Starting phenix.real_space_refine on Fri Feb 16 22:49:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/02_2024/5z3u_6882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/02_2024/5z3u_6882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/02_2024/5z3u_6882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/02_2024/5z3u_6882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/02_2024/5z3u_6882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/02_2024/5z3u_6882_updated.pdb" } resolution = 4.31 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= 0.014 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 29 5.16 5 Be 1 3.05 5 C 9648 2.51 5 N 3088 2.21 5 O 3702 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 880": "NH1" <-> "NH2" Residue "O TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O ARG 1076": "NH1" <-> "NH2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1164": "NH1" <-> "NH2" Residue "O ARG 1196": "NH1" <-> "NH2" Residue "O TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1349": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16766 Number of models: 1 Model: "" Number of chains: 12 Chain: "O" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4723 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 558} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.07, per 1000 atoms: 0.54 Number of scatterers: 16766 At special positions: 0 Unit cell: (142.56, 124.08, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 29 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3702 8.00 N 3088 7.00 C 9648 6.00 Be 1 4.00 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: 8.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 2 sheets defined 57.3% alpha, 1.7% beta 144 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'O' and resid 675 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 770 through 783 Processing helix chain 'O' and resid 798 through 812 Processing helix chain 'O' and resid 829 through 837 Processing helix chain 'O' and resid 851 through 863 removed outlier: 4.441A pdb=" N ALA O 863 " --> pdb=" O ALA O 859 " (cutoff:3.500A) Processing helix chain 'O' and resid 874 through 883 removed outlier: 3.657A pdb=" N LYS O 878 " --> pdb=" O TYR O 875 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU O 879 " --> pdb=" O ILE O 876 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA O 881 " --> pdb=" O LYS O 878 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU O 883 " --> pdb=" O ARG O 880 " (cutoff:3.500A) Processing helix chain 'O' and resid 896 through 898 No H-bonds generated for 'chain 'O' and resid 896 through 898' Processing helix chain 'O' and resid 905 through 913 Processing helix chain 'O' and resid 934 through 941 Processing helix chain 'O' and resid 949 through 959 removed outlier: 3.951A pdb=" N PHE O 952 " --> pdb=" O VAL O 949 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP O 953 " --> pdb=" O LYS O 950 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU O 954 " --> pdb=" O SER O 951 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN O 957 " --> pdb=" O GLU O 954 " (cutoff:3.500A) Proline residue: O 959 - end of helix Processing helix chain 'O' and resid 968 through 989 Proline residue: O 989 - end of helix Processing helix chain 'O' and resid 996 through 999 No H-bonds generated for 'chain 'O' and resid 996 through 999' Processing helix chain 'O' and resid 1017 through 1025 removed outlier: 4.283A pdb=" N MET O1022 " --> pdb=" O LEU O1018 " (cutoff:3.500A) Processing helix chain 'O' and resid 1051 through 1060 Processing helix chain 'O' and resid 1066 through 1071 Processing helix chain 'O' and resid 1087 through 1102 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1114 through 1126 Processing helix chain 'O' and resid 1141 through 1150 Processing helix chain 'O' and resid 1187 through 1196 removed outlier: 4.085A pdb=" N ARG O1196 " --> pdb=" O GLN O1192 " (cutoff:3.500A) Processing helix chain 'O' and resid 1217 through 1234 removed outlier: 3.622A pdb=" N LYS O1234 " --> pdb=" O ASP O1230 " (cutoff:3.500A) Processing helix chain 'O' and resid 1236 through 1239 No H-bonds generated for 'chain 'O' and resid 1236 through 1239' Processing helix chain 'O' and resid 1249 through 1268 Processing helix chain 'O' and resid 1280 through 1287 Processing helix chain 'O' and resid 1291 through 1296 Processing helix chain 'O' and resid 1298 through 1300 No H-bonds generated for 'chain 'O' and resid 1298 through 1300' Processing helix chain 'O' and resid 1337 through 1346 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 76 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 47 through 73 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.767A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) 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 131 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 76 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 43 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.767A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'O' and resid 868 through 871 removed outlier: 6.512A pdb=" N TYR O 819 " --> pdb=" O VAL O 869 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR O 871 " --> pdb=" O TYR O 819 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL O 821 " --> pdb=" O THR O 871 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'O' and resid 1208 through 1210 removed outlier: 6.609A pdb=" N VAL O1178 " --> pdb=" O LEU O1209 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE O1159 " --> pdb=" O VAL O1106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE O1108 " --> pdb=" O PHE O1159 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE O1110 " --> pdb=" O LEU O1161 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU O1131 " --> pdb=" O CYS O1158 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 8.68 Time building geometry restraints manager: 9.27 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: 3252 1.33 - 1.45: 5341 1.45 - 1.57: 8415 1.57 - 1.69: 587 1.69 - 1.81: 55 Bond restraints: 17650 Sorted by residual: bond pdb=" BE BEF O1503 " pdb=" F2 BEF O1503 " ideal model delta sigma weight residual 1.476 1.708 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" BE BEF O1503 " pdb=" F1 BEF O1503 " ideal model delta sigma weight residual 1.476 1.703 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" BE BEF O1503 " pdb=" F3 BEF O1503 " ideal model delta sigma weight residual 1.476 1.686 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CB VAL G 100 " pdb=" CG1 VAL G 100 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" CB VAL C 100 " pdb=" CG1 VAL C 100 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.31e+00 ... (remaining 17645 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.58: 1223 104.58 - 112.38: 10032 112.38 - 120.17: 7383 120.17 - 127.97: 6008 127.97 - 135.77: 436 Bond angle restraints: 25082 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 103.41 110.24 -6.83 9.40e-01 1.13e+00 5.27e+01 angle pdb=" F1 BEF O1503 " pdb=" BE BEF O1503 " pdb=" F3 BEF O1503 " ideal model delta sigma weight residual 120.12 99.63 20.49 3.00e+00 1.11e-01 4.66e+01 angle pdb=" F2 BEF O1503 " pdb=" BE BEF O1503 " pdb=" F3 BEF O1503 " ideal model delta sigma weight residual 119.96 105.24 14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" N ILE O 861 " pdb=" CA ILE O 861 " pdb=" C ILE O 861 " ideal model delta sigma weight residual 112.29 108.34 3.95 9.40e-01 1.13e+00 1.76e+01 angle pdb=" CB ARG B 35 " pdb=" CG ARG B 35 " pdb=" CD ARG B 35 " ideal model delta sigma weight residual 111.30 101.71 9.59 2.30e+00 1.89e-01 1.74e+01 ... (remaining 25077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 8358 31.19 - 62.39: 1520 62.39 - 93.58: 39 93.58 - 124.77: 0 124.77 - 155.97: 3 Dihedral angle restraints: 9920 sinusoidal: 6003 harmonic: 3917 Sorted by residual: dihedral pdb=" CA TYR O 810 " pdb=" C TYR O 810 " pdb=" N GLU O 811 " pdb=" CA GLU O 811 " ideal model delta harmonic sigma weight residual 180.00 149.38 30.62 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA GLY O1166 " pdb=" C GLY O1166 " pdb=" N GLY O1167 " pdb=" CA GLY O1167 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N THR B 96 " pdb=" CA THR B 96 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 9917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1894 0.048 - 0.097: 803 0.097 - 0.145: 137 0.145 - 0.194: 18 0.194 - 0.242: 4 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASP O1184 " pdb=" N ASP O1184 " pdb=" C ASP O1184 " pdb=" CB ASP O1184 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ARG D 76 " pdb=" N ARG D 76 " pdb=" C ARG D 76 " pdb=" CB ARG D 76 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2853 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 121 " -0.036 2.00e-02 2.50e+03 1.85e-02 9.38e+00 pdb=" N9 DA J 121 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA J 121 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA J 121 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA J 121 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA J 121 " -0.035 2.00e-02 2.50e+03 pdb=" N6 DA J 121 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA J 121 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA J 121 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 121 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA J 121 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.038 2.00e-02 2.50e+03 1.82e-02 9.11e+00 pdb=" N9 DA I 39 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.027 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 100 " -0.036 2.00e-02 2.50e+03 1.75e-02 8.40e+00 pdb=" N9 DA J 100 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA J 100 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA J 100 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA J 100 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 100 " -0.032 2.00e-02 2.50e+03 pdb=" N6 DA J 100 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA J 100 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 100 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DA J 100 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA J 100 " 0.021 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 277 2.60 - 3.18: 15415 3.18 - 3.75: 29583 3.75 - 4.33: 39252 4.33 - 4.90: 57043 Nonbonded interactions: 141570 Sorted by model distance: nonbonded pdb=" OD2 ASP O 894 " pdb="MG MG O1501 " model vdw 2.030 2.170 nonbonded pdb=" O2A ADP O1502 " pdb=" F2 BEF O1503 " model vdw 2.120 2.390 nonbonded pdb=" NH1 ARG B 39 " pdb=" O LYS B 44 " model vdw 2.144 2.520 nonbonded pdb=" O SER O 972 " pdb=" OG1 THR O 976 " model vdw 2.145 2.440 nonbonded pdb=" O3B ADP O1502 " pdb=" F2 BEF O1503 " model vdw 2.151 2.390 ... (remaining 141565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 1.880 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 55.320 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.232 17650 Z= 0.677 Angle : 0.979 20.487 25082 Z= 0.534 Chirality : 0.051 0.242 2856 Planarity : 0.005 0.065 2163 Dihedral : 24.079 155.965 7376 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -5.01 (0.16), residues: 1313 helix: -3.59 (0.11), residues: 783 sheet: -2.74 (0.59), residues: 62 loop : -2.52 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O 831 HIS 0.014 0.003 HIS B 75 PHE 0.032 0.003 PHE O 946 TYR 0.036 0.004 TYR O 810 ARG 0.008 0.001 ARG O 862 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 1.347 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: O 769 ASP cc_start: 0.7632 (p0) cc_final: 0.7302 (t0) REVERT: O 790 LEU cc_start: 0.6813 (tp) cc_final: 0.6418 (mp) REVERT: O 803 ILE cc_start: 0.8338 (mt) cc_final: 0.7909 (mt) REVERT: O 810 TYR cc_start: 0.5671 (m-80) cc_final: 0.5362 (m-80) REVERT: O 812 MET cc_start: 0.7655 (mtm) cc_final: 0.7418 (tpp) REVERT: O 854 ARG cc_start: 0.6229 (mtm-85) cc_final: 0.4782 (ttp80) REVERT: O 876 ILE cc_start: 0.8527 (pp) cc_final: 0.8257 (tt) REVERT: O 888 TRP cc_start: 0.5310 (m100) cc_final: 0.4883 (m100) REVERT: O 897 HIS cc_start: 0.8691 (p90) cc_final: 0.8028 (p90) REVERT: O 915 HIS cc_start: 0.7652 (m-70) cc_final: 0.7170 (t-170) REVERT: O 930 ASN cc_start: 0.7820 (m-40) cc_final: 0.7370 (t0) REVERT: O 932 PRO cc_start: 0.6273 (Cg_exo) cc_final: 0.5928 (Cg_endo) REVERT: O 1015 MET cc_start: 0.5562 (tpt) cc_final: 0.5340 (tmm) REVERT: O 1116 MET cc_start: 0.8497 (ptm) cc_final: 0.7967 (mtt) REVERT: O 1183 THR cc_start: 0.7213 (m) cc_final: 0.6939 (p) REVERT: O 1293 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6830 (mm-30) REVERT: O 1338 GLU cc_start: 0.3751 (tm-30) cc_final: 0.3145 (pm20) REVERT: A 52 ARG cc_start: 0.8493 (mtt90) cc_final: 0.7863 (mtm-85) REVERT: A 131 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7984 (mtt-85) REVERT: B 74 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 77 LYS cc_start: 0.9159 (mttt) cc_final: 0.8642 (mtmt) REVERT: C 84 GLN cc_start: 0.8441 (tp40) cc_final: 0.8223 (tp40) REVERT: C 95 LYS cc_start: 0.8822 (tptm) cc_final: 0.8319 (ttmm) REVERT: D 59 MET cc_start: 0.9241 (mmm) cc_final: 0.8979 (tpp) REVERT: D 82 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8649 (mttp) REVERT: D 90 GLU cc_start: 0.8341 (mp0) cc_final: 0.8034 (mp0) REVERT: E 49 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7942 (ttm-80) REVERT: E 68 GLN cc_start: 0.8297 (tt0) cc_final: 0.7982 (tm-30) REVERT: E 81 ASP cc_start: 0.9098 (m-30) cc_final: 0.8558 (t70) REVERT: E 83 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8327 (mtm180) REVERT: F 79 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8155 (mptt) REVERT: F 88 TYR cc_start: 0.7820 (m-10) cc_final: 0.7432 (m-10) REVERT: F 91 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8763 (ttpt) REVERT: G 35 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8116 (mtp85) REVERT: G 61 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8405 (tp30) REVERT: G 95 LYS cc_start: 0.8282 (tptm) cc_final: 0.7798 (tppt) REVERT: H 31 LYS cc_start: 0.8365 (tptt) cc_final: 0.7450 (mmtp) REVERT: H 33 SER cc_start: 0.8079 (p) cc_final: 0.7735 (m) REVERT: H 36 ILE cc_start: 0.9042 (pt) cc_final: 0.8755 (pt) REVERT: H 76 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.7253 (ptp-110) REVERT: H 81 ASN cc_start: 0.8479 (m-40) cc_final: 0.8239 (m-40) REVERT: H 82 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8322 (mmtt) REVERT: H 115 VAL cc_start: 0.9138 (t) cc_final: 0.8937 (p) REVERT: H 117 LYS cc_start: 0.8252 (tttp) cc_final: 0.8015 (ttmt) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.4094 time to fit residues: 192.6660 Evaluate side-chains 207 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 142 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 749 HIS O 890 HIS ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN O1104 HIS O1111 GLN O1189 GLN O1192 GLN A 76 GLN B 93 GLN D 46 HIS E 68 GLN F 75 HIS G 24 GLN G 104 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17650 Z= 0.192 Angle : 0.637 7.209 25082 Z= 0.362 Chirality : 0.038 0.199 2856 Planarity : 0.005 0.052 2163 Dihedral : 28.462 161.690 4678 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.09 % Allowed : 1.66 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.55 (0.21), residues: 1313 helix: -0.42 (0.17), residues: 802 sheet: -2.35 (0.59), residues: 57 loop : -1.77 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O1083 HIS 0.009 0.001 HIS O 984 PHE 0.028 0.002 PHE O 835 TYR 0.028 0.002 TYR O 810 ARG 0.006 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 1.599 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: O 769 ASP cc_start: 0.7113 (p0) cc_final: 0.6846 (t0) REVERT: O 790 LEU cc_start: 0.7100 (tp) cc_final: 0.6681 (mp) REVERT: O 803 ILE cc_start: 0.8436 (mt) cc_final: 0.8129 (mt) REVERT: O 810 TYR cc_start: 0.4819 (m-80) cc_final: 0.4536 (m-80) REVERT: O 812 MET cc_start: 0.7524 (mtm) cc_final: 0.7132 (mmt) REVERT: O 854 ARG cc_start: 0.5936 (mtm-85) cc_final: 0.4315 (ttp-110) REVERT: O 879 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7302 (mt-10) REVERT: O 888 TRP cc_start: 0.5656 (m100) cc_final: 0.5281 (m100) REVERT: O 891 MET cc_start: 0.8097 (tmm) cc_final: 0.7661 (tmm) REVERT: O 897 HIS cc_start: 0.8275 (p90) cc_final: 0.7779 (p90) REVERT: O 980 ILE cc_start: 0.5988 (mt) cc_final: 0.5707 (mm) REVERT: O 1116 MET cc_start: 0.8511 (ptm) cc_final: 0.8262 (ptp) REVERT: O 1144 GLU cc_start: 0.8883 (tt0) cc_final: 0.8407 (mp0) REVERT: O 1293 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6616 (mm-30) REVERT: O 1294 MET cc_start: 0.6822 (tpt) cc_final: 0.6429 (tpt) REVERT: A 120 MET cc_start: 0.8666 (mtt) cc_final: 0.8344 (mtm) REVERT: B 84 MET cc_start: 0.7577 (mmp) cc_final: 0.6707 (mtm) REVERT: C 24 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8385 (mm-40) REVERT: C 75 LYS cc_start: 0.7525 (mmmm) cc_final: 0.7273 (mmmm) REVERT: C 95 LYS cc_start: 0.8877 (tptm) cc_final: 0.8358 (ttmm) REVERT: D 56 MET cc_start: 0.8418 (mmp) cc_final: 0.7872 (tmm) REVERT: D 82 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8357 (mmtt) REVERT: E 48 LEU cc_start: 0.8954 (mp) cc_final: 0.8596 (mt) REVERT: E 49 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8035 (mtp85) REVERT: E 60 LEU cc_start: 0.8377 (mt) cc_final: 0.8147 (mp) REVERT: E 81 ASP cc_start: 0.9024 (m-30) cc_final: 0.8496 (t70) REVERT: E 131 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7927 (tpp80) REVERT: F 74 GLU cc_start: 0.8692 (tp30) cc_final: 0.8420 (tp30) REVERT: F 79 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8279 (mptt) REVERT: F 91 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8630 (ttpt) REVERT: F 96 THR cc_start: 0.8234 (m) cc_final: 0.7758 (p) REVERT: G 95 LYS cc_start: 0.8471 (tptm) cc_final: 0.7798 (tppt) REVERT: H 31 LYS cc_start: 0.8316 (tptt) cc_final: 0.7371 (mttp) REVERT: H 32 GLU cc_start: 0.7174 (pp20) cc_final: 0.6922 (pp20) REVERT: H 33 SER cc_start: 0.7975 (p) cc_final: 0.7750 (m) REVERT: H 56 MET cc_start: 0.8684 (tpp) cc_final: 0.8365 (tpp) REVERT: H 82 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8407 (mmtt) REVERT: H 115 VAL cc_start: 0.8971 (t) cc_final: 0.8633 (p) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.3505 time to fit residues: 137.5117 Evaluate side-chains 198 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 681 HIS ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 984 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 17650 Z= 0.398 Angle : 0.733 9.325 25082 Z= 0.404 Chirality : 0.043 0.213 2856 Planarity : 0.005 0.048 2163 Dihedral : 28.695 159.917 4678 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.19 (0.22), residues: 1313 helix: -0.05 (0.18), residues: 791 sheet: -1.90 (0.58), residues: 69 loop : -1.80 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 777 HIS 0.011 0.002 HIS O 913 PHE 0.016 0.002 PHE O1159 TYR 0.034 0.003 TYR O 810 ARG 0.006 0.001 ARG O 854 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: O 790 LEU cc_start: 0.6866 (tp) cc_final: 0.6503 (mp) REVERT: O 810 TYR cc_start: 0.5029 (m-80) cc_final: 0.4581 (m-80) REVERT: O 812 MET cc_start: 0.7568 (mtm) cc_final: 0.7174 (mmt) REVERT: O 897 HIS cc_start: 0.8468 (p90) cc_final: 0.7878 (p90) REVERT: O 980 ILE cc_start: 0.6146 (mt) cc_final: 0.5850 (mm) REVERT: O 1116 MET cc_start: 0.8624 (ptm) cc_final: 0.8318 (ptp) REVERT: A 76 GLN cc_start: 0.8342 (pp30) cc_final: 0.7970 (pp30) REVERT: A 77 ASP cc_start: 0.8103 (m-30) cc_final: 0.7589 (m-30) REVERT: A 120 MET cc_start: 0.8851 (mtt) cc_final: 0.8639 (mtm) REVERT: B 84 MET cc_start: 0.7473 (mmp) cc_final: 0.6745 (mtm) REVERT: C 75 LYS cc_start: 0.7282 (mmmm) cc_final: 0.6878 (mmmm) REVERT: C 95 LYS cc_start: 0.8756 (tptm) cc_final: 0.8259 (ttmm) REVERT: D 32 GLU cc_start: 0.8230 (mp0) cc_final: 0.7936 (mp0) REVERT: D 82 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8144 (mmtt) REVERT: D 118 TYR cc_start: 0.9365 (t80) cc_final: 0.9161 (t80) REVERT: E 59 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8420 (pt0) REVERT: E 68 GLN cc_start: 0.8381 (tt0) cc_final: 0.7953 (tm-30) REVERT: E 81 ASP cc_start: 0.9129 (m-30) cc_final: 0.8708 (t70) REVERT: F 74 GLU cc_start: 0.8744 (tp30) cc_final: 0.8530 (tp30) REVERT: F 79 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8164 (mttp) REVERT: F 88 TYR cc_start: 0.7941 (m-10) cc_final: 0.7730 (m-10) REVERT: F 91 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8726 (ttpt) REVERT: F 96 THR cc_start: 0.8394 (m) cc_final: 0.8042 (p) REVERT: G 95 LYS cc_start: 0.8335 (tptm) cc_final: 0.7693 (tppt) REVERT: H 31 LYS cc_start: 0.8329 (tptt) cc_final: 0.7503 (mttm) REVERT: H 56 MET cc_start: 0.8929 (tpp) cc_final: 0.8710 (tpp) REVERT: H 82 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8413 (mmtt) REVERT: H 115 VAL cc_start: 0.9189 (t) cc_final: 0.8953 (p) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3305 time to fit residues: 102.6361 Evaluate side-chains 173 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 30.0000 chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 928 GLN D 92 GLN F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17650 Z= 0.275 Angle : 0.632 7.445 25082 Z= 0.358 Chirality : 0.038 0.180 2856 Planarity : 0.005 0.058 2163 Dihedral : 28.387 161.719 4678 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.47 (0.23), residues: 1313 helix: 0.58 (0.19), residues: 785 sheet: -1.45 (0.60), residues: 69 loop : -1.63 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 777 HIS 0.006 0.001 HIS G 31 PHE 0.015 0.002 PHE O1159 TYR 0.030 0.002 TYR O 810 ARG 0.013 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.7107 (tp) cc_final: 0.6514 (mp) REVERT: O 810 TYR cc_start: 0.4769 (m-80) cc_final: 0.4357 (m-80) REVERT: O 812 MET cc_start: 0.7572 (mtm) cc_final: 0.7246 (mmt) REVERT: O 897 HIS cc_start: 0.8397 (p90) cc_final: 0.7795 (p90) REVERT: O 980 ILE cc_start: 0.6054 (mt) cc_final: 0.5810 (mt) REVERT: O 1116 MET cc_start: 0.8467 (ptm) cc_final: 0.8220 (ptp) REVERT: A 60 LEU cc_start: 0.9226 (mp) cc_final: 0.8985 (mp) REVERT: A 120 MET cc_start: 0.8699 (mtt) cc_final: 0.8447 (mtm) REVERT: B 31 LYS cc_start: 0.9075 (tttm) cc_final: 0.8683 (mtmt) REVERT: B 84 MET cc_start: 0.7547 (mmp) cc_final: 0.6787 (mtm) REVERT: C 35 ARG cc_start: 0.8646 (mtm180) cc_final: 0.8434 (ttm110) REVERT: C 95 LYS cc_start: 0.8801 (tptm) cc_final: 0.8259 (ttmm) REVERT: D 82 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8116 (mmtt) REVERT: E 59 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8475 (pt0) REVERT: E 68 GLN cc_start: 0.8329 (tt0) cc_final: 0.8058 (tp40) REVERT: E 81 ASP cc_start: 0.9078 (m-30) cc_final: 0.8698 (t70) REVERT: F 74 GLU cc_start: 0.8710 (tp30) cc_final: 0.8491 (tp30) REVERT: F 79 LYS cc_start: 0.8809 (mmtp) cc_final: 0.8255 (mttp) REVERT: F 88 TYR cc_start: 0.8011 (m-10) cc_final: 0.7706 (m-10) REVERT: F 91 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8550 (ttpt) REVERT: F 96 THR cc_start: 0.8402 (m) cc_final: 0.8054 (p) REVERT: G 95 LYS cc_start: 0.8220 (tptm) cc_final: 0.7586 (tppt) REVERT: H 31 LYS cc_start: 0.7915 (tptt) cc_final: 0.7020 (mttm) REVERT: H 56 MET cc_start: 0.8892 (tpp) cc_final: 0.8594 (tpp) REVERT: H 82 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8360 (mmtt) REVERT: H 115 VAL cc_start: 0.9232 (t) cc_final: 0.8978 (p) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3152 time to fit residues: 103.2726 Evaluate side-chains 180 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17650 Z= 0.217 Angle : 0.592 7.386 25082 Z= 0.337 Chirality : 0.036 0.173 2856 Planarity : 0.004 0.049 2163 Dihedral : 28.282 163.103 4678 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.06 (0.23), residues: 1313 helix: 0.88 (0.19), residues: 792 sheet: -1.03 (0.64), residues: 69 loop : -1.47 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 777 HIS 0.004 0.001 HIS O 913 PHE 0.016 0.001 PHE O1159 TYR 0.027 0.002 TYR O 810 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.7136 (tp) cc_final: 0.6477 (mp) REVERT: O 810 TYR cc_start: 0.4785 (m-80) cc_final: 0.4489 (m-80) REVERT: O 812 MET cc_start: 0.7577 (mtm) cc_final: 0.7210 (mmt) REVERT: O 815 ILE cc_start: 0.5475 (mp) cc_final: 0.5181 (pt) REVERT: O 879 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7407 (mt-10) REVERT: O 897 HIS cc_start: 0.8396 (p90) cc_final: 0.7837 (p90) REVERT: O 944 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7060 (mmmt) REVERT: O 1030 ARG cc_start: 0.6462 (ptm-80) cc_final: 0.6218 (tpm170) REVERT: O 1116 MET cc_start: 0.8543 (ptm) cc_final: 0.8315 (ptp) REVERT: O 1190 ASP cc_start: 0.6639 (t70) cc_final: 0.6316 (t0) REVERT: B 84 MET cc_start: 0.7520 (mmp) cc_final: 0.6756 (mtm) REVERT: C 95 LYS cc_start: 0.8799 (tptm) cc_final: 0.8249 (ttmm) REVERT: D 82 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8109 (mmtt) REVERT: D 118 TYR cc_start: 0.9255 (t80) cc_final: 0.8782 (t80) REVERT: E 59 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8471 (pt0) REVERT: E 68 GLN cc_start: 0.8297 (tt0) cc_final: 0.8031 (tp40) REVERT: E 81 ASP cc_start: 0.9001 (m-30) cc_final: 0.8556 (t70) REVERT: F 74 GLU cc_start: 0.8712 (tp30) cc_final: 0.8509 (tp30) REVERT: F 79 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8130 (mttp) REVERT: F 84 MET cc_start: 0.7950 (tpp) cc_final: 0.7569 (mtm) REVERT: F 91 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8579 (tttt) REVERT: F 96 THR cc_start: 0.8295 (m) cc_final: 0.7983 (p) REVERT: G 95 LYS cc_start: 0.8209 (tptm) cc_final: 0.7545 (tppt) REVERT: H 31 LYS cc_start: 0.7890 (tptt) cc_final: 0.6911 (mttm) REVERT: H 43 LYS cc_start: 0.8626 (mttm) cc_final: 0.8375 (mmtp) REVERT: H 49 THR cc_start: 0.8851 (m) cc_final: 0.8241 (p) REVERT: H 82 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8359 (mmtt) REVERT: H 102 GLU cc_start: 0.7925 (tp30) cc_final: 0.7327 (tp30) REVERT: H 115 VAL cc_start: 0.9246 (t) cc_final: 0.9004 (p) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3411 time to fit residues: 112.3929 Evaluate side-chains 180 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 40.0000 chunk 79 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN E 68 GLN H 46 HIS H 79 HIS H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17650 Z= 0.356 Angle : 0.669 8.638 25082 Z= 0.374 Chirality : 0.039 0.163 2856 Planarity : 0.005 0.056 2163 Dihedral : 28.461 162.463 4678 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.35 (0.23), residues: 1313 helix: 0.60 (0.19), residues: 790 sheet: -1.06 (0.65), residues: 69 loop : -1.50 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 831 HIS 0.010 0.001 HIS C 31 PHE 0.018 0.002 PHE O1159 TYR 0.031 0.002 TYR F 88 ARG 0.006 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: O 677 THR cc_start: 0.2916 (m) cc_final: 0.2682 (m) REVERT: O 790 LEU cc_start: 0.7172 (tp) cc_final: 0.6581 (mp) REVERT: O 812 MET cc_start: 0.7456 (mtm) cc_final: 0.7100 (mmt) REVERT: O 897 HIS cc_start: 0.8438 (p90) cc_final: 0.7899 (p90) REVERT: O 944 LYS cc_start: 0.7949 (ttpt) cc_final: 0.6998 (mmmt) REVERT: O 1116 MET cc_start: 0.8614 (ptm) cc_final: 0.8377 (ptp) REVERT: A 59 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8058 (pt0) REVERT: B 84 MET cc_start: 0.7553 (mmp) cc_final: 0.6800 (mtm) REVERT: C 95 LYS cc_start: 0.8768 (tptm) cc_final: 0.8262 (ttmm) REVERT: D 82 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8145 (mmtt) REVERT: E 59 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8531 (pt0) REVERT: E 68 GLN cc_start: 0.8354 (tt0) cc_final: 0.7926 (tm-30) REVERT: E 81 ASP cc_start: 0.8998 (m-30) cc_final: 0.8717 (t70) REVERT: F 27 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8676 (mm-40) REVERT: F 74 GLU cc_start: 0.8742 (tp30) cc_final: 0.8502 (tp30) REVERT: F 77 LYS cc_start: 0.8905 (mttm) cc_final: 0.8655 (mmtt) REVERT: F 79 LYS cc_start: 0.8745 (mmtp) cc_final: 0.8301 (mttp) REVERT: F 84 MET cc_start: 0.7753 (tpp) cc_final: 0.7311 (mtm) REVERT: F 91 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8609 (tttt) REVERT: F 96 THR cc_start: 0.8403 (m) cc_final: 0.8093 (p) REVERT: G 95 LYS cc_start: 0.8216 (tptm) cc_final: 0.7612 (tppt) REVERT: H 31 LYS cc_start: 0.7729 (tptt) cc_final: 0.6796 (mttm) REVERT: H 43 LYS cc_start: 0.8634 (mttm) cc_final: 0.8367 (mmtp) REVERT: H 79 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8453 (t70) REVERT: H 82 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8485 (mmtt) REVERT: H 115 VAL cc_start: 0.9265 (t) cc_final: 0.9014 (p) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.3185 time to fit residues: 100.0402 Evaluate side-chains 175 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17650 Z= 0.178 Angle : 0.577 8.391 25082 Z= 0.328 Chirality : 0.036 0.219 2856 Planarity : 0.004 0.050 2163 Dihedral : 28.130 163.757 4678 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.15 (0.24), residues: 1313 helix: 1.01 (0.19), residues: 800 sheet: -0.83 (0.65), residues: 69 loop : -1.37 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O1083 HIS 0.006 0.001 HIS C 31 PHE 0.018 0.001 PHE O1159 TYR 0.023 0.001 TYR O 810 ARG 0.008 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 677 THR cc_start: 0.3000 (m) cc_final: 0.2767 (m) REVERT: O 790 LEU cc_start: 0.7183 (tp) cc_final: 0.6676 (mp) REVERT: O 812 MET cc_start: 0.7436 (mtm) cc_final: 0.7064 (mmt) REVERT: O 879 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7375 (mt-10) REVERT: O 891 MET cc_start: 0.7682 (tmm) cc_final: 0.7434 (tmm) REVERT: O 897 HIS cc_start: 0.8348 (p90) cc_final: 0.7783 (p90) REVERT: O 923 THR cc_start: 0.7158 (t) cc_final: 0.6940 (t) REVERT: O 944 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7018 (mmmt) REVERT: O 1026 MET cc_start: 0.4008 (mmt) cc_final: 0.3738 (mmt) REVERT: O 1116 MET cc_start: 0.8497 (ptm) cc_final: 0.8223 (ptp) REVERT: A 59 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7987 (pt0) REVERT: B 84 MET cc_start: 0.7581 (mmp) cc_final: 0.6726 (mtm) REVERT: C 95 LYS cc_start: 0.8699 (tptm) cc_final: 0.8140 (ttmm) REVERT: D 82 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8089 (mmtt) REVERT: D 96 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8637 (ttm-80) REVERT: E 59 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8490 (pt0) REVERT: E 68 GLN cc_start: 0.8245 (tt0) cc_final: 0.7930 (tp40) REVERT: E 81 ASP cc_start: 0.8861 (m-30) cc_final: 0.8563 (t70) REVERT: E 108 ASN cc_start: 0.8699 (t0) cc_final: 0.8463 (t0) REVERT: F 27 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8543 (mm-40) REVERT: F 79 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8234 (mttp) REVERT: F 91 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8608 (tttt) REVERT: F 96 THR cc_start: 0.8287 (m) cc_final: 0.8006 (p) REVERT: G 95 LYS cc_start: 0.8228 (tptm) cc_final: 0.7645 (tppt) REVERT: G 104 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8201 (mt0) REVERT: H 31 LYS cc_start: 0.7708 (tptt) cc_final: 0.6729 (mttm) REVERT: H 36 ILE cc_start: 0.8869 (tt) cc_final: 0.8558 (mt) REVERT: H 43 LYS cc_start: 0.8532 (mttm) cc_final: 0.8237 (mmtp) REVERT: H 49 THR cc_start: 0.8873 (m) cc_final: 0.8277 (p) REVERT: H 82 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8477 (mmtt) REVERT: H 102 GLU cc_start: 0.7900 (tp30) cc_final: 0.7465 (tp30) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3184 time to fit residues: 107.0194 Evaluate side-chains 188 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17650 Z= 0.163 Angle : 0.568 10.708 25082 Z= 0.320 Chirality : 0.035 0.215 2856 Planarity : 0.004 0.050 2163 Dihedral : 27.972 164.192 4678 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.09 % Allowed : 0.70 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.53 (0.24), residues: 1313 helix: 1.28 (0.19), residues: 804 sheet: -0.69 (0.66), residues: 69 loop : -1.18 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O1083 HIS 0.009 0.001 HIS H 79 PHE 0.016 0.001 PHE O1159 TYR 0.021 0.001 TYR O 810 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: O 677 THR cc_start: 0.3222 (m) cc_final: 0.3021 (m) REVERT: O 812 MET cc_start: 0.7322 (mtm) cc_final: 0.6960 (mmt) REVERT: O 879 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7554 (mt-10) REVERT: O 891 MET cc_start: 0.7665 (tmm) cc_final: 0.7431 (tmm) REVERT: O 897 HIS cc_start: 0.8322 (p90) cc_final: 0.7787 (p90) REVERT: O 944 LYS cc_start: 0.7928 (ttpt) cc_final: 0.6964 (mmmt) REVERT: O 991 LEU cc_start: 0.7456 (mp) cc_final: 0.7244 (mm) REVERT: O 1026 MET cc_start: 0.3495 (mmt) cc_final: 0.3203 (mmt) REVERT: O 1053 MET cc_start: 0.8133 (tpt) cc_final: 0.7516 (mmt) REVERT: O 1116 MET cc_start: 0.8486 (ptm) cc_final: 0.8267 (ptp) REVERT: B 84 MET cc_start: 0.7626 (mmp) cc_final: 0.6619 (mtm) REVERT: C 38 ASN cc_start: 0.9224 (m-40) cc_final: 0.8359 (p0) REVERT: C 71 ARG cc_start: 0.8083 (tmm-80) cc_final: 0.7875 (tmm-80) REVERT: C 78 ILE cc_start: 0.8861 (mt) cc_final: 0.8643 (mt) REVERT: C 95 LYS cc_start: 0.8716 (tptm) cc_final: 0.8167 (ttmm) REVERT: D 82 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8057 (mmtt) REVERT: E 48 LEU cc_start: 0.8831 (mp) cc_final: 0.8549 (mt) REVERT: E 59 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8578 (pt0) REVERT: E 68 GLN cc_start: 0.8195 (tt0) cc_final: 0.7895 (tp40) REVERT: E 81 ASP cc_start: 0.8786 (m-30) cc_final: 0.8532 (t70) REVERT: E 108 ASN cc_start: 0.8742 (t0) cc_final: 0.8450 (t0) REVERT: F 52 GLU cc_start: 0.7827 (mp0) cc_final: 0.7388 (mm-30) REVERT: F 74 GLU cc_start: 0.8350 (tp30) cc_final: 0.8119 (tp30) REVERT: F 79 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8217 (mttp) REVERT: F 91 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8573 (tttt) REVERT: F 96 THR cc_start: 0.8296 (m) cc_final: 0.7989 (p) REVERT: G 95 LYS cc_start: 0.8071 (tptm) cc_final: 0.7423 (tppt) REVERT: G 104 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8185 (mt0) REVERT: H 31 LYS cc_start: 0.7897 (tptt) cc_final: 0.6868 (mttm) REVERT: H 32 GLU cc_start: 0.7576 (pp20) cc_final: 0.7198 (pp20) REVERT: H 39 TYR cc_start: 0.8632 (t80) cc_final: 0.8310 (t80) REVERT: H 79 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8516 (t70) REVERT: H 82 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8473 (mmtt) REVERT: H 102 GLU cc_start: 0.7880 (tp30) cc_final: 0.7413 (tp30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3223 time to fit residues: 105.0371 Evaluate side-chains 180 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17650 Z= 0.306 Angle : 0.656 10.644 25082 Z= 0.360 Chirality : 0.039 0.212 2856 Planarity : 0.005 0.052 2163 Dihedral : 28.215 162.828 4678 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.13 (0.24), residues: 1313 helix: 0.99 (0.19), residues: 786 sheet: -0.88 (0.67), residues: 69 loop : -1.30 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 838 HIS 0.007 0.001 HIS C 31 PHE 0.016 0.002 PHE O1159 TYR 0.034 0.002 TYR F 88 ARG 0.027 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.570 Fit side-chains REVERT: O 677 THR cc_start: 0.1888 (m) cc_final: 0.1660 (m) REVERT: O 778 MET cc_start: 0.8907 (tmm) cc_final: 0.8455 (tmm) REVERT: O 812 MET cc_start: 0.7449 (mtm) cc_final: 0.7016 (mmt) REVERT: O 879 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7281 (mt-10) REVERT: O 891 MET cc_start: 0.7767 (tmm) cc_final: 0.7300 (tmm) REVERT: O 897 HIS cc_start: 0.8389 (p90) cc_final: 0.7904 (p90) REVERT: O 944 LYS cc_start: 0.7894 (ttpt) cc_final: 0.6938 (mmmt) REVERT: O 1053 MET cc_start: 0.7781 (tpt) cc_final: 0.7404 (mmt) REVERT: O 1113 THR cc_start: 0.8805 (p) cc_final: 0.8401 (t) REVERT: O 1116 MET cc_start: 0.8478 (ptm) cc_final: 0.8243 (ptp) REVERT: O 1144 GLU cc_start: 0.8831 (tt0) cc_final: 0.8473 (mp0) REVERT: A 59 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8098 (pt0) REVERT: B 84 MET cc_start: 0.7466 (mmp) cc_final: 0.6752 (mtm) REVERT: C 95 LYS cc_start: 0.8785 (tptm) cc_final: 0.8271 (ttmm) REVERT: D 82 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8148 (mmtt) REVERT: E 59 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8578 (pt0) REVERT: E 68 GLN cc_start: 0.8168 (tt0) cc_final: 0.7751 (tm-30) REVERT: F 52 GLU cc_start: 0.7912 (mp0) cc_final: 0.7665 (tp30) REVERT: F 74 GLU cc_start: 0.8472 (tp30) cc_final: 0.8247 (tp30) REVERT: F 79 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8215 (mttp) REVERT: F 91 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8633 (tttt) REVERT: F 96 THR cc_start: 0.8351 (m) cc_final: 0.8064 (p) REVERT: G 95 LYS cc_start: 0.8242 (tptm) cc_final: 0.7624 (tppt) REVERT: G 104 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8237 (mt0) REVERT: H 31 LYS cc_start: 0.7941 (tptt) cc_final: 0.6980 (mttm) REVERT: H 32 GLU cc_start: 0.7430 (pp20) cc_final: 0.7213 (pp20) REVERT: H 82 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8478 (mmtt) REVERT: H 102 GLU cc_start: 0.8042 (tp30) cc_final: 0.7645 (tp30) REVERT: H 115 VAL cc_start: 0.9267 (t) cc_final: 0.9019 (p) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3186 time to fit residues: 96.1710 Evaluate side-chains 167 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17650 Z= 0.202 Angle : 0.597 11.123 25082 Z= 0.332 Chirality : 0.036 0.210 2856 Planarity : 0.004 0.052 2163 Dihedral : 28.024 163.598 4678 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.40 (0.24), residues: 1313 helix: 1.19 (0.19), residues: 800 sheet: -0.73 (0.67), residues: 69 loop : -1.26 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 955 HIS 0.008 0.001 HIS H 79 PHE 0.016 0.001 PHE O1159 TYR 0.025 0.002 TYR F 88 ARG 0.007 0.000 ARG C 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: O 677 THR cc_start: 0.1961 (m) cc_final: 0.1732 (m) REVERT: O 778 MET cc_start: 0.8707 (tmm) cc_final: 0.8200 (tmm) REVERT: O 812 MET cc_start: 0.7411 (mtm) cc_final: 0.7029 (mmt) REVERT: O 879 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7458 (mt-10) REVERT: O 891 MET cc_start: 0.7752 (tmm) cc_final: 0.7298 (tmm) REVERT: O 897 HIS cc_start: 0.8337 (p90) cc_final: 0.7846 (p90) REVERT: O 944 LYS cc_start: 0.7909 (ttpt) cc_final: 0.6919 (mmmt) REVERT: O 1053 MET cc_start: 0.7777 (tpt) cc_final: 0.7359 (mmt) REVERT: O 1113 THR cc_start: 0.8703 (p) cc_final: 0.8198 (t) REVERT: O 1114 GLN cc_start: 0.7741 (mp10) cc_final: 0.7499 (tp40) REVERT: O 1116 MET cc_start: 0.8376 (ptm) cc_final: 0.8138 (ptp) REVERT: A 59 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8053 (pt0) REVERT: B 84 MET cc_start: 0.7497 (mmp) cc_final: 0.6720 (mtm) REVERT: C 95 LYS cc_start: 0.8783 (tptm) cc_final: 0.8282 (ttmm) REVERT: D 82 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8108 (mmtt) REVERT: E 59 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8625 (pt0) REVERT: E 68 GLN cc_start: 0.8183 (tt0) cc_final: 0.7947 (tp40) REVERT: F 52 GLU cc_start: 0.7874 (mp0) cc_final: 0.7582 (tp30) REVERT: F 74 GLU cc_start: 0.8454 (tp30) cc_final: 0.8210 (tp30) REVERT: F 79 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8261 (mttp) REVERT: F 91 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8692 (tttt) REVERT: F 96 THR cc_start: 0.8321 (m) cc_final: 0.8037 (p) REVERT: G 95 LYS cc_start: 0.8220 (tptm) cc_final: 0.7566 (tppt) REVERT: G 104 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8174 (mt0) REVERT: H 31 LYS cc_start: 0.7878 (tptt) cc_final: 0.6905 (mttm) REVERT: H 32 GLU cc_start: 0.7505 (pp20) cc_final: 0.7184 (pp20) REVERT: H 79 HIS cc_start: 0.8889 (OUTLIER) cc_final: 0.8523 (t70) REVERT: H 82 LYS cc_start: 0.8889 (mtpt) cc_final: 0.8520 (mmtt) REVERT: H 102 GLU cc_start: 0.7940 (tp30) cc_final: 0.7531 (tp30) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.3138 time to fit residues: 94.3432 Evaluate side-chains 169 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.129929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099767 restraints weight = 34043.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098589 restraints weight = 60195.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098914 restraints weight = 61210.854| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17650 Z= 0.224 Angle : 0.602 10.924 25082 Z= 0.334 Chirality : 0.036 0.202 2856 Planarity : 0.004 0.052 2163 Dihedral : 28.038 163.068 4678 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.40 (0.24), residues: 1313 helix: 1.22 (0.19), residues: 787 sheet: -0.59 (0.67), residues: 68 loop : -1.25 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 838 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.001 PHE O1159 TYR 0.026 0.002 TYR F 88 ARG 0.008 0.000 ARG C 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.98 seconds wall clock time: 52 minutes 45.97 seconds (3165.97 seconds total)