Starting phenix.real_space_refine on Sun Mar 17 07:23:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy3_9749/03_2024/6iy3_9749_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy3_9749/03_2024/6iy3_9749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy3_9749/03_2024/6iy3_9749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy3_9749/03_2024/6iy3_9749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy3_9749/03_2024/6iy3_9749_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy3_9749/03_2024/6iy3_9749_updated.pdb" } resolution = 3.67 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= 0.001 sd= 0.010 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 296 5.49 5 S 27 5.16 5 C 9834 2.51 5 N 3167 2.21 5 O 3749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 898": "NH1" <-> "NH2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1076": "NH1" <-> "NH2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O ARG 1142": "NH1" <-> "NH2" Residue "O ARG 1164": "NH1" <-> "NH2" Residue "O PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1268": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17073 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2972 Classifications: {'DNA': 147} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3056 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "O" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4791 Unusual residues: {'ADP': 1} Classifications: {'peptide': 580, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 563, None: 1} Not linked: pdbres="GLY O1348 " pdbres="ADP O2000 " Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.44, per 1000 atoms: 0.55 Number of scatterers: 17073 At special positions: 0 Unit cell: (141.24, 130.68, 132, 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 27 16.00 P 296 15.00 O 3749 8.00 N 3167 7.00 C 9834 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: 8.38 Conformation dependent library (CDL) restraints added in 2.0 seconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 2 sheets defined 54.7% alpha, 1.2% beta 108 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 8.26 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.526A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 57 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'O' and resid 672 through 682 Processing helix chain 'O' and resid 684 through 688 Processing helix chain 'O' and resid 745 through 748 No H-bonds generated for 'chain 'O' and resid 745 through 748' Processing helix chain 'O' and resid 769 through 783 Processing helix chain 'O' and resid 798 through 811 Processing helix chain 'O' and resid 828 through 838 removed outlier: 3.693A pdb=" N ALA O 836 " --> pdb=" O SER O 832 " (cutoff:3.500A) Processing helix chain 'O' and resid 851 through 861 removed outlier: 4.872A pdb=" N ALA O 856 " --> pdb=" O ASN O 852 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS O 857 " --> pdb=" O GLU O 853 " (cutoff:3.500A) Processing helix chain 'O' and resid 873 through 884 removed outlier: 4.132A pdb=" N ILE O 877 " --> pdb=" O PHE O 873 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA O 881 " --> pdb=" O ILE O 877 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU O 882 " --> pdb=" O LYS O 878 " (cutoff:3.500A) Processing helix chain 'O' and resid 896 through 899 No H-bonds generated for 'chain 'O' and resid 896 through 899' Processing helix chain 'O' and resid 905 through 911 Processing helix chain 'O' and resid 934 through 937 No H-bonds generated for 'chain 'O' and resid 934 through 937' Processing helix chain 'O' and resid 944 through 949 Processing helix chain 'O' and resid 952 through 957 Processing helix chain 'O' and resid 977 through 986 Processing helix chain 'O' and resid 1021 through 1030 removed outlier: 3.531A pdb=" N ARG O1030 " --> pdb=" O LEU O1027 " (cutoff:3.500A) Processing helix chain 'O' and resid 1051 through 1060 removed outlier: 3.560A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE O1058 " --> pdb=" O GLN O1054 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS O1059 " --> pdb=" O LEU O1055 " (cutoff:3.500A) Processing helix chain 'O' and resid 1069 through 1072 No H-bonds generated for 'chain 'O' and resid 1069 through 1072' Processing helix chain 'O' and resid 1083 through 1085 No H-bonds generated for 'chain 'O' and resid 1083 through 1085' Processing helix chain 'O' and resid 1087 through 1102 removed outlier: 3.836A pdb=" N LEU O1091 " --> pdb=" O GLY O1087 " (cutoff:3.500A) Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1113 through 1125 Processing helix chain 'O' and resid 1140 through 1149 removed outlier: 4.077A pdb=" N LEU O1146 " --> pdb=" O ARG O1142 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG O1147 " --> pdb=" O SER O1143 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU O1148 " --> pdb=" O GLU O1144 " (cutoff:3.500A) Processing helix chain 'O' and resid 1188 through 1193 Processing helix chain 'O' and resid 1195 through 1198 No H-bonds generated for 'chain 'O' and resid 1195 through 1198' Processing helix chain 'O' and resid 1217 through 1229 Processing helix chain 'O' and resid 1231 through 1242 removed outlier: 3.840A pdb=" N GLY O1239 " --> pdb=" O ILE O1236 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS O1240 " --> pdb=" O GLN O1237 " (cutoff:3.500A) Processing helix chain 'O' and resid 1249 through 1262 removed outlier: 4.801A pdb=" N LEU O1254 " --> pdb=" O GLN O1250 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA O1260 " --> pdb=" O SER O1256 " (cutoff:3.500A) Processing helix chain 'O' and resid 1265 through 1267 No H-bonds generated for 'chain 'O' and resid 1265 through 1267' Processing helix chain 'O' and resid 1280 through 1287 Processing helix chain 'O' and resid 1291 through 1303 Processing helix chain 'O' and resid 1338 through 1343 Processing sheet with id= A, first strand: chain 'O' and resid 819 through 822 removed outlier: 6.667A pdb=" N HIS O 890 " --> pdb=" O LEU O 820 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ILE O 822 " --> pdb=" O HIS O 890 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE O 892 " --> pdb=" O ILE O 822 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'O' and resid 1158 through 1160 removed outlier: 6.490A pdb=" N VAL O1106 " --> pdb=" O PHE O1159 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR O1177 " --> pdb=" O LEU O1107 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE O1109 " --> pdb=" O THR O1177 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE O1179 " --> pdb=" O PHE O1109 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG O1207 " --> pdb=" O VAL O1178 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE O1180 " --> pdb=" O ARG O1207 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU O1209 " --> pdb=" O ILE O1180 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 473 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 270 hydrogen bonds 540 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 9.15 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3068 1.33 - 1.45: 5432 1.45 - 1.57: 8824 1.57 - 1.68: 589 1.68 - 1.80: 51 Bond restraints: 17964 Sorted by residual: bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 5.02e+00 bond pdb=" CB VAL G 100 " pdb=" CG1 VAL G 100 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CB PRO F 32 " pdb=" CG PRO F 32 " ideal model delta sigma weight residual 1.492 1.392 0.100 5.00e-02 4.00e+02 4.01e+00 bond pdb=" C2' DC I 58 " pdb=" C1' DC I 58 " ideal model delta sigma weight residual 1.525 1.488 0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C3' DC I 23 " pdb=" O3' DC I 23 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.18e+00 ... (remaining 17959 not shown) Histogram of bond angle deviations from ideal: 95.31 - 103.38: 755 103.38 - 111.46: 8810 111.46 - 119.54: 7620 119.54 - 127.62: 7793 127.62 - 135.70: 512 Bond angle restraints: 25490 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 103.25 109.92 -6.67 1.05e+00 9.07e-01 4.03e+01 angle pdb=" C ASN O1049 " pdb=" N ASN O1050 " pdb=" CA ASN O1050 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C3' DG J 109 " pdb=" C2' DG J 109 " pdb=" C1' DG J 109 " ideal model delta sigma weight residual 101.60 95.31 6.29 1.50e+00 4.44e-01 1.76e+01 angle pdb=" C3' DC I 24 " pdb=" C2' DC I 24 " pdb=" C1' DC I 24 " ideal model delta sigma weight residual 101.60 95.80 5.80 1.50e+00 4.44e-01 1.50e+01 angle pdb=" C THR F 30 " pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 120.26 125.43 -5.17 1.34e+00 5.57e-01 1.49e+01 ... (remaining 25485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 8500 34.96 - 69.92: 1570 69.92 - 104.88: 65 104.88 - 139.84: 4 139.84 - 174.80: 3 Dihedral angle restraints: 10142 sinusoidal: 6156 harmonic: 3986 Sorted by residual: dihedral pdb=" CA PRO O 932 " pdb=" C PRO O 932 " pdb=" N GLU O 933 " pdb=" CA GLU O 933 " ideal model delta harmonic sigma weight residual -180.00 -142.93 -37.07 0 5.00e+00 4.00e-02 5.50e+01 dihedral pdb=" O2A ADP O2000 " pdb=" O3A ADP O2000 " pdb=" PA ADP O2000 " pdb=" PB ADP O2000 " ideal model delta sinusoidal sigma weight residual 300.00 131.19 168.81 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP O2000 " pdb=" O5' ADP O2000 " pdb=" PA ADP O2000 " pdb=" O2A ADP O2000 " ideal model delta sinusoidal sigma weight residual -60.00 83.52 -143.52 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 10139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2076 0.061 - 0.122: 682 0.122 - 0.183: 118 0.183 - 0.243: 12 0.243 - 0.304: 4 Chirality restraints: 2892 Sorted by residual: chirality pdb=" CA ASN O1050 " pdb=" N ASN O1050 " pdb=" C ASN O1050 " pdb=" CB ASN O1050 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C1' DC I 24 " pdb=" O4' DC I 24 " pdb=" C2' DC I 24 " pdb=" N1 DC I 24 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2889 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 122 " -0.039 2.00e-02 2.50e+03 1.88e-02 8.82e+00 pdb=" N1 DT J 122 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DT J 122 " 0.014 2.00e-02 2.50e+03 pdb=" O2 DT J 122 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DT J 122 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT J 122 " -0.025 2.00e-02 2.50e+03 pdb=" O4 DT J 122 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT J 122 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT J 122 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DT J 122 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO H 103 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 946 " 0.021 2.00e-02 2.50e+03 1.90e-02 6.33e+00 pdb=" CG PHE O 946 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE O 946 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE O 946 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE O 946 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE O 946 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE O 946 " -0.002 2.00e-02 2.50e+03 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3684 2.79 - 3.32: 15033 3.32 - 3.84: 32127 3.84 - 4.37: 37004 4.37 - 4.90: 54378 Nonbonded interactions: 142226 Sorted by model distance: nonbonded pdb=" OP1 DC J 95 " pdb=" OG SER O 904 " model vdw 2.260 2.440 nonbonded pdb=" NE2 GLN O1111 " pdb=" OD1 ASP O1184 " model vdw 2.293 2.520 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.295 2.440 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.296 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.303 2.520 ... (remaining 142221 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 37 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = (chain 'G' and resid 11 through 117) } ncs_group { reference = (chain 'D' and resid 29 through 125) selection = chain 'H' } 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.860 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 56.040 Find NCS groups from input model: 0.700 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.009 0.100 17964 Z= 0.538 Angle : 1.078 13.260 25490 Z= 0.611 Chirality : 0.060 0.304 2892 Planarity : 0.007 0.072 2204 Dihedral : 26.116 174.797 7552 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.24 % Favored : 91.54 % Rotamer: Outliers : 0.42 % Allowed : 2.04 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.98 (0.17), residues: 1335 helix: -2.21 (0.13), residues: 782 sheet: -3.27 (0.48), residues: 72 loop : -3.03 (0.23), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O1083 HIS 0.015 0.003 HIS O 984 PHE 0.044 0.005 PHE O 946 TYR 0.027 0.004 TYR B 51 ARG 0.010 0.001 ARG O 854 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 290 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8545 (p) cc_final: 0.8171 (t) REVERT: A 120 MET cc_start: 0.8067 (mtp) cc_final: 0.7802 (mtp) REVERT: C 15 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8377 (mttm) REVERT: D 59 MET cc_start: 0.8721 (tpp) cc_final: 0.8334 (tpp) REVERT: E 108 ASN cc_start: 0.8783 (t0) cc_final: 0.8559 (t0) REVERT: E 133 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7509 (mt-10) REVERT: G 77 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8110 (ttm-80) REVERT: O 933 GLU cc_start: 0.6393 (tp30) cc_final: 0.5535 (tp30) REVERT: O 1124 ARG cc_start: 0.7370 (mmm160) cc_final: 0.7075 (ptp-110) REVERT: O 1182 ASP cc_start: 0.7276 (p0) cc_final: 0.7005 (p0) REVERT: O 1266 LYS cc_start: 0.6543 (mttt) cc_final: 0.6002 (tptp) REVERT: O 1267 LYS cc_start: 0.7480 (mttt) cc_final: 0.6708 (tptt) REVERT: O 1287 LEU cc_start: 0.7373 (pp) cc_final: 0.7148 (pp) REVERT: O 1294 MET cc_start: 0.6690 (mmm) cc_final: 0.6314 (mmm) outliers start: 5 outliers final: 2 residues processed: 293 average time/residue: 0.4442 time to fit residues: 172.1712 Evaluate side-chains 183 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 931 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 31 HIS D 47 GLN D 67 ASN D 82 HIS D 84 ASN E 68 GLN G 38 ASN H 49 HIS H 95 GLN O 685 GLN O 776 GLN O 783 ASN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 858 GLN ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1188 HIS O1192 GLN O1347 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17964 Z= 0.310 Angle : 0.718 12.548 25490 Z= 0.403 Chirality : 0.042 0.175 2892 Planarity : 0.005 0.057 2204 Dihedral : 30.646 178.668 4735 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 2.12 % Allowed : 8.58 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1335 helix: -0.39 (0.17), residues: 794 sheet: -3.22 (0.53), residues: 63 loop : -2.58 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O1083 HIS 0.008 0.001 HIS F 75 PHE 0.034 0.002 PHE O 946 TYR 0.014 0.002 TYR B 51 ARG 0.006 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.580 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 87 SER cc_start: 0.8702 (p) cc_final: 0.8479 (t) REVERT: A 94 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 120 MET cc_start: 0.8209 (mtp) cc_final: 0.7861 (ttm) REVERT: C 15 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8237 (mtmm) REVERT: D 59 MET cc_start: 0.8579 (tpp) cc_final: 0.8236 (tpp) REVERT: E 41 TYR cc_start: 0.7916 (m-80) cc_final: 0.7627 (m-80) REVERT: F 92 ARG cc_start: 0.8738 (ptm-80) cc_final: 0.8479 (ptm-80) REVERT: G 71 ARG cc_start: 0.8056 (mtp-110) cc_final: 0.7567 (ptp-170) REVERT: G 101 THR cc_start: 0.9398 (p) cc_final: 0.9181 (p) REVERT: O 858 GLN cc_start: 0.7713 (tp40) cc_final: 0.7457 (mt0) REVERT: O 1022 MET cc_start: 0.3837 (tmm) cc_final: 0.3545 (tmm) REVERT: O 1124 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6941 (ptp-110) REVERT: O 1147 ARG cc_start: 0.8248 (tmm-80) cc_final: 0.7274 (mmm160) REVERT: O 1182 ASP cc_start: 0.7397 (p0) cc_final: 0.6995 (p0) REVERT: O 1266 LYS cc_start: 0.6660 (mttt) cc_final: 0.6026 (tptp) REVERT: O 1267 LYS cc_start: 0.7458 (mttt) cc_final: 0.6744 (tptt) REVERT: O 1294 MET cc_start: 0.6583 (mmm) cc_final: 0.6204 (mmt) outliers start: 25 outliers final: 17 residues processed: 213 average time/residue: 0.3602 time to fit residues: 108.4764 Evaluate side-chains 177 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 907 SER Chi-restraints excluded: chain O residue 912 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 1188 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN O 776 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN O1192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17964 Z= 0.175 Angle : 0.609 9.086 25490 Z= 0.347 Chirality : 0.037 0.149 2892 Planarity : 0.004 0.052 2204 Dihedral : 29.836 177.465 4735 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.78 % Allowed : 11.81 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.78 (0.22), residues: 1335 helix: 0.69 (0.18), residues: 793 sheet: -2.57 (0.54), residues: 71 loop : -2.28 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O1083 HIS 0.036 0.002 HIS O1188 PHE 0.026 0.002 PHE O 946 TYR 0.016 0.002 TYR D 83 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8502 (p) cc_final: 0.8071 (t) REVERT: C 15 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8138 (mtmm) REVERT: D 59 MET cc_start: 0.8446 (tpp) cc_final: 0.8060 (tpp) REVERT: D 85 LYS cc_start: 0.8224 (mptt) cc_final: 0.7925 (mmmt) REVERT: D 108 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7969 (tptp) REVERT: F 27 GLN cc_start: 0.8862 (mm110) cc_final: 0.8436 (mm-40) REVERT: G 71 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7325 (ptp-170) REVERT: O 794 MET cc_start: 0.6572 (tmm) cc_final: 0.6289 (tmm) REVERT: O 1124 ARG cc_start: 0.7484 (mmm160) cc_final: 0.6910 (ptp-110) REVERT: O 1147 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7789 (tmm-80) REVERT: O 1182 ASP cc_start: 0.7548 (p0) cc_final: 0.7028 (p0) REVERT: O 1267 LYS cc_start: 0.7249 (mttt) cc_final: 0.6688 (tptt) outliers start: 21 outliers final: 11 residues processed: 217 average time/residue: 0.3259 time to fit residues: 101.6218 Evaluate side-chains 170 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 912 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 928 GLN O1019 GLN O1071 GLN O1189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17964 Z= 0.350 Angle : 0.696 10.164 25490 Z= 0.386 Chirality : 0.041 0.175 2892 Planarity : 0.005 0.054 2204 Dihedral : 30.080 170.702 4735 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.40 % Allowed : 12.15 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.68 (0.23), residues: 1335 helix: 0.74 (0.19), residues: 795 sheet: -2.66 (0.56), residues: 72 loop : -2.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP O1083 HIS 0.007 0.001 HIS F 75 PHE 0.027 0.002 PHE O1063 TYR 0.020 0.002 TYR D 83 ARG 0.006 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 120 MET cc_start: 0.8087 (mtp) cc_final: 0.7779 (ttm) REVERT: C 15 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8296 (mtmm) REVERT: D 59 MET cc_start: 0.8571 (tpp) cc_final: 0.8212 (tpp) REVERT: D 85 LYS cc_start: 0.8231 (mptt) cc_final: 0.7916 (mmmt) REVERT: G 71 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7428 (ptp-170) REVERT: O 794 MET cc_start: 0.6801 (tmm) cc_final: 0.6511 (tmm) REVERT: O 990 PHE cc_start: 0.7527 (m-80) cc_final: 0.7298 (m-80) REVERT: O 1022 MET cc_start: 0.3448 (tmm) cc_final: 0.3168 (tmm) REVERT: O 1053 MET cc_start: 0.8819 (tpp) cc_final: 0.8488 (tpp) REVERT: O 1123 LEU cc_start: 0.7890 (mt) cc_final: 0.7635 (mp) REVERT: O 1124 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7066 (ptp-110) REVERT: O 1182 ASP cc_start: 0.7428 (p0) cc_final: 0.7210 (p0) REVERT: O 1185 TRP cc_start: 0.7232 (m100) cc_final: 0.7012 (m100) REVERT: O 1218 GLU cc_start: 0.7191 (pt0) cc_final: 0.6990 (pt0) REVERT: O 1267 LYS cc_start: 0.7524 (mttt) cc_final: 0.7221 (tptt) outliers start: 40 outliers final: 27 residues processed: 200 average time/residue: 0.3394 time to fit residues: 96.9706 Evaluate side-chains 182 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 907 SER Chi-restraints excluded: chain O residue 912 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 104 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17964 Z= 0.253 Angle : 0.634 10.747 25490 Z= 0.355 Chirality : 0.038 0.157 2892 Planarity : 0.004 0.053 2204 Dihedral : 29.877 169.285 4735 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.14 % Allowed : 12.57 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.29 (0.23), residues: 1335 helix: 1.06 (0.19), residues: 793 sheet: -2.56 (0.60), residues: 63 loop : -2.03 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP O1083 HIS 0.005 0.001 HIS F 75 PHE 0.026 0.002 PHE O1063 TYR 0.018 0.002 TYR D 83 ARG 0.011 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 59 MET cc_start: 0.8538 (tpp) cc_final: 0.8205 (tpp) REVERT: D 85 LYS cc_start: 0.8266 (mptt) cc_final: 0.7930 (mmmt) REVERT: G 71 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7526 (ptp-170) REVERT: O 794 MET cc_start: 0.6882 (tmm) cc_final: 0.6517 (tmm) REVERT: O 875 TYR cc_start: 0.7147 (m-80) cc_final: 0.6796 (m-80) REVERT: O 1022 MET cc_start: 0.3818 (tmm) cc_final: 0.3613 (tmm) REVERT: O 1053 MET cc_start: 0.8844 (tpp) cc_final: 0.8634 (tpp) REVERT: O 1182 ASP cc_start: 0.7491 (p0) cc_final: 0.7260 (p0) REVERT: O 1263 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6751 (tp30) REVERT: O 1267 LYS cc_start: 0.7740 (mttt) cc_final: 0.7209 (tptt) outliers start: 37 outliers final: 24 residues processed: 185 average time/residue: 0.3244 time to fit residues: 87.1510 Evaluate side-chains 172 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 775 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 912 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1263 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 154 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17964 Z= 0.190 Angle : 0.597 11.892 25490 Z= 0.336 Chirality : 0.037 0.243 2892 Planarity : 0.004 0.056 2204 Dihedral : 29.541 170.042 4735 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.55 % Allowed : 13.59 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.10 (0.24), residues: 1335 helix: 1.37 (0.19), residues: 793 sheet: -2.27 (0.59), residues: 72 loop : -1.84 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP O1083 HIS 0.003 0.001 HIS O 681 PHE 0.023 0.002 PHE O1063 TYR 0.018 0.001 TYR C 57 ARG 0.008 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8616 (mt) REVERT: D 59 MET cc_start: 0.8495 (tpp) cc_final: 0.8149 (tpp) REVERT: D 85 LYS cc_start: 0.8211 (mptt) cc_final: 0.7863 (mmmt) REVERT: D 108 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7916 (ttpt) REVERT: F 79 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7926 (mttp) REVERT: G 71 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7376 (ptp-170) REVERT: O 875 TYR cc_start: 0.7095 (m-80) cc_final: 0.6841 (m-80) REVERT: O 1182 ASP cc_start: 0.7464 (p0) cc_final: 0.7199 (p0) REVERT: O 1267 LYS cc_start: 0.7829 (mttt) cc_final: 0.7217 (tptt) outliers start: 30 outliers final: 20 residues processed: 182 average time/residue: 0.3169 time to fit residues: 84.2337 Evaluate side-chains 171 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 923 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1188 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 8.9990 chunk 17 optimal weight: 0.0170 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1019 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 17964 Z= 0.481 Angle : 0.773 11.687 25490 Z= 0.424 Chirality : 0.045 0.183 2892 Planarity : 0.005 0.058 2204 Dihedral : 30.102 159.481 4735 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.57 % Allowed : 13.76 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.52 (0.23), residues: 1335 helix: 0.85 (0.19), residues: 783 sheet: -2.37 (0.59), residues: 72 loop : -2.04 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP O1083 HIS 0.009 0.002 HIS F 75 PHE 0.032 0.003 PHE O1063 TYR 0.023 0.003 TYR D 83 ARG 0.011 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 152 time to evaluate : 1.599 Fit side-chains REVERT: D 59 MET cc_start: 0.8656 (tpp) cc_final: 0.8304 (tpp) REVERT: D 85 LYS cc_start: 0.8225 (mptt) cc_final: 0.7942 (mmmt) REVERT: H 68 ASP cc_start: 0.8572 (t0) cc_final: 0.8323 (t0) REVERT: O 794 MET cc_start: 0.6954 (tmm) cc_final: 0.6600 (tmm) REVERT: O 834 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6744 (mm-30) REVERT: O 875 TYR cc_start: 0.7586 (m-80) cc_final: 0.7190 (m-80) REVERT: O 1022 MET cc_start: 0.4068 (tmm) cc_final: 0.3612 (tmm) outliers start: 42 outliers final: 31 residues processed: 178 average time/residue: 0.3235 time to fit residues: 84.0531 Evaluate side-chains 170 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 809 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 907 SER Chi-restraints excluded: chain O residue 918 TYR Chi-restraints excluded: chain O residue 923 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1019 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17964 Z= 0.313 Angle : 0.673 11.353 25490 Z= 0.375 Chirality : 0.040 0.165 2892 Planarity : 0.004 0.057 2204 Dihedral : 29.969 161.755 4735 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.97 % Allowed : 15.80 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.38 (0.24), residues: 1335 helix: 0.97 (0.19), residues: 788 sheet: -2.33 (0.59), residues: 72 loop : -2.03 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP O1083 HIS 0.007 0.001 HIS F 75 PHE 0.028 0.002 PHE O1063 TYR 0.019 0.002 TYR D 83 ARG 0.013 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: D 59 MET cc_start: 0.8594 (tpp) cc_final: 0.8260 (tpp) REVERT: H 120 LYS cc_start: 0.8442 (tptt) cc_final: 0.8208 (tptt) REVERT: O 834 GLU cc_start: 0.7623 (mm-30) cc_final: 0.6798 (mm-30) REVERT: O 875 TYR cc_start: 0.7496 (m-80) cc_final: 0.7140 (m-80) REVERT: O 1022 MET cc_start: 0.4056 (tmm) cc_final: 0.3609 (tmm) REVERT: O 1157 LEU cc_start: 0.5630 (mt) cc_final: 0.5118 (pt) outliers start: 35 outliers final: 32 residues processed: 165 average time/residue: 0.3134 time to fit residues: 78.1174 Evaluate side-chains 169 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 809 LEU Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 918 TYR Chi-restraints excluded: chain O residue 923 THR Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 143 optimal weight: 0.0030 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1019 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17964 Z= 0.176 Angle : 0.606 13.690 25490 Z= 0.338 Chirality : 0.036 0.170 2892 Planarity : 0.004 0.065 2204 Dihedral : 29.422 171.635 4735 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.78 % Allowed : 17.25 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.23 (0.24), residues: 1335 helix: 1.40 (0.19), residues: 793 sheet: -1.98 (0.62), residues: 71 loop : -1.71 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP O1083 HIS 0.004 0.001 HIS O 984 PHE 0.024 0.002 PHE O 946 TYR 0.019 0.001 TYR C 57 ARG 0.013 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.8417 (tpp) cc_final: 0.8107 (tpp) REVERT: E 90 MET cc_start: 0.7238 (mmm) cc_final: 0.6746 (mmt) REVERT: O 794 MET cc_start: 0.6730 (tmm) cc_final: 0.6420 (tmm) REVERT: O 834 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6907 (mm-30) REVERT: O 1157 LEU cc_start: 0.5455 (mt) cc_final: 0.5007 (pt) outliers start: 21 outliers final: 17 residues processed: 172 average time/residue: 0.2885 time to fit residues: 74.9183 Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 0.3980 chunk 126 optimal weight: 20.0000 chunk 13 optimal weight: 0.0040 chunk 98 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1019 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17964 Z= 0.317 Angle : 0.670 12.439 25490 Z= 0.369 Chirality : 0.040 0.186 2892 Planarity : 0.004 0.065 2204 Dihedral : 29.677 166.690 4735 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.21 % Allowed : 17.16 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.03 (0.24), residues: 1335 helix: 1.24 (0.19), residues: 791 sheet: -2.06 (0.61), residues: 72 loop : -1.77 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.004 TRP O1083 HIS 0.006 0.001 HIS F 75 PHE 0.028 0.002 PHE O1063 TYR 0.017 0.002 TYR C 57 ARG 0.015 0.001 ARG H 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: C 111 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8580 (mt) REVERT: D 59 MET cc_start: 0.8574 (tpp) cc_final: 0.8235 (tpp) REVERT: O 794 MET cc_start: 0.6871 (tmm) cc_final: 0.6542 (tmm) REVERT: O 834 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6750 (mm-30) REVERT: O 876 ILE cc_start: 0.8298 (mm) cc_final: 0.8015 (mm) REVERT: O 1022 MET cc_start: 0.4098 (tmm) cc_final: 0.3576 (tmm) REVERT: O 1157 LEU cc_start: 0.5647 (mt) cc_final: 0.5170 (pt) outliers start: 26 outliers final: 23 residues processed: 161 average time/residue: 0.2941 time to fit residues: 71.5974 Evaluate side-chains 164 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 754 ASP Chi-restraints excluded: chain O residue 763 VAL Chi-restraints excluded: chain O residue 775 LEU Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 1013 CYS Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 127 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1019 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.142132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104900 restraints weight = 37012.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104417 restraints weight = 36613.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.105260 restraints weight = 34878.087| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17964 Z= 0.181 Angle : 0.606 13.283 25490 Z= 0.337 Chirality : 0.036 0.168 2892 Planarity : 0.004 0.071 2204 Dihedral : 29.320 173.068 4735 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.95 % Allowed : 17.50 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.34 (0.24), residues: 1335 helix: 1.47 (0.19), residues: 793 sheet: -1.89 (0.63), residues: 71 loop : -1.62 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP O1083 HIS 0.003 0.001 HIS F 75 PHE 0.025 0.002 PHE O1063 TYR 0.021 0.001 TYR C 57 ARG 0.014 0.000 ARG H 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2749.30 seconds wall clock time: 50 minutes 37.30 seconds (3037.30 seconds total)