Starting phenix.real_space_refine on Mon Dec 11 05:08:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0y_6700/12_2023/5x0y_6700.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0y_6700/12_2023/5x0y_6700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0y_6700/12_2023/5x0y_6700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0y_6700/12_2023/5x0y_6700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0y_6700/12_2023/5x0y_6700.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x0y_6700/12_2023/5x0y_6700.pdb" } resolution = 4.69 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= 0.003 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 9677 2.51 5 N 3098 2.21 5 O 3702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 23": "NH1" <-> "NH2" Residue "O PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1076": "NH1" <-> "NH2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1164": "NH1" <-> "NH2" Residue "O PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1349": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16798 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: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} 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: 19 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: 9.39, per 1000 atoms: 0.56 Number of scatterers: 16798 At special positions: 0 Unit cell: (143.88, 126.72, 128.04, 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 3702 8.00 N 3098 7.00 C 9677 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: 11.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 11 sheets defined 67.5% alpha, 3.3% beta 145 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 8.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.563A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.923A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.999A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.255A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.563A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 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: 3.668A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.602A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.254A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.658A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'O' and resid 671 through 689 Processing helix chain 'O' and resid 744 through 749 Processing helix chain 'O' and resid 769 through 784 Processing helix chain 'O' and resid 797 through 812 Processing helix chain 'O' and resid 824 through 838 removed outlier: 4.593A pdb=" N SER O 829 " --> pdb=" O LEU O 825 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASN O 830 " --> pdb=" O SER O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 863 removed outlier: 4.108A pdb=" N GLU O 853 " --> pdb=" O GLY O 849 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 854 " --> pdb=" O SER O 850 " (cutoff:3.500A) Processing helix chain 'O' and resid 872 through 886 removed outlier: 5.199A pdb=" N ALA O 881 " --> pdb=" O ILE O 877 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU O 882 " --> pdb=" O LYS O 878 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL O 886 " --> pdb=" O LEU O 882 " (cutoff:3.500A) Processing helix chain 'O' and resid 895 through 901 removed outlier: 3.971A pdb=" N ASN O 901 " --> pdb=" O ARG O 898 " (cutoff:3.500A) Processing helix chain 'O' and resid 905 through 914 Processing helix chain 'O' and resid 932 through 942 removed outlier: 3.969A pdb=" N LEU O 937 " --> pdb=" O GLU O 933 " (cutoff:3.500A) Processing helix chain 'O' and resid 942 through 958 Processing helix chain 'O' and resid 973 through 979 removed outlier: 4.293A pdb=" N LEU O 978 " --> pdb=" O GLU O 974 " (cutoff:3.500A) Processing helix chain 'O' and resid 980 through 988 Processing helix chain 'O' and resid 995 through 1000 Processing helix chain 'O' and resid 1020 through 1032 Processing helix chain 'O' and resid 1049 through 1061 removed outlier: 3.963A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) Processing helix chain 'O' and resid 1066 through 1073 Processing helix chain 'O' and resid 1081 through 1086 removed outlier: 4.465A pdb=" N ALA O1086 " --> pdb=" O ILE O1082 " (cutoff:3.500A) Processing helix chain 'O' and resid 1086 through 1103 removed outlier: 3.774A pdb=" N GLU O1090 " --> pdb=" O ALA O1086 " (cutoff:3.500A) Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1113 through 1127 removed outlier: 3.864A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP O1121 " --> pdb=" O ASP O1117 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE O1126 " --> pdb=" O PHE O1122 " (cutoff:3.500A) Processing helix chain 'O' and resid 1138 through 1150 Processing helix chain 'O' and resid 1163 through 1168 Processing helix chain 'O' and resid 1187 through 1196 Processing helix chain 'O' and resid 1216 through 1243 removed outlier: 3.671A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY O1233 " --> pdb=" O LEU O1229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS O1234 " --> pdb=" O ASP O1230 " (cutoff:3.500A) Processing helix chain 'O' and resid 1246 through 1267 removed outlier: 4.110A pdb=" N GLN O1250 " --> pdb=" O THR O1246 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG O1255 " --> pdb=" O GLU O1251 " (cutoff:3.500A) Processing helix chain 'O' and resid 1279 through 1287 removed outlier: 4.138A pdb=" N ILE O1283 " --> pdb=" O LYS O1279 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1307 removed outlier: 3.706A pdb=" N MET O1294 " --> pdb=" O ASN O1290 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1348 removed outlier: 3.986A pdb=" N GLU O1341 " --> pdb=" O ARG O1337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.876A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.133A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.156A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.766A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (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: 7.200A 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 868 through 871 removed outlier: 6.195A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL O 889 " --> pdb=" O TYR O 918 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LEU O 920 " --> pdb=" O VAL O 889 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET O 891 " --> pdb=" O LEU O 920 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N LEU O 922 " --> pdb=" O MET O 891 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE O 893 " --> pdb=" O LEU O 922 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY O 788 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE O 789 " --> pdb=" O LEU O 992 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 1007 through 1008 removed outlier: 7.087A pdb=" N VAL O1007 " --> pdb=" O ILE O1208 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 1130 through 1132 removed outlier: 6.196A pdb=" N VAL O1106 " --> pdb=" O PHE O1159 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 11.60 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: 2846 1.32 - 1.44: 5676 1.44 - 1.56: 8524 1.56 - 1.68: 582 1.68 - 1.80: 53 Bond restraints: 17681 Sorted by residual: bond pdb=" C LYS O 757 " pdb=" N GLN O 758 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.07e-02 2.33e+03 1.35e+01 bond pdb=" C1' DC J 108 " pdb=" N1 DC J 108 " ideal model delta sigma weight residual 1.490 1.413 0.077 3.00e-02 1.11e+03 6.62e+00 bond pdb=" C1' DT J 51 " pdb=" N1 DT J 51 " ideal model delta sigma weight residual 1.490 1.414 0.076 3.00e-02 1.11e+03 6.38e+00 bond pdb=" C1' DT J 109 " pdb=" N1 DT J 109 " ideal model delta sigma weight residual 1.490 1.420 0.070 3.00e-02 1.11e+03 5.45e+00 bond pdb=" CG GLN O1173 " pdb=" CD GLN O1173 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.11e+00 ... (remaining 17676 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.25: 1153 104.25 - 111.78: 9602 111.78 - 119.31: 5659 119.31 - 126.84: 7904 126.84 - 134.36: 794 Bond angle restraints: 25112 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 103.25 110.38 -7.13 1.05e+00 9.07e-01 4.61e+01 angle pdb=" N PRO O 932 " pdb=" CA PRO O 932 " pdb=" C PRO O 932 " ideal model delta sigma weight residual 113.86 105.96 7.90 1.25e+00 6.40e-01 4.00e+01 angle pdb=" C TRP O1185 " pdb=" N ASN O1186 " pdb=" CA ASN O1186 " ideal model delta sigma weight residual 121.80 134.36 -12.56 2.44e+00 1.68e-01 2.65e+01 angle pdb=" CA ARG O1299 " pdb=" CB ARG O1299 " pdb=" CG ARG O1299 " ideal model delta sigma weight residual 114.10 104.38 9.72 2.00e+00 2.50e-01 2.36e+01 angle pdb=" CA ARG O1031 " pdb=" CB ARG O1031 " pdb=" CG ARG O1031 " ideal model delta sigma weight residual 114.10 104.44 9.66 2.00e+00 2.50e-01 2.33e+01 ... (remaining 25107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 8380 35.11 - 70.23: 1512 70.23 - 105.34: 48 105.34 - 140.45: 5 140.45 - 175.56: 3 Dihedral angle restraints: 9948 sinusoidal: 6014 harmonic: 3934 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 180.00 133.10 46.90 0 5.00e+00 4.00e-02 8.80e+01 dihedral pdb=" CA LYS O 768 " pdb=" C LYS O 768 " pdb=" N ASP O 769 " pdb=" CA ASP O 769 " ideal model delta harmonic sigma weight residual -180.00 -142.86 -37.14 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA THR E 58 " pdb=" C THR E 58 " pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta harmonic sigma weight residual -180.00 -146.24 -33.76 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1895 0.049 - 0.099: 772 0.099 - 0.148: 167 0.148 - 0.198: 23 0.198 - 0.247: 2 Chirality restraints: 2859 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 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1' DC I 42 " pdb=" O4' DC I 42 " pdb=" C2' DC I 42 " pdb=" N1 DC I 42 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG O1299 " pdb=" N ARG O1299 " pdb=" C ARG O1299 " pdb=" CB ARG O1299 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 2856 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 16 " 0.005 2.00e-02 2.50e+03 2.79e-02 1.75e+01 pdb=" N1 DC J 16 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 16 " 0.067 2.00e-02 2.50e+03 pdb=" O2 DC J 16 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DC J 16 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC J 16 " 0.018 2.00e-02 2.50e+03 pdb=" N4 DC J 16 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC J 16 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC J 16 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 24 " 0.002 2.00e-02 2.50e+03 2.48e-02 1.38e+01 pdb=" N1 DC I 24 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 24 " 0.062 2.00e-02 2.50e+03 pdb=" O2 DC I 24 " -0.039 2.00e-02 2.50e+03 pdb=" N3 DC I 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 24 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 24 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 24 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC I 24 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 131 " -0.049 2.00e-02 2.50e+03 2.12e-02 1.23e+01 pdb=" N9 DA I 131 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DA I 131 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA I 131 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 131 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA I 131 " -0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 131 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 131 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 131 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 131 " 0.004 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 260 2.53 - 3.12: 16288 3.12 - 3.71: 33264 3.71 - 4.31: 43391 4.31 - 4.90: 60499 Nonbonded interactions: 153702 Sorted by model distance: nonbonded pdb=" O2 DC I 111 " pdb=" N2 DG J 37 " model vdw 1.932 2.496 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 1.964 2.440 nonbonded pdb=" N6 DA I 60 " pdb=" O4 DT J 87 " model vdw 1.987 2.520 nonbonded pdb=" NE2 GLN O1173 " pdb=" O ARG O1199 " model vdw 2.063 2.520 nonbonded pdb=" NH2 ARG O1105 " pdb=" O PHE O1149 " model vdw 2.090 2.520 ... (remaining 153697 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 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 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: 0.720 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: 4.320 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 60.690 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.012 0.077 17681 Z= 0.676 Angle : 1.121 14.254 25112 Z= 0.612 Chirality : 0.054 0.247 2859 Planarity : 0.006 0.048 2171 Dihedral : 26.087 175.563 7394 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 49.72 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.84 % Favored : 88.70 % Rotamer: Outliers : 0.26 % Allowed : 0.70 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.13 % Twisted General : 0.46 % 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: -5.59 (0.16), residues: 1319 helix: -4.42 (0.09), residues: 799 sheet: -2.49 (0.70), residues: 38 loop : -2.04 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.006 TRP O 955 HIS 0.017 0.004 HIS O 984 PHE 0.044 0.004 PHE O 946 TYR 0.045 0.004 TYR F 98 ARG 0.019 0.001 ARG O1264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 371 time to evaluate : 1.564 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 374 average time/residue: 0.3976 time to fit residues: 203.5101 Evaluate side-chains 194 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1697 time to fit residues: 2.4364 ------------------------------------------------------------------------------- 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: 9.9990 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 73 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 749 HIS ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1051 GLN O1054 GLN O1111 GLN ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17681 Z= 0.246 Angle : 0.751 10.414 25112 Z= 0.429 Chirality : 0.042 0.172 2859 Planarity : 0.006 0.058 2171 Dihedral : 31.335 178.205 4676 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.08 % Favored : 94.77 % Rotamer: Outliers : 0.26 % Allowed : 1.83 % Favored : 97.91 % 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: -2.14 (0.21), residues: 1319 helix: -1.17 (0.16), residues: 854 sheet: -1.60 (0.61), residues: 60 loop : -1.56 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP O 955 HIS 0.010 0.002 HIS B 75 PHE 0.044 0.003 PHE O 946 TYR 0.031 0.003 TYR O1226 ARG 0.013 0.001 ARG O 880 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 330 time to evaluate : 1.694 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 331 average time/residue: 0.3879 time to fit residues: 178.5940 Evaluate side-chains 225 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1517 time to fit residues: 2.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 44 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 68 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1049 ASN O1051 GLN ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17681 Z= 0.257 Angle : 0.706 12.612 25112 Z= 0.402 Chirality : 0.040 0.156 2859 Planarity : 0.006 0.070 2171 Dihedral : 30.855 178.098 4676 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 0.17 % Allowed : 3.05 % Favored : 96.78 % 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: 1319 helix: 0.20 (0.18), residues: 846 sheet: -1.01 (0.61), residues: 63 loop : -1.42 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 955 HIS 0.007 0.002 HIS D 106 PHE 0.043 0.002 PHE O 946 TYR 0.026 0.002 TYR H 80 ARG 0.009 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 311 time to evaluate : 1.562 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 outliers start: 2 outliers final: 1 residues processed: 312 average time/residue: 0.3364 time to fit residues: 148.7697 Evaluate side-chains 212 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1567 time to fit residues: 2.3161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17681 Z= 0.213 Angle : 0.673 11.426 25112 Z= 0.383 Chirality : 0.038 0.157 2859 Planarity : 0.005 0.054 2171 Dihedral : 30.505 177.975 4676 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.93 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 0.10 (0.23), residues: 1319 helix: 0.70 (0.18), residues: 866 sheet: -0.50 (0.65), residues: 63 loop : -1.10 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 935 HIS 0.008 0.001 HIS B 75 PHE 0.041 0.002 PHE O 946 TYR 0.033 0.002 TYR B 98 ARG 0.006 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.462 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.3622 time to fit residues: 153.2345 Evaluate side-chains 216 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17681 Z= 0.212 Angle : 0.662 11.075 25112 Z= 0.375 Chirality : 0.037 0.139 2859 Planarity : 0.005 0.056 2171 Dihedral : 30.256 177.024 4676 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % 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: 0.23 (0.23), residues: 1319 helix: 0.72 (0.18), residues: 874 sheet: -0.01 (0.69), residues: 63 loop : -0.98 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 955 HIS 0.007 0.001 HIS B 75 PHE 0.022 0.002 PHE E 104 TYR 0.037 0.002 TYR D 80 ARG 0.006 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.547 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: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.3312 time to fit residues: 141.4787 Evaluate side-chains 209 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.0010 chunk 137 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN H 92 GLN ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 911 ASN O 929 ASN ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17681 Z= 0.190 Angle : 0.648 10.821 25112 Z= 0.367 Chirality : 0.037 0.147 2859 Planarity : 0.005 0.053 2171 Dihedral : 30.006 177.044 4676 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1319 helix: 0.85 (0.18), residues: 878 sheet: 0.35 (0.70), residues: 65 loop : -0.91 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 955 HIS 0.008 0.001 HIS O 913 PHE 0.023 0.002 PHE O1110 TYR 0.023 0.002 TYR O 744 ARG 0.004 0.000 ARG O1031 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.564 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 outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3450 time to fit residues: 146.6183 Evaluate side-chains 204 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.0470 chunk 17 optimal weight: 0.0570 chunk 87 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN C 68 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN O 685 GLN ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1050 ASN O1073 ASN ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17681 Z= 0.213 Angle : 0.653 10.777 25112 Z= 0.370 Chirality : 0.037 0.131 2859 Planarity : 0.005 0.071 2171 Dihedral : 29.882 176.643 4676 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1319 helix: 0.77 (0.18), residues: 876 sheet: 0.56 (0.71), residues: 63 loop : -1.04 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 955 HIS 0.008 0.001 HIS O1061 PHE 0.023 0.003 PHE A 67 TYR 0.040 0.002 TYR D 80 ARG 0.006 0.001 ARG O1076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.663 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 outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.3265 time to fit residues: 129.0202 Evaluate side-chains 192 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN E 125 GLN G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17681 Z= 0.286 Angle : 0.697 11.057 25112 Z= 0.395 Chirality : 0.039 0.270 2859 Planarity : 0.005 0.064 2171 Dihedral : 29.979 176.469 4676 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1319 helix: 0.56 (0.18), residues: 876 sheet: 0.11 (0.68), residues: 63 loop : -1.24 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 777 HIS 0.015 0.002 HIS B 75 PHE 0.027 0.003 PHE A 67 TYR 0.027 0.002 TYR D 80 ARG 0.006 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.530 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 outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3345 time to fit residues: 122.5081 Evaluate side-chains 177 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 687 ASN ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17681 Z= 0.208 Angle : 0.661 10.778 25112 Z= 0.373 Chirality : 0.037 0.191 2859 Planarity : 0.005 0.054 2171 Dihedral : 29.783 177.631 4676 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1319 helix: 0.66 (0.18), residues: 882 sheet: 0.49 (0.71), residues: 61 loop : -1.08 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 955 HIS 0.005 0.001 HIS F 75 PHE 0.034 0.002 PHE O1089 TYR 0.023 0.002 TYR B 98 ARG 0.007 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.506 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 outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3476 time to fit residues: 133.7942 Evaluate side-chains 194 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 104 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1189 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1198 HIS ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 17681 Z= 0.390 Angle : 0.786 11.791 25112 Z= 0.442 Chirality : 0.042 0.273 2859 Planarity : 0.006 0.085 2171 Dihedral : 30.039 176.221 4676 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1319 helix: 0.21 (0.17), residues: 874 sheet: -0.12 (0.68), residues: 61 loop : -1.40 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP O 777 HIS 0.007 0.002 HIS F 75 PHE 0.028 0.003 PHE A 104 TYR 0.033 0.003 TYR O1226 ARG 0.015 0.001 ARG O1164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.446 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 outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3264 time to fit residues: 105.8188 Evaluate side-chains 162 residues out of total 1171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.041233 restraints weight = 124323.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042443 restraints weight = 74300.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.043293 restraints weight = 52220.172| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17681 Z= 0.226 Angle : 0.675 10.821 25112 Z= 0.381 Chirality : 0.038 0.198 2859 Planarity : 0.005 0.058 2171 Dihedral : 29.847 178.021 4676 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1319 helix: 0.55 (0.18), residues: 876 sheet: 0.15 (0.69), residues: 61 loop : -1.21 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 955 HIS 0.012 0.001 HIS O1061 PHE 0.025 0.002 PHE O 835 TYR 0.027 0.002 TYR O1226 ARG 0.011 0.001 ARG O1164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.02 seconds wall clock time: 62 minutes 56.47 seconds (3776.47 seconds total)