Starting phenix.real_space_refine (version: dev) on Tue Apr 5 23:55:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/04_2022/5z3u_6882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/04_2022/5z3u_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_6882/04_2022/5z3u_6882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/04_2022/5z3u_6882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/04_2022/5z3u_6882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3u_6882/04_2022/5z3u_6882_updated.pdb" } resolution = 4.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: {'PTRANS': 15, 'TRANS': 558, 'PCIS': 1} 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, 'BEF': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.73, per 1000 atoms: 0.58 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: 8.79 Conformation dependent library (CDL) restraints added in 1.7 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: 6.97 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: 8.96 Time building geometry restraints manager: 9.13 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=" F2 BEF O1503 " pdb="BE 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=" F1 BEF O1503 " pdb="BE 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=" F3 BEF O1503 " pdb="BE 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: 8165 31.19 - 62.39: 1457 62.39 - 93.58: 39 93.58 - 124.77: 0 124.77 - 155.97: 3 Dihedral angle restraints: 9664 sinusoidal: 5747 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 9661 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 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. 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.640 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.150 Process input model: 54.210 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 24.033 155.965 7120 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 0.09 % 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 *********************** 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 : 1.537 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 outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.3940 time to fit residues: 187.2710 Evaluate side-chains 189 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8694 ------------------------------------------------------------------------------- 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: 0.9990 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 O1025 GLN O1104 HIS O1111 GLN O1189 GLN O1192 GLN A 76 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 104 GLN H 81 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17650 Z= 0.219 Angle : 0.646 7.081 25082 Z= 0.366 Chirality : 0.039 0.201 2856 Planarity : 0.005 0.052 2163 Dihedral : 28.936 161.245 4422 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.09 % 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: -1.80 (0.21), residues: 1313 helix: -0.60 (0.17), residues: 799 sheet: -2.30 (0.58), residues: 62 loop : -1.92 (0.25), residues: 452 *********************** 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 255 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.3272 time to fit residues: 121.8000 Evaluate side-chains 180 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0206 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 142 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- 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 O1104 HIS D 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 17650 Z= 0.296 Angle : 0.659 8.005 25082 Z= 0.370 Chirality : 0.039 0.182 2856 Planarity : 0.005 0.050 2163 Dihedral : 28.899 161.235 4422 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.00 % 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: -0.88 (0.22), residues: 1313 helix: 0.28 (0.18), residues: 779 sheet: -1.71 (0.58), residues: 69 loop : -1.83 (0.25), residues: 465 *********************** 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 230 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3024 time to fit residues: 101.4634 Evaluate side-chains 164 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9398 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 chunk 143 optimal weight: 30.0000 chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 0.9980 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3549 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= 0.256 Angle : 0.621 7.336 25082 Z= 0.351 Chirality : 0.037 0.177 2856 Planarity : 0.005 0.067 2163 Dihedral : 28.755 163.104 4422 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.00 % 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: -0.45 (0.23), residues: 1313 helix: 0.54 (0.19), residues: 797 sheet: -1.01 (0.65), residues: 63 loop : -1.64 (0.27), residues: 453 *********************** 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 226 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3304 time to fit residues: 106.9654 Evaluate side-chains 169 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9271 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 40.0000 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 77 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 84 GLN C 89 ASN D 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 17650 Z= 0.266 Angle : 0.620 7.356 25082 Z= 0.350 Chirality : 0.037 0.172 2856 Planarity : 0.005 0.056 2163 Dihedral : 28.756 163.857 4422 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % 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: -0.36 (0.23), residues: 1313 helix: 0.60 (0.19), residues: 796 sheet: -0.74 (0.67), residues: 63 loop : -1.62 (0.28), residues: 454 *********************** 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 219 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3064 time to fit residues: 98.7690 Evaluate side-chains 161 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9429 ------------------------------------------------------------------------------- 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: 10.0000 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 125 GLN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4039 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= 0.251 Angle : 0.615 7.598 25082 Z= 0.347 Chirality : 0.037 0.173 2856 Planarity : 0.005 0.052 2163 Dihedral : 28.709 164.255 4422 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.00 % 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: -0.24 (0.23), residues: 1313 helix: 0.67 (0.19), residues: 797 sheet: -0.85 (0.67), residues: 63 loop : -1.50 (0.28), residues: 453 *********************** 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 211 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.557 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3037 time to fit residues: 94.6786 Evaluate side-chains 164 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9861 ------------------------------------------------------------------------------- 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: 0.0060 chunk 86 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4313 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= 0.192 Angle : 0.578 8.043 25082 Z= 0.328 Chirality : 0.035 0.211 2856 Planarity : 0.004 0.050 2163 Dihedral : 28.551 165.047 4422 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.09 % 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: 0.08 (0.24), residues: 1313 helix: 0.96 (0.19), residues: 807 sheet: -0.70 (0.67), residues: 63 loop : -1.50 (0.28), residues: 443 *********************** 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 220 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.3157 time to fit residues: 101.9663 Evaluate side-chains 174 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9909 ------------------------------------------------------------------------------- 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: 0.0470 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 108 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4586 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= 0.182 Angle : 0.577 7.949 25082 Z= 0.326 Chirality : 0.036 0.221 2856 Planarity : 0.004 0.050 2163 Dihedral : 28.470 165.162 4422 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.09 % 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: 0.31 (0.24), residues: 1313 helix: 1.16 (0.19), residues: 798 sheet: -0.59 (0.68), residues: 63 loop : -1.39 (0.28), residues: 452 *********************** 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 213 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.550 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.3205 time to fit residues: 99.7614 Evaluate side-chains 166 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9421 ------------------------------------------------------------------------------- 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: 5.9990 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 947 ASN O1215 ASN A 108 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 17650 Z= 0.426 Angle : 0.734 10.723 25082 Z= 0.403 Chirality : 0.042 0.213 2856 Planarity : 0.006 0.066 2163 Dihedral : 28.927 163.451 4422 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.00 % 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: -0.36 (0.23), residues: 1313 helix: 0.60 (0.18), residues: 783 sheet: -0.72 (0.69), residues: 62 loop : -1.57 (0.28), residues: 468 *********************** 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 194 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.543 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3047 time to fit residues: 87.3296 Evaluate side-chains 158 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9062 ------------------------------------------------------------------------------- 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: 8.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4705 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= 0.201 Angle : 0.599 7.618 25082 Z= 0.335 Chirality : 0.036 0.213 2856 Planarity : 0.004 0.054 2163 Dihedral : 28.566 164.807 4422 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.00 % 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: 0.19 (0.24), residues: 1313 helix: 1.07 (0.19), residues: 793 sheet: -0.58 (0.73), residues: 58 loop : -1.43 (0.29), residues: 462 ********************** 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 200 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.598 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2978 time to fit residues: 88.1636 Evaluate side-chains 160 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9626 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100745 restraints weight = 33770.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099969 restraints weight = 50628.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099699 restraints weight = 46991.480| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4971 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= 0.179 Angle : 0.585 7.908 25082 Z= 0.327 Chirality : 0.035 0.205 2856 Planarity : 0.004 0.052 2163 Dihedral : 28.398 164.478 4422 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.00 % 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: 0.31 (0.24), residues: 1313 helix: 1.16 (0.19), residues: 802 sheet: -0.34 (0.74), residues: 57 loop : -1.43 (0.29), residues: 454 =============================================================================== Job complete usr+sys time: 2615.42 seconds wall clock time: 48 minutes 41.66 seconds (2921.66 seconds total)