Starting phenix.real_space_refine on Sun Mar 17 07:29:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy2_9748/03_2024/6iy2_9748_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy2_9748/03_2024/6iy2_9748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy2_9748/03_2024/6iy2_9748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy2_9748/03_2024/6iy2_9748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy2_9748/03_2024/6iy2_9748_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iy2_9748/03_2024/6iy2_9748_updated.pdb" } resolution = 3.47 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 9843 2.51 5 N 3171 2.21 5 O 3751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "O PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 898": "NH1" <-> "NH2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1076": "NH1" <-> "NH2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1142": "NH1" <-> "NH2" Residue "O ARG 1164": "NH1" <-> "NH2" Residue "O PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1268": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17088 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: 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: "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: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 789 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} 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: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" 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: "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: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3057 Classifications: {'DNA': 147} Modifications used: {'p5*END': 1} 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: 8.97, per 1000 atoms: 0.52 Number of scatterers: 17088 At special positions: 0 Unit cell: (142.56, 128.04, 126.72, 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 3751 8.00 N 3171 7.00 C 9843 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: 6.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 2 sheets defined 54.2% alpha, 2.2% beta 110 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 8.53 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 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 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 122 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 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 41 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 21 removed outlier: 3.627A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 17 through 21' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 67 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 56 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 681 Processing helix chain 'O' and resid 685 through 688 No H-bonds generated for 'chain 'O' and resid 685 through 688' Processing helix chain 'O' and resid 744 through 747 No H-bonds generated for 'chain 'O' and resid 744 through 747' Processing helix chain 'O' and resid 769 through 783 Processing helix chain 'O' and resid 798 through 811 Processing helix chain 'O' and resid 825 through 838 removed outlier: 5.777A pdb=" N SER O 829 " --> pdb=" O SER O 826 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O 837 " --> pdb=" O GLU O 834 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP O 838 " --> pdb=" O PHE O 835 " (cutoff:3.500A) Processing helix chain 'O' and resid 851 through 861 Processing helix chain 'O' and resid 874 through 885 removed outlier: 5.887A pdb=" N ALA O 881 " --> pdb=" O ILE O 877 " (cutoff:3.500A) removed outlier: 6.974A 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 933 through 937 Processing helix chain 'O' and resid 944 through 947 No H-bonds generated for 'chain 'O' and resid 944 through 947' Processing helix chain 'O' and resid 953 through 959 Proline residue: O 959 - end of helix Processing helix chain 'O' and resid 975 through 986 removed outlier: 3.898A pdb=" N LEU O 978 " --> pdb=" O GLU O 975 " (cutoff:3.500A) Processing helix chain 'O' and resid 1021 through 1030 removed outlier: 3.625A pdb=" N MET O1026 " --> pdb=" O MET O1022 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O1028 " --> pdb=" O GLN O1024 " (cutoff:3.500A) Processing helix chain 'O' and resid 1051 through 1060 removed outlier: 3.506A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) removed outlier: 3.782A 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 1087 through 1102 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: 4.613A pdb=" N LEU O1146 " --> pdb=" O ARG O1142 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG O1147 " --> pdb=" O SER O1143 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU O1148 " --> pdb=" O GLU O1144 " (cutoff:3.500A) Processing helix chain 'O' and resid 1188 through 1197 removed outlier: 5.104A pdb=" N ASP O1195 " --> pdb=" O LEU O1191 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA O1197 " --> pdb=" O ALA O1193 " (cutoff:3.500A) Processing helix chain 'O' and resid 1217 through 1229 Processing helix chain 'O' and resid 1231 through 1241 removed outlier: 3.799A pdb=" N GLY O1239 " --> pdb=" O ILE O1236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS O1240 " --> pdb=" O GLN O1237 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE O1241 " --> pdb=" O ALA O1238 " (cutoff:3.500A) Processing helix chain 'O' and resid 1252 through 1262 removed outlier: 4.035A pdb=" N ALA O1260 " --> pdb=" O SER O1256 " (cutoff:3.500A) Processing helix chain 'O' and resid 1264 through 1268 Processing helix chain 'O' and resid 1280 through 1286 Processing helix chain 'O' and resid 1291 through 1306 Processing helix chain 'O' and resid 1338 through 1345 removed outlier: 4.156A pdb=" N ALA O1344 " --> pdb=" O SER O1340 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL O1345 " --> pdb=" O GLU O1341 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'O' and resid 819 through 822 removed outlier: 6.094A pdb=" N HIS O 890 " --> pdb=" O LEU O 820 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE O 822 " --> pdb=" O HIS O 890 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE O 892 " --> pdb=" O ILE O 822 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR O 918 " --> pdb=" O MET O 891 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE O 893 " --> pdb=" O TYR O 918 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU O 920 " --> pdb=" O ILE O 893 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'O' and resid 1007 through 1013 removed outlier: 3.608A pdb=" N ARG O1210 " --> pdb=" O LYS O1009 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU O1209 " --> pdb=" O VAL O1178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE O1109 " --> pdb=" O ILE O1179 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O1131 " --> pdb=" O CYS O1158 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 7.54 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: 3006 1.33 - 1.45: 5543 1.45 - 1.57: 8790 1.57 - 1.69: 589 1.69 - 1.80: 51 Bond restraints: 17979 Sorted by residual: bond pdb=" CB ASP A 123 " pdb=" CG ASP A 123 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" CG LEU C 83 " pdb=" CD1 LEU C 83 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" CB ILE C 78 " pdb=" CG2 ILE C 78 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" C3' DA J 23 " pdb=" O3' DA J 23 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 bond pdb=" C2' DC J 58 " pdb=" C1' DC J 58 " ideal model delta sigma weight residual 1.525 1.480 0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 17974 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.16: 1480 105.16 - 112.86: 9999 112.86 - 120.56: 8314 120.56 - 128.26: 5308 128.26 - 135.96: 406 Bond angle restraints: 25507 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 103.52 110.39 -6.87 1.06e+00 8.90e-01 4.20e+01 angle pdb=" C ASN O1049 " pdb=" N ASN O1050 " pdb=" CA ASN O1050 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C ASN O 930 " pdb=" N LEU O 931 " pdb=" CA LEU O 931 " ideal model delta sigma weight residual 121.80 133.56 -11.76 2.44e+00 1.68e-01 2.32e+01 angle pdb=" C GLU O 933 " pdb=" N LEU O 934 " pdb=" CA LEU O 934 " ideal model delta sigma weight residual 121.19 128.57 -7.38 1.59e+00 3.96e-01 2.15e+01 angle pdb=" C PHE O1065 " pdb=" N GLU O1066 " pdb=" CA GLU O1066 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 ... (remaining 25502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8520 35.43 - 70.86: 1596 70.86 - 106.29: 32 106.29 - 141.72: 4 141.72 - 177.15: 1 Dihedral angle restraints: 10153 sinusoidal: 6163 harmonic: 3990 Sorted by residual: dihedral pdb=" CA PHE O1110 " pdb=" C PHE O1110 " pdb=" N GLN O1111 " pdb=" CA GLN O1111 " ideal model delta harmonic sigma weight residual 180.00 144.71 35.29 0 5.00e+00 4.00e-02 4.98e+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 -60.00 80.97 -140.97 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O1B ADP O2000 " pdb=" O3A ADP O2000 " pdb=" PB ADP O2000 " pdb=" PA ADP O2000 " ideal model delta sinusoidal sigma weight residual -60.00 73.65 -133.65 1 2.00e+01 2.50e-03 4.06e+01 ... (remaining 10150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2027 0.058 - 0.117: 713 0.117 - 0.175: 133 0.175 - 0.234: 14 0.234 - 0.292: 5 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 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CG LEU O1123 " pdb=" CB LEU O1123 " pdb=" CD1 LEU O1123 " pdb=" CD2 LEU O1123 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2889 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 30 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C ARG D 30 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG D 30 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS D 31 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O1139 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C SER O1139 " 0.048 2.00e-02 2.50e+03 pdb=" O SER O1139 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP O1140 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 121 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.037 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3479 2.78 - 3.31: 14866 3.31 - 3.84: 32586 3.84 - 4.37: 37110 4.37 - 4.90: 54725 Nonbonded interactions: 142766 Sorted by model distance: nonbonded pdb=" N2 DG J 32 " pdb=" O2 DC I 116 " model vdw 2.248 2.496 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.269 2.440 nonbonded pdb=" OG1 THR C 76 " pdb=" OP1 DA I 133 " model vdw 2.271 2.440 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.290 2.520 nonbonded pdb=" OP1 DT I 97 " pdb=" ND2 ASN O1186 " model vdw 2.291 2.520 ... (remaining 142761 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' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 119) selection = (chain 'G' and resid 11 through 119) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 2.750 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 52.300 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.010 0.110 17979 Z= 0.622 Angle : 1.094 11.882 25507 Z= 0.614 Chirality : 0.060 0.292 2892 Planarity : 0.007 0.065 2206 Dihedral : 25.750 177.154 7561 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.55 % Favored : 92.22 % Rotamer: Outliers : 0.59 % Allowed : 2.04 % Favored : 97.37 % 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: -4.13 (0.18), residues: 1337 helix: -2.25 (0.14), residues: 797 sheet: -3.70 (0.51), residues: 66 loop : -3.23 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP O1083 HIS 0.017 0.003 HIS O 984 PHE 0.038 0.005 PHE C 25 TYR 0.042 0.004 TYR B 51 ARG 0.010 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8254 (tp30) cc_final: 0.8039 (tp30) REVERT: B 59 LYS cc_start: 0.8798 (tttt) cc_final: 0.8476 (tttm) REVERT: C 95 LYS cc_start: 0.8990 (tttp) cc_final: 0.8753 (ttpt) REVERT: D 30 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6722 (tpm170) REVERT: D 68 ASP cc_start: 0.8085 (t0) cc_final: 0.7776 (t0) REVERT: E 79 LYS cc_start: 0.8353 (tptt) cc_final: 0.8053 (tttp) REVERT: H 59 MET cc_start: 0.8056 (tpp) cc_final: 0.7689 (tpp) REVERT: H 122 THR cc_start: 0.9069 (m) cc_final: 0.8724 (p) REVERT: O 800 ILE cc_start: 0.7524 (mt) cc_final: 0.7221 (mp) REVERT: O 1309 GLU cc_start: 0.6802 (tp30) cc_final: 0.5829 (pm20) outliers start: 7 outliers final: 4 residues processed: 281 average time/residue: 0.3910 time to fit residues: 149.7148 Evaluate side-chains 160 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 949 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 31 HIS C 73 ASN C 104 GLN D 82 HIS E 113 HIS E 125 GLN F 25 ASN F 64 ASN F 93 GLN G 68 ASN O 687 ASN O 749 HIS ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 911 ASN O 928 GLN O1104 HIS ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17979 Z= 0.215 Angle : 0.640 9.987 25507 Z= 0.361 Chirality : 0.038 0.155 2892 Planarity : 0.005 0.050 2206 Dihedral : 30.167 175.572 4739 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 2.63 % Allowed : 7.47 % Favored : 89.90 % 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: -2.14 (0.21), residues: 1337 helix: -0.35 (0.17), residues: 802 sheet: -3.56 (0.48), residues: 77 loop : -2.88 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O1083 HIS 0.007 0.001 HIS D 82 PHE 0.020 0.002 PHE O 782 TYR 0.017 0.001 TYR B 51 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7536 (p0) REVERT: B 59 LYS cc_start: 0.8587 (tttt) cc_final: 0.8264 (tttm) REVERT: C 95 LYS cc_start: 0.9025 (tttp) cc_final: 0.8754 (ttpt) REVERT: D 30 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6523 (tpm170) REVERT: E 79 LYS cc_start: 0.8209 (tptt) cc_final: 0.7833 (tttp) REVERT: G 90 ASP cc_start: 0.8151 (t0) cc_final: 0.7706 (t0) REVERT: G 92 GLU cc_start: 0.7791 (pm20) cc_final: 0.7349 (pm20) REVERT: H 59 MET cc_start: 0.7853 (tpp) cc_final: 0.7405 (tpp) REVERT: H 122 THR cc_start: 0.9095 (m) cc_final: 0.8799 (p) REVERT: O 949 VAL cc_start: 0.0468 (OUTLIER) cc_final: 0.0204 (t) REVERT: O 1309 GLU cc_start: 0.6751 (tp30) cc_final: 0.5882 (pm20) outliers start: 31 outliers final: 21 residues processed: 198 average time/residue: 0.3198 time to fit residues: 94.0801 Evaluate side-chains 169 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 0.0770 chunk 131 optimal weight: 0.0970 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN F 25 ASN F 93 GLN ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17979 Z= 0.187 Angle : 0.584 7.987 25507 Z= 0.331 Chirality : 0.036 0.147 2892 Planarity : 0.004 0.050 2206 Dihedral : 29.732 176.316 4739 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.40 % Allowed : 8.66 % Favored : 87.95 % 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: -0.96 (0.22), residues: 1337 helix: 0.66 (0.18), residues: 796 sheet: -2.97 (0.53), residues: 77 loop : -2.53 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O1083 HIS 0.003 0.001 HIS O1104 PHE 0.020 0.001 PHE O1063 TYR 0.015 0.001 TYR H 83 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7327 (p0) REVERT: B 59 LYS cc_start: 0.8502 (tttt) cc_final: 0.8069 (tttm) REVERT: C 95 LYS cc_start: 0.9025 (tttp) cc_final: 0.8744 (ttpt) REVERT: E 79 LYS cc_start: 0.8162 (tptt) cc_final: 0.7835 (tttp) REVERT: G 92 GLU cc_start: 0.7798 (pm20) cc_final: 0.7533 (pm20) REVERT: H 59 MET cc_start: 0.7817 (tpp) cc_final: 0.7375 (tpp) REVERT: H 122 THR cc_start: 0.9101 (m) cc_final: 0.8768 (p) REVERT: O 675 LYS cc_start: 0.7013 (mttt) cc_final: 0.6610 (mmtt) REVERT: O 1015 MET cc_start: 0.5577 (mmt) cc_final: 0.5325 (mmm) REVERT: O 1224 ARG cc_start: 0.7286 (ttt180) cc_final: 0.7037 (ttm170) REVERT: O 1257 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7699 (mm) REVERT: O 1309 GLU cc_start: 0.6468 (tp30) cc_final: 0.5566 (pm20) outliers start: 40 outliers final: 26 residues processed: 189 average time/residue: 0.2960 time to fit residues: 84.1137 Evaluate side-chains 174 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 827 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1162 SER Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1257 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN O 749 HIS ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 801 GLN ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 17979 Z= 0.466 Angle : 0.735 9.374 25507 Z= 0.406 Chirality : 0.044 0.227 2892 Planarity : 0.006 0.052 2206 Dihedral : 30.171 177.309 4738 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.18 % Favored : 92.74 % Rotamer: Outliers : 4.16 % Allowed : 10.70 % Favored : 85.14 % 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: -1.21 (0.23), residues: 1337 helix: 0.35 (0.18), residues: 795 sheet: -2.85 (0.54), residues: 78 loop : -2.44 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 838 HIS 0.006 0.001 HIS A 39 PHE 0.024 0.003 PHE O1063 TYR 0.046 0.002 TYR H 83 ARG 0.006 0.001 ARG O1268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7617 (p0) REVERT: B 59 LYS cc_start: 0.8571 (tttt) cc_final: 0.8194 (tttm) REVERT: C 95 LYS cc_start: 0.8980 (tttp) cc_final: 0.8673 (ttpt) REVERT: E 41 TYR cc_start: 0.8806 (m-10) cc_final: 0.8565 (m-10) REVERT: E 79 LYS cc_start: 0.8494 (tptt) cc_final: 0.8158 (tttp) REVERT: G 56 GLU cc_start: 0.8180 (tt0) cc_final: 0.7955 (tt0) REVERT: G 90 ASP cc_start: 0.8197 (t0) cc_final: 0.7946 (t0) REVERT: G 92 GLU cc_start: 0.7986 (pm20) cc_final: 0.7676 (pm20) REVERT: H 59 MET cc_start: 0.8160 (tpp) cc_final: 0.7735 (tpp) REVERT: H 122 THR cc_start: 0.9290 (m) cc_final: 0.9033 (p) REVERT: O 871 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8771 (p) REVERT: O 886 VAL cc_start: 0.6642 (OUTLIER) cc_final: 0.6423 (t) REVERT: O 949 VAL cc_start: -0.1069 (OUTLIER) cc_final: -0.1563 (t) outliers start: 49 outliers final: 30 residues processed: 179 average time/residue: 0.2795 time to fit residues: 76.6605 Evaluate side-chains 167 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 827 THR Chi-restraints excluded: chain O residue 831 TRP Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN O 749 HIS ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17979 Z= 0.312 Angle : 0.641 7.951 25507 Z= 0.359 Chirality : 0.039 0.160 2892 Planarity : 0.004 0.047 2206 Dihedral : 29.985 177.561 4736 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 4.41 % Allowed : 11.71 % Favored : 83.87 % 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: -0.79 (0.23), residues: 1337 helix: 0.66 (0.19), residues: 790 sheet: -2.55 (0.60), residues: 69 loop : -2.24 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP O 838 HIS 0.005 0.001 HIS B 75 PHE 0.021 0.002 PHE O1063 TYR 0.017 0.002 TYR H 83 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 144 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 59 LYS cc_start: 0.8540 (tttt) cc_final: 0.8188 (tttm) REVERT: C 15 LYS cc_start: 0.7658 (tptm) cc_final: 0.7260 (tppt) REVERT: C 35 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7798 (ttp80) REVERT: C 95 LYS cc_start: 0.9022 (tttp) cc_final: 0.8738 (ttpt) REVERT: E 41 TYR cc_start: 0.8722 (m-10) cc_final: 0.8459 (m-10) REVERT: E 79 LYS cc_start: 0.8438 (tptt) cc_final: 0.8076 (tttp) REVERT: E 123 ASP cc_start: 0.8376 (m-30) cc_final: 0.8121 (m-30) REVERT: G 50 TYR cc_start: 0.9016 (t80) cc_final: 0.8671 (t80) REVERT: G 92 GLU cc_start: 0.8094 (pm20) cc_final: 0.7880 (pm20) REVERT: H 59 MET cc_start: 0.8050 (tpp) cc_final: 0.7676 (tpp) REVERT: H 122 THR cc_start: 0.9245 (m) cc_final: 0.8925 (p) REVERT: O 749 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6540 (m170) REVERT: O 794 MET cc_start: 0.6956 (tmm) cc_final: 0.5804 (tmm) REVERT: O 949 VAL cc_start: -0.1140 (OUTLIER) cc_final: -0.1505 (t) REVERT: O 1015 MET cc_start: 0.6076 (mmt) cc_final: 0.5682 (mtp) REVERT: O 1190 ASP cc_start: 0.7742 (t0) cc_final: 0.6952 (t0) REVERT: O 1337 ARG cc_start: 0.7380 (mmt-90) cc_final: 0.5986 (mmm160) outliers start: 52 outliers final: 39 residues processed: 182 average time/residue: 0.2841 time to fit residues: 78.7923 Evaluate side-chains 182 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 749 HIS Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 827 THR Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 75 HIS O 749 HIS ** O 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17979 Z= 0.204 Angle : 0.587 8.684 25507 Z= 0.331 Chirality : 0.036 0.145 2892 Planarity : 0.004 0.043 2206 Dihedral : 29.697 177.156 4735 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.99 % Allowed : 12.65 % Favored : 83.36 % 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: -0.31 (0.24), residues: 1337 helix: 1.01 (0.19), residues: 802 sheet: -2.04 (0.62), residues: 69 loop : -2.10 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 888 HIS 0.009 0.001 HIS O 749 PHE 0.020 0.002 PHE O1063 TYR 0.012 0.001 TYR D 40 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7461 (p0) REVERT: B 59 LYS cc_start: 0.8504 (tttt) cc_final: 0.8163 (tttm) REVERT: C 15 LYS cc_start: 0.7577 (tptm) cc_final: 0.7208 (tppt) REVERT: C 35 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: C 95 LYS cc_start: 0.9026 (tttp) cc_final: 0.8741 (ttpt) REVERT: E 79 LYS cc_start: 0.8433 (tptt) cc_final: 0.8048 (tttp) REVERT: E 81 ASP cc_start: 0.7107 (t70) cc_final: 0.6492 (t70) REVERT: G 92 GLU cc_start: 0.8099 (pm20) cc_final: 0.7889 (pm20) REVERT: H 47 GLN cc_start: 0.8074 (mt0) cc_final: 0.7699 (tt0) REVERT: H 59 MET cc_start: 0.7938 (tpp) cc_final: 0.7569 (tpp) REVERT: H 122 THR cc_start: 0.9242 (m) cc_final: 0.8865 (p) REVERT: O 794 MET cc_start: 0.6857 (tmm) cc_final: 0.6471 (tpp) REVERT: O 949 VAL cc_start: -0.1105 (OUTLIER) cc_final: -0.1450 (t) REVERT: O 1190 ASP cc_start: 0.7798 (t0) cc_final: 0.7147 (t0) outliers start: 47 outliers final: 36 residues processed: 183 average time/residue: 0.3036 time to fit residues: 82.3668 Evaluate side-chains 183 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS F 25 ASN O 749 HIS O 776 GLN ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1202 GLN ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 17979 Z= 0.475 Angle : 0.722 8.441 25507 Z= 0.398 Chirality : 0.043 0.160 2892 Planarity : 0.005 0.051 2206 Dihedral : 30.164 178.524 4735 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 4.41 % Allowed : 12.56 % Favored : 83.02 % 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: -0.85 (0.23), residues: 1337 helix: 0.58 (0.18), residues: 789 sheet: -2.31 (0.61), residues: 69 loop : -2.23 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP O1083 HIS 0.007 0.001 HIS B 75 PHE 0.023 0.003 PHE O1063 TYR 0.017 0.002 TYR O1023 ARG 0.005 0.001 ARG O1224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7621 (p0) REVERT: B 59 LYS cc_start: 0.8579 (tttt) cc_final: 0.8189 (tttm) REVERT: C 15 LYS cc_start: 0.7669 (tptm) cc_final: 0.7280 (tppt) REVERT: C 35 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7753 (ttp80) REVERT: C 95 LYS cc_start: 0.8993 (tttp) cc_final: 0.8686 (ttpt) REVERT: E 79 LYS cc_start: 0.8536 (tptt) cc_final: 0.8165 (tttp) REVERT: E 81 ASP cc_start: 0.7352 (t70) cc_final: 0.6738 (t70) REVERT: E 123 ASP cc_start: 0.8391 (m-30) cc_final: 0.8146 (m-30) REVERT: G 92 GLU cc_start: 0.8019 (pm20) cc_final: 0.7819 (pm20) REVERT: H 59 MET cc_start: 0.8144 (tpp) cc_final: 0.7721 (tpp) REVERT: O 794 MET cc_start: 0.6834 (tmm) cc_final: 0.6328 (tpp) REVERT: O 949 VAL cc_start: -0.1161 (OUTLIER) cc_final: -0.1571 (t) REVERT: O 1015 MET cc_start: 0.5662 (mmt) cc_final: 0.5333 (mtp) REVERT: O 1058 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7517 (pt) REVERT: O 1190 ASP cc_start: 0.7877 (t0) cc_final: 0.7110 (t0) REVERT: O 1218 GLU cc_start: 0.7702 (tt0) cc_final: 0.7412 (tt0) outliers start: 52 outliers final: 42 residues processed: 179 average time/residue: 0.2962 time to fit residues: 79.5072 Evaluate side-chains 182 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 136 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 831 TRP Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 877 ILE Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1058 ILE Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 749 HIS ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17979 Z= 0.240 Angle : 0.607 8.856 25507 Z= 0.340 Chirality : 0.037 0.148 2892 Planarity : 0.004 0.042 2206 Dihedral : 29.843 178.258 4735 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 4.41 % Allowed : 13.07 % Favored : 82.51 % 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: -0.39 (0.24), residues: 1337 helix: 0.94 (0.19), residues: 794 sheet: -1.93 (0.64), residues: 69 loop : -2.09 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 888 HIS 0.004 0.001 HIS B 75 PHE 0.020 0.002 PHE O1063 TYR 0.016 0.001 TYR G 57 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 146 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7554 (p0) REVERT: B 59 LYS cc_start: 0.8524 (tttt) cc_final: 0.8176 (tttm) REVERT: C 15 LYS cc_start: 0.7578 (tptm) cc_final: 0.7211 (tppt) REVERT: C 35 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7936 (ttp80) REVERT: C 95 LYS cc_start: 0.9029 (tttp) cc_final: 0.8750 (ttpt) REVERT: E 79 LYS cc_start: 0.8470 (tptt) cc_final: 0.8076 (tttp) REVERT: E 81 ASP cc_start: 0.7212 (t70) cc_final: 0.6596 (t70) REVERT: G 50 TYR cc_start: 0.8975 (t80) cc_final: 0.8627 (t80) REVERT: G 90 ASP cc_start: 0.8151 (t0) cc_final: 0.7939 (t0) REVERT: G 92 GLU cc_start: 0.8139 (pm20) cc_final: 0.7738 (pm20) REVERT: H 59 MET cc_start: 0.7994 (tpp) cc_final: 0.7641 (tpp) REVERT: H 122 THR cc_start: 0.9278 (m) cc_final: 0.8924 (p) REVERT: O 794 MET cc_start: 0.6828 (tmm) cc_final: 0.5679 (tmm) REVERT: O 935 TRP cc_start: 0.4333 (OUTLIER) cc_final: 0.3926 (p90) REVERT: O 1015 MET cc_start: 0.5638 (mmt) cc_final: 0.5221 (mtp) REVERT: O 1058 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7241 (pt) REVERT: O 1181 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.5947 (m-80) REVERT: O 1190 ASP cc_start: 0.7681 (t0) cc_final: 0.7150 (t0) REVERT: O 1218 GLU cc_start: 0.7633 (tt0) cc_final: 0.7359 (tt0) outliers start: 52 outliers final: 41 residues processed: 185 average time/residue: 0.2872 time to fit residues: 80.0597 Evaluate side-chains 183 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 749 HIS Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 827 THR Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1058 ILE Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1181 PHE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 0.0470 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 749 HIS ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17979 Z= 0.304 Angle : 0.645 9.850 25507 Z= 0.356 Chirality : 0.039 0.239 2892 Planarity : 0.004 0.043 2206 Dihedral : 29.899 178.358 4735 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.26 % Favored : 92.67 % Rotamer: Outliers : 4.24 % Allowed : 13.50 % Favored : 82.26 % 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: -0.44 (0.24), residues: 1337 helix: 0.88 (0.19), residues: 796 sheet: -1.85 (0.64), residues: 69 loop : -2.12 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O1083 HIS 0.005 0.001 HIS B 75 PHE 0.021 0.002 PHE O1063 TYR 0.020 0.002 TYR G 57 ARG 0.003 0.000 ARG O1224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7565 (p0) REVERT: B 59 LYS cc_start: 0.8550 (tttt) cc_final: 0.8198 (tttm) REVERT: C 15 LYS cc_start: 0.7565 (tptm) cc_final: 0.7191 (tppt) REVERT: C 35 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7891 (ttp80) REVERT: C 95 LYS cc_start: 0.9028 (tttp) cc_final: 0.8692 (ttmt) REVERT: E 79 LYS cc_start: 0.8534 (tptt) cc_final: 0.8133 (tttp) REVERT: E 81 ASP cc_start: 0.7237 (t70) cc_final: 0.6627 (t70) REVERT: G 50 TYR cc_start: 0.9046 (t80) cc_final: 0.8687 (t80) REVERT: G 90 ASP cc_start: 0.8149 (t0) cc_final: 0.7919 (t0) REVERT: G 92 GLU cc_start: 0.8150 (pm20) cc_final: 0.7741 (pm20) REVERT: H 59 MET cc_start: 0.8029 (tpp) cc_final: 0.7655 (tpp) REVERT: O 794 MET cc_start: 0.6797 (tmm) cc_final: 0.6300 (tpp) REVERT: O 935 TRP cc_start: 0.4309 (OUTLIER) cc_final: 0.3866 (p90) REVERT: O 1058 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7524 (pt) REVERT: O 1190 ASP cc_start: 0.7727 (t0) cc_final: 0.7215 (t0) REVERT: O 1218 GLU cc_start: 0.7668 (tt0) cc_final: 0.7385 (tt0) REVERT: O 1337 ARG cc_start: 0.7135 (mmt-90) cc_final: 0.5920 (mmm160) outliers start: 50 outliers final: 40 residues processed: 176 average time/residue: 0.2859 time to fit residues: 75.8910 Evaluate side-chains 180 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 827 THR Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1058 ILE Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 0.0370 chunk 161 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 749 HIS ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17979 Z= 0.228 Angle : 0.615 13.809 25507 Z= 0.339 Chirality : 0.037 0.313 2892 Planarity : 0.004 0.042 2206 Dihedral : 29.744 178.256 4735 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.82 % Allowed : 13.92 % Favored : 82.26 % 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: -0.13 (0.24), residues: 1337 helix: 1.14 (0.19), residues: 792 sheet: -1.62 (0.66), residues: 69 loop : -2.00 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O1185 HIS 0.004 0.001 HIS B 75 PHE 0.019 0.002 PHE O1063 TYR 0.017 0.001 TYR G 57 ARG 0.003 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 59 LYS cc_start: 0.8524 (tttt) cc_final: 0.8180 (tttm) REVERT: C 15 LYS cc_start: 0.7561 (tptm) cc_final: 0.7211 (tppt) REVERT: C 35 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (ttp80) REVERT: C 95 LYS cc_start: 0.9031 (tttp) cc_final: 0.8754 (ttpt) REVERT: E 79 LYS cc_start: 0.8362 (tptt) cc_final: 0.7953 (tttp) REVERT: E 81 ASP cc_start: 0.7076 (t70) cc_final: 0.6474 (t70) REVERT: G 50 TYR cc_start: 0.8975 (t80) cc_final: 0.8575 (t80) REVERT: G 90 ASP cc_start: 0.8150 (t0) cc_final: 0.7927 (t0) REVERT: G 92 GLU cc_start: 0.8177 (pm20) cc_final: 0.7773 (pm20) REVERT: H 59 MET cc_start: 0.7987 (tpp) cc_final: 0.7640 (tpp) REVERT: H 122 THR cc_start: 0.9274 (m) cc_final: 0.8919 (p) REVERT: O 749 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6544 (m90) REVERT: O 794 MET cc_start: 0.6865 (tmm) cc_final: 0.6249 (tpp) REVERT: O 935 TRP cc_start: 0.4288 (OUTLIER) cc_final: 0.3676 (p90) REVERT: O 1015 MET cc_start: 0.5876 (mmt) cc_final: 0.5459 (mtp) REVERT: O 1190 ASP cc_start: 0.7719 (t0) cc_final: 0.7211 (t0) REVERT: O 1218 GLU cc_start: 0.7651 (tt0) cc_final: 0.7385 (tt0) REVERT: O 1337 ARG cc_start: 0.7150 (mmt-90) cc_final: 0.5896 (mmm160) outliers start: 45 outliers final: 39 residues processed: 176 average time/residue: 0.2934 time to fit residues: 78.4210 Evaluate side-chains 184 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 749 HIS Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 827 THR Chi-restraints excluded: chain O residue 850 SER Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 935 TRP Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097306 restraints weight = 36774.054| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.18 r_work: 0.3135 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17979 Z= 0.174 Angle : 0.591 13.357 25507 Z= 0.326 Chirality : 0.036 0.319 2892 Planarity : 0.004 0.044 2206 Dihedral : 29.504 177.589 4735 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 2.55 % Allowed : 15.45 % Favored : 82.00 % 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: 0.31 (0.24), residues: 1337 helix: 1.50 (0.19), residues: 794 sheet: -1.30 (0.68), residues: 63 loop : -1.86 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 888 HIS 0.006 0.001 HIS O 749 PHE 0.018 0.001 PHE O1063 TYR 0.014 0.001 TYR G 57 ARG 0.004 0.000 ARG O 750 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.86 seconds wall clock time: 55 minutes 44.37 seconds (3344.37 seconds total)