planarity : 0.005 0.061 2163 Dihedral : 28.962 147.704 4669 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 5.24 % Allowed : 16.24 % Favored : 78.52 % 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: -0.29 (0.22), residues: 1314 helix: 0.47 (0.18), residues: 841 sheet: -1.68 (0.49), residues: 72 loop : -1.15 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP O 935 HIS 0.006 0.002 HIS O1188 PHE 0.042 0.003 PHE O 946 TYR 0.030 0.002 TYR F 88 ARG 0.006 0.001 ARG C 77 *********************** 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 329 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 269 time to evaluate : 1.366 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 76 GLN cc_start: 0.7912 (mp10) cc_final: 0.7304 (mp10) REVERT: A 105 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8548 (tm-30) REVERT: A 125 GLN cc_start: 0.9094 (mt0) cc_final: 0.8810 (mm-40) REVERT: B 27 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8828 (mp10) REVERT: B 31 LYS cc_start: 0.9383 (ttpt) cc_final: 0.9097 (tttm) REVERT: B 63 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 80 THR cc_start: 0.8798 (p) cc_final: 0.8520 (p) REVERT: C 84 GLN cc_start: 0.9585 (OUTLIER) cc_final: 0.9070 (tp40) REVERT: D 56 MET cc_start: 0.9020 (tpp) cc_final: 0.8604 (tpp) REVERT: D 82 LYS cc_start: 0.9318 (mtpt) cc_final: 0.9066 (mmmt) REVERT: D 83 ARG cc_start: 0.8874 (mpt180) cc_final: 0.8671 (mpt180) REVERT: D 117 LYS cc_start: 0.8818 (tttp) cc_final: 0.8091 (ttmt) REVERT: E 41 TYR cc_start: 0.7899 (m-80) cc_final: 0.7697 (m-80) REVERT: E 56 LYS cc_start: 0.9109 (tttp) cc_final: 0.8450 (tppt) REVERT: E 79 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8708 (ttmm) REVERT: E 108 ASN cc_start: 0.9544 (t0) cc_final: 0.9165 (t0) REVERT: E 120 MET cc_start: 0.9056 (mtp) cc_final: 0.8849 (mtm) REVERT: F 95 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8911 (mtp85) REVERT: G 38 ASN cc_start: 0.8919 (t0) cc_final: 0.8706 (t0) REVERT: G 64 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8309 (tm-30) REVERT: G 84 GLN cc_start: 0.9153 (tp40) cc_final: 0.8435 (tm-30) REVERT: O 888 TRP cc_start: 0.6152 (m100) cc_final: 0.5946 (m100) outliers start: 60 outliers final: 43 residues processed: 301 average time/residue: 0.3363 time to fit residues: 146.5376 Evaluate side-chains 287 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 242 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 43 VAL 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 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER 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 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 1065 PHE Chi-restraints excluded: chain O residue 1139 SER Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.0010 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN C 73 ASN E 108 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** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17630 Z= 0.207 Angle : 0.626 11.111 25047 Z= 0.354 Chirality : 0.037 0.162 2854 Planarity : 0.005 0.081 2163 Dihedral : 28.706 147.617 4669 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 3.93 % Allowed : 16.86 % Favored : 79.21 % 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: 0.25 (0.23), residues: 1314 helix: 0.88 (0.18), residues: 856 sheet: -1.38 (0.51), residues: 72 loop : -0.97 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP O 935 HIS 0.004 0.001 HIS B 75 PHE 0.040 0.002 PHE O 946 TYR 0.038 0.002 TYR F 88 ARG 0.006 0.000 ARG H 76 *********************** 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 328 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 283 time to evaluate : 1.610 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 54 TYR cc_start: 0.8887 (m-10) cc_final: 0.8507 (m-10) REVERT: A 76 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: A 105 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8537 (tm-30) REVERT: A 125 GLN cc_start: 0.9107 (mt0) cc_final: 0.8821 (mm-40) REVERT: B 31 LYS cc_start: 0.9343 (ttpt) cc_final: 0.9071 (tttm) REVERT: B 59 LYS cc_start: 0.8928 (tttt) cc_final: 0.8454 (tttt) REVERT: B 63 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8179 (mt-10) REVERT: B 80 THR cc_start: 0.8743 (p) cc_final: 0.8458 (p) REVERT: D 56 MET cc_start: 0.8972 (tpp) cc_final: 0.8656 (tpp) REVERT: D 82 LYS cc_start: 0.9358 (mtpt) cc_final: 0.9112 (mmmt) REVERT: D 117 LYS cc_start: 0.8909 (tttp) cc_final: 0.8167 (ttmt) REVERT: E 56 LYS cc_start: 0.9004 (tttp) cc_final: 0.8365 (tppt) REVERT: E 107 THR cc_start: 0.9653 (m) cc_final: 0.9447 (p) REVERT: E 108 ASN cc_start: 0.9505 (t0) cc_final: 0.9220 (t0) REVERT: E 120 MET cc_start: 0.8977 (mtp) cc_final: 0.8757 (mtm) REVERT: F 27 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8361 (mp10) REVERT: G 64 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8241 (tm-30) REVERT: G 84 GLN cc_start: 0.9109 (tp40) cc_final: 0.8581 (tm-30) REVERT: H 85 THR cc_start: 0.8901 (m) cc_final: 0.8484 (t) REVERT: O 1337 ARG cc_start: 0.5950 (mmp80) cc_final: 0.5512 (mmp80) outliers start: 45 outliers final: 31 residues processed: 306 average time/residue: 0.3190 time to fit residues: 141.0612 Evaluate side-chains 283 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 GLU 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 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 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 G residue 23 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 923 THR 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 1184 ASP Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 0.0070 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17630 Z= 0.209 Angle : 0.633 14.727 25047 Z= 0.354 Chirality : 0.037 0.149 2854 Planarity : 0.004 0.080 2163 Dihedral : 28.589 146.339 4669 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 3.49 % Allowed : 17.90 % Favored : 78.60 % 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: 0.53 (0.23), residues: 1314 helix: 1.12 (0.18), residues: 851 sheet: -0.99 (0.53), residues: 72 loop : -1.00 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP O 888 HIS 0.007 0.001 HIS B 75 PHE 0.054 0.002 PHE O 946 TYR 0.026 0.002 TYR F 88 ARG 0.009 0.000 ARG O1268 *********************** 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 301 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 261 time to evaluate : 1.475 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 105 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 120 MET cc_start: 0.8856 (mmm) cc_final: 0.8618 (mmm) REVERT: A 125 GLN cc_start: 0.9255 (mt0) cc_final: 0.8895 (mm-40) REVERT: B 31 LYS cc_start: 0.9355 (ttpt) cc_final: 0.9054 (tttp) REVERT: B 59 LYS cc_start: 0.8960 (tttt) cc_final: 0.8402 (tttt) REVERT: B 63 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 80 THR cc_start: 0.8768 (p) cc_final: 0.8475 (p) REVERT: D 56 MET cc_start: 0.8988 (tpp) cc_final: 0.8690 (tpp) REVERT: D 82 LYS cc_start: 0.9316 (mtpt) cc_final: 0.9111 (mmmt) REVERT: D 117 LYS cc_start: 0.8912 (tttp) cc_final: 0.8177 (ttmt) REVERT: E 56 LYS cc_start: 0.9006 (tttp) cc_final: 0.8400 (tppt) REVERT: E 120 MET cc_start: 0.8982 (mtp) cc_final: 0.8736 (mtm) REVERT: E 125 GLN cc_start: 0.8777 (mt0) cc_final: 0.8508 (mp10) REVERT: F 27 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8328 (mp10) REVERT: G 38 ASN cc_start: 0.8607 (t0) cc_final: 0.8322 (p0) REVERT: G 64 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8261 (tm-30) REVERT: G 84 GLN cc_start: 0.9079 (tp40) cc_final: 0.8423 (tm-30) REVERT: H 59 MET cc_start: 0.9001 (mmm) cc_final: 0.8726 (mmm) REVERT: H 85 THR cc_start: 0.8894 (m) cc_final: 0.8475 (t) REVERT: O 777 TRP cc_start: 0.6219 (t60) cc_final: 0.5888 (t60) outliers start: 40 outliers final: 33 residues processed: 277 average time/residue: 0.3056 time to fit residues: 124.3408 Evaluate side-chains 276 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP 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 85 ASP Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 871 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.0270 chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 939 ASN O1025 GLN O1073 ASN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17630 Z= 0.319 Angle : 0.690 11.600 25047 Z= 0.384 Chirality : 0.039 0.139 2854 Planarity : 0.005 0.097 2163 Dihedral : 28.662 146.153 4669 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 4.63 % Allowed : 17.21 % Favored : 78.17 % 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: 0.34 (0.23), residues: 1314 helix: 0.99 (0.18), residues: 852 sheet: -0.95 (0.55), residues: 72 loop : -1.16 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP O 888 HIS 0.008 0.001 HIS O1061 PHE 0.053 0.002 PHE O 946 TYR 0.028 0.002 TYR F 88 ARG 0.009 0.001 ARG O1268 *********************** REFINEMENT MACRO_CYCLE 7 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 305 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 252 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 125 GLN cc_start: 0.9201 (mt0) cc_final: 0.8919 (mm-40) REVERT: B 31 LYS cc_start: 0.9329 (ttpt) cc_final: 0.9051 (tttp) REVERT: B 80 THR cc_start: 0.8856 (p) cc_final: 0.8577 (p) REVERT: C 84 GLN cc_start: 0.9597 (OUTLIER) cc_final: 0.9119 (tp40) REVERT: D 56 MET cc_start: 0.9013 (tpp) cc_final: 0.8744 (tpp) REVERT: D 117 LYS cc_start: 0.8993 (tttp) cc_final: 0.8226 (ttmt) REVERT: E 56 LYS cc_start: 0.9038 (tttp) cc_final: 0.8692 (tppt) REVERT: F 27 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8394 (mp10) REVERT: F 98 TYR cc_start: 0.9122 (m-10) cc_final: 0.8780 (m-80) REVERT: G 84 GLN cc_start: 0.9128 (tp40) cc_final: 0.8424 (tm-30) REVERT: O 1112 MET cc_start: 0.6032 (tpp) cc_final: 0.5554 (tpp) REVERT: O 1294 MET cc_start: 0.4397 (mmm) cc_final: 0.4139 (mmp) outliers start: 53 outliers final: 45 residues processed: 283 average time/residue: 0.2985 time to fit residues: 124.7833 Evaluate side-chains 278 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 232 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 43 VAL 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 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 923 THR 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 1184 ASP Chi-restraints excluded: chain O residue 1198 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 119 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN B 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** O 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN O1198 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17630 Z= 0.310 Angle : 0.694 12.671 25047 Z= 0.386 Chirality : 0.039 0.156 2854 Planarity : 0.005 0.093 2163 Dihedral : 28.631 146.675 4669 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 4.37 % Allowed : 18.86 % Favored : 76.77 % 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: 0.35 (0.23), residues: 1314 helix: 1.03 (0.18), residues: 846 sheet: -0.87 (0.55), residues: 72 loop : -1.21 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP O 935 HIS 0.007 0.001 HIS B 75 PHE 0.051 0.002 PHE O 946 TYR 0.047 0.002 TYR F 51 ARG 0.008 0.001 ARG O1268 *********************** REFINEMENT MACRO_CYCLE 8 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 297 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 247 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8625 (tm-30) REVERT: A 125 GLN cc_start: 0.9215 (mt0) cc_final: 0.8955 (mm-40) REVERT: B 31 LYS cc_start: 0.9354 (ttpt) cc_final: 0.9062 (tttm) REVERT: B 63 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8205 (mt-10) REVERT: B 80 THR cc_start: 0.8869 (p) cc_final: 0.8577 (p) REVERT: C 84 GLN cc_start: 0.9614 (OUTLIER) cc_final: 0.9133 (tp40) REVERT: D 56 MET cc_start: 0.9005 (tpp) cc_final: 0.8723 (tpp) REVERT: D 117 LYS cc_start: 0.8989 (tttp) cc_final: 0.8070 (ttmm) REVERT: E 56 LYS cc_start: 0.8963 (tttp) cc_final: 0.8442 (tppt) REVERT: F 98 TYR cc_start: 0.9210 (m-10) cc_final: 0.8742 (m-80) REVERT: G 64 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8603 (tm-30) REVERT: G 84 GLN cc_start: 0.9124 (tp40) cc_final: 0.8482 (tm-30) REVERT: O 1294 MET cc_start: 0.4193 (mmm) cc_final: 0.3748 (mmp) outliers start: 50 outliers final: 46 residues processed: 273 average time/residue: 0.2903 time to fit residues: 117.5076 Evaluate side-chains 280 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 43 VAL 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 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 923 THR 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 1184 ASP Chi-restraints excluded: chain O residue 1241 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17630 Z= 0.275 Angle : 0.683 11.845 25047 Z= 0.380 Chirality : 0.039 0.222 2854 Planarity : 0.005 0.086 2163 Dihedral : 28.537 146.673 4669 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 4.37 % Allowed : 19.39 % Favored : 76.24 % 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: 0.39 (0.23), residues: 1314 helix: 1.04 (0.18), residues: 857 sheet: -0.70 (0.56), residues: 76 loop : -1.24 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP O 777 HIS 0.007 0.001 HIS O1061 PHE 0.051 0.003 PHE O1122 TYR 0.054 0.003 TYR F 51 ARG 0.009 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 9 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 293 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 125 GLN cc_start: 0.9227 (mt0) cc_final: 0.8909 (mm-40) REVERT: B 31 LYS cc_start: 0.9341 (ttpt) cc_final: 0.9052 (tttm) REVERT: B 63 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 80 THR cc_start: 0.8859 (p) cc_final: 0.8580 (p) REVERT: C 84 GLN cc_start: 0.9620 (OUTLIER) cc_final: 0.8940 (tp40) REVERT: D 56 MET cc_start: 0.9017 (tpp) cc_final: 0.8729 (tpp) REVERT: D 117 LYS cc_start: 0.8975 (tttp) cc_final: 0.8058 (ttmm) REVERT: E 56 LYS cc_start: 0.8948 (tttp) cc_final: 0.8502 (tppt) REVERT: F 98 TYR cc_start: 0.9187 (m-10) cc_final: 0.8722 (m-80) REVERT: G 64 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8609 (tm-30) REVERT: G 84 GLN cc_start: 0.9126 (tp40) cc_final: 0.8512 (tm-30) outliers start: 50 outliers final: 47 residues processed: 269 average time/residue: 0.2907 time to fit residues: 115.6874 Evaluate side-chains 282 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 43 VAL 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 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 SER 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 763 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 923 THR Chi-restraints excluded: chain O residue 944 LYS 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 1184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 125 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17630 Z= 0.295 Angle : 0.698 11.981 25047 Z= 0.390 Chirality : 0.039 0.215 2854 Planarity : 0.005 0.082 2163 Dihedral : 28.516 146.611 4669 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 4.72 % Allowed : 19.48 % Favored : 75.81 % 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: 0.32 (0.23), residues: 1314 helix: 0.99 (0.18), residues: 855 sheet: -0.50 (0.57), residues: 70 loop : -1.32 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP O 777 HIS 0.007 0.001 HIS O1061 PHE 0.049 0.002 PHE O 946 TYR 0.052 0.003 TYR F 51 ARG 0.008 0.001 ARG D 89 ********************** REFINEMENT MACRO_CYCLE 10 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 297 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8699 (tm-30) REVERT: A 125 GLN cc_start: 0.9237 (mt0) cc_final: 0.8907 (mm-40) REVERT: B 31 LYS cc_start: 0.9356 (ttpt) cc_final: 0.9061 (tttm) REVERT: B 63 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 80 THR cc_start: 0.8909 (p) cc_final: 0.8644 (p) REVERT: C 84 GLN cc_start: 0.9611 (OUTLIER) cc_final: 0.9109 (tp40) REVERT: D 56 MET cc_start: 0.9030 (tpp) cc_final: 0.8748 (tpp) REVERT: D 110 GLU cc_start: 0.8644 (tp30) cc_final: 0.8360 (tm-30) REVERT: D 117 LYS cc_start: 0.8977 (tttp) cc_final: 0.8087 (ttmm) REVERT: E 56 LYS cc_start: 0.8943 (tttp) cc_final: 0.8502 (tppt) REVERT: E 125 GLN cc_start: 0.8523 (mp10) cc_final: 0.8165 (mp10) REVERT: G 64 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8592 (tm-30) REVERT: G 84 GLN cc_start: 0.9119 (tp40) cc_final: 0.8488 (tm-30) REVERT: O 992 LEU cc_start: 0.7348 (tp) cc_final: 0.6704 (tp) outliers start: 54 outliers final: 52 residues processed: 270 average time/residue: 0.3006 time to fit residues: 120.1748 Evaluate side-chains 283 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 43 VAL 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 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 SER 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 763 VAL Chi-restraints excluded: chain O residue 821 VAL Chi-restraints excluded: chain O residue 829 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 923 THR Chi-restraints excluded: chain O residue 944 LYS 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 1184 ASP Chi-restraints excluded: chain O residue 1198 HIS Chi-restraints excluded: chain O residue 1241 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.0040 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.086428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064406 restraints weight = 61475.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.065747 restraints weight = 36435.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066617 restraints weight = 26333.161| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17630 Z= 0.204 Angle : 0.659 11.168 25047 Z= 0.370 Chirality : 0.038 0.199 2854 Planarity : 0.005 0.083 2163 Dihedral : 28.347 146.661 4669 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.06 % Allowed : 21.22 % Favored : 75.72 % 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: 0.61 (0.23), residues: 1314 helix: 1.21 (0.18), residues: 857 sheet: -0.08 (0.60), residues: 60 loop : -1.25 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP O 777 HIS 0.007 0.001 HIS O1061 PHE 0.055 0.002 PHE O1122 TYR 0.041 0.002 TYR F 51 ARG 0.008 0.001 ARG D 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.75 seconds wall clock time: 62 minutes 13.44 seconds (3733.44 seconds total)