Starting phenix.real_space_refine on Tue Nov 18 18:48:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z3u_6882/11_2025/5z3u_6882.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z3u_6882/11_2025/5z3u_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 { model { file = "/net/cci-nas-00/data/ceres_data/5z3u_6882/11_2025/5z3u_6882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z3u_6882/11_2025/5z3u_6882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5z3u_6882/11_2025/5z3u_6882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z3u_6882/11_2025/5z3u_6882.map" } 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 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. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ASN:plan1': 2, 'PHE:plan': 1} 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: 3.77, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.66 Conformation dependent library (CDL) restraints added in 580.4 milliseconds 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... Secondary structure from input PDB file: 64 helices and 13 sheets defined 64.5% alpha, 3.6% beta 144 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'O' and resid 674 through 688 Processing helix chain 'O' and resid 744 through 748 removed outlier: 3.825A pdb=" N ALA O 748 " --> pdb=" O TYR O 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 744 through 748' Processing helix chain 'O' and resid 769 through 784 Processing helix chain 'O' and resid 797 through 813 Processing helix chain 'O' and resid 828 through 838 Processing helix chain 'O' and resid 852 through 861 Processing helix chain 'O' and resid 862 through 864 No H-bonds generated for 'chain 'O' and resid 862 through 864' Processing helix chain 'O' and resid 874 through 879 Processing helix chain 'O' and resid 879 through 884 Processing helix chain 'O' and resid 895 through 899 Processing helix chain 'O' and resid 904 through 914 removed outlier: 3.574A pdb=" N LEU O 908 " --> pdb=" O SER O 904 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR O 914 " --> pdb=" O LEU O 910 " (cutoff:3.500A) Processing helix chain 'O' and resid 933 through 942 removed outlier: 3.777A pdb=" N LEU O 942 " --> pdb=" O LEU O 938 " (cutoff:3.500A) Processing helix chain 'O' and resid 948 through 951 Processing helix chain 'O' and resid 952 through 957 Processing helix chain 'O' and resid 968 through 988 Processing helix chain 'O' and resid 995 through 1000 removed outlier: 3.762A pdb=" N VAL O 999 " --> pdb=" O LEU O 995 " (cutoff:3.500A) Processing helix chain 'O' and resid 1016 through 1026 removed outlier: 4.283A pdb=" N MET O1022 " --> pdb=" O LEU O1018 " (cutoff:3.500A) Processing helix chain 'O' and resid 1050 through 1061 Processing helix chain 'O' and resid 1065 through 1072 removed outlier: 3.996A pdb=" N GLU O1069 " --> pdb=" O PHE O1065 " (cutoff:3.500A) Processing helix chain 'O' and resid 1086 through 1103 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1114 through 1127 removed outlier: 3.761A pdb=" N ILE O1118 " --> pdb=" O GLN O1114 " (cutoff:3.500A) Processing helix chain 'O' and resid 1140 through 1151 Processing helix chain 'O' and resid 1186 through 1195 removed outlier: 3.596A pdb=" N ASP O1190 " --> pdb=" O ASN O1186 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1234 removed outlier: 3.702A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS O1234 " --> pdb=" O ASP O1230 " (cutoff:3.500A) Processing helix chain 'O' and resid 1235 through 1240 Processing helix chain 'O' and resid 1248 through 1269 Processing helix chain 'O' and resid 1279 through 1288 removed outlier: 4.009A pdb=" N ILE O1283 " --> pdb=" O LYS O1279 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1297 Processing helix chain 'O' and resid 1298 through 1301 Processing helix chain 'O' and resid 1337 through 1347 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.633A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.545A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.723A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.855A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.767A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.942A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.633A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.545A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.511A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.843A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.767A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.942A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 789 through 790 Processing sheet with id=AA2, first strand: chain 'O' and resid 868 through 872 removed outlier: 3.518A pdb=" N VAL O 823 " --> pdb=" O THR O 871 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU O 820 " --> pdb=" O ILE O 892 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 888 through 890 removed outlier: 6.061A pdb=" N VAL O 889 " --> pdb=" O TYR O 918 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 1130 through 1132 removed outlier: 6.751A pdb=" N LEU O1131 " --> pdb=" O ILE O1160 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N SER O1162 " --> pdb=" O LEU O1131 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL O1106 " --> pdb=" O PHE O1159 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU O1161 " --> pdb=" O VAL O1106 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE O1108 " --> pdb=" O LEU O1161 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU O1107 " --> pdb=" O ILE O1179 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL O1178 " --> pdb=" O LEU O1209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.538A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 119 removed outlier: 7.413A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.811A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.095A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 119 removed outlier: 7.471A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.734A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 77 through 78 593 hydrogen bonds defined for protein. 1755 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: 4.30 Time building geometry restraints manager: 2.13 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: 0.00 - 4.10: 24924 4.10 - 8.19: 140 8.19 - 12.29: 16 12.29 - 16.39: 1 16.39 - 20.49: 1 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: 272 2.60 - 3.18: 15346 3.18 - 3.75: 29535 3.75 - 4.33: 39092 4.33 - 4.90: 57005 Nonbonded interactions: 141250 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 2.990 nonbonded pdb=" NH1 ARG B 39 " pdb=" O LYS B 44 " model vdw 2.144 3.120 nonbonded pdb=" O SER O 972 " pdb=" OG1 THR O 976 " model vdw 2.145 3.040 nonbonded pdb=" O3B ADP O1502 " pdb=" F2 BEF O1503 " model vdw 2.151 2.990 ... (remaining 141245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.230 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.620 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- 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= 0.506 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG O 862 TYR 0.036 0.004 TYR O 810 PHE 0.032 0.003 PHE O 946 TRP 0.018 0.003 TRP O 831 HIS 0.014 0.003 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.01138 (17650) covalent geometry : angle 0.97893 (25082) hydrogen bonds : bond 0.11866 ( 961) hydrogen bonds : angle 9.14371 ( 2491) *********************** 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 to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 0.526 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: 0.7301 (t0) REVERT: O 790 LEU cc_start: 0.6813 (tp) cc_final: 0.6415 (mp) REVERT: O 803 ILE cc_start: 0.8338 (mt) cc_final: 0.7912 (mt) REVERT: O 810 TYR cc_start: 0.5671 (m-80) cc_final: 0.5364 (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: 0.4892 (ttp80) REVERT: O 876 ILE cc_start: 0.8527 (pp) cc_final: 0.8261 (tt) REVERT: O 888 TRP cc_start: 0.5310 (m100) cc_final: 0.4885 (m100) REVERT: O 897 HIS cc_start: 0.8691 (p90) cc_final: 0.8027 (p90) REVERT: O 915 HIS cc_start: 0.7652 (m-70) cc_final: 0.7171 (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: 0.5338 (tmm) REVERT: O 1116 MET cc_start: 0.8497 (ptm) cc_final: 0.7965 (mtt) REVERT: O 1183 THR cc_start: 0.7213 (m) cc_final: 0.6934 (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: 0.3146 (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: 0.8641 (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: 0.8980 (tpp) REVERT: D 82 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8650 (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: 0.8326 (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: 0.8406 (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: 0.7451 (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: 0.7252 (ptp-110) REVERT: H 81 ASN cc_start: 0.8479 (m-40) cc_final: 0.8238 (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: 0.2050 time to fit residues: 96.1318 Evaluate side-chains 207 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O1111 GLN O1192 GLN A 76 GLN B 25 ASN B 75 HIS B 93 GLN E 68 GLN F 75 HIS G 104 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101105 restraints weight = 33983.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100399 restraints weight = 64285.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100382 restraints weight = 62088.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100347 restraints weight = 49782.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100302 restraints weight = 54387.732| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2666 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= 0.161 Angle : 0.648 7.253 25082 Z= 0.367 Chirality : 0.038 0.209 2856 Planarity : 0.005 0.052 2163 Dihedral : 28.412 162.118 4678 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1313 helix: 0.06 (0.18), residues: 804 sheet: -2.35 (0.59), residues: 57 loop : -1.91 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.028 0.002 TYR O1226 PHE 0.031 0.002 PHE O 835 TRP 0.014 0.002 TRP O1185 HIS 0.009 0.001 HIS O1061 Details of bonding type rmsd covalent geometry : bond 0.00325 (17650) covalent geometry : angle 0.64774 (25082) hydrogen bonds : bond 0.04453 ( 961) hydrogen bonds : angle 4.75445 ( 2491) *********************** 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 293 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8226 (tp) cc_final: 0.7512 (mp) REVERT: O 794 MET cc_start: 0.5398 (ppp) cc_final: 0.4882 (ppp) REVERT: O 803 ILE cc_start: 0.8112 (mt) cc_final: 0.7893 (mt) REVERT: O 810 TYR cc_start: 0.3978 (m-80) cc_final: 0.3551 (m-80) REVERT: O 854 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.5088 (ttp-110) REVERT: O 876 ILE cc_start: 0.9054 (pt) cc_final: 0.8552 (tt) REVERT: O 980 ILE cc_start: 0.5948 (mt) cc_final: 0.5526 (mm) REVERT: A 77 ASP cc_start: 0.6808 (m-30) cc_final: 0.6021 (m-30) REVERT: B 30 THR cc_start: 0.9080 (t) cc_final: 0.8722 (m) REVERT: B 84 MET cc_start: 0.6681 (mmp) cc_final: 0.6190 (mtm) REVERT: C 81 ARG cc_start: 0.8697 (tpt170) cc_final: 0.8467 (tpt170) REVERT: C 89 ASN cc_start: 0.7924 (m-40) cc_final: 0.7639 (m-40) REVERT: C 95 LYS cc_start: 0.8920 (tptm) cc_final: 0.8401 (ttmm) REVERT: D 68 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7914 (mm-30) REVERT: D 90 GLU cc_start: 0.8015 (mp0) cc_final: 0.7724 (mp0) REVERT: D 96 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7565 (ttp80) REVERT: E 108 ASN cc_start: 0.9032 (t0) cc_final: 0.8760 (t0) REVERT: E 129 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7320 (tpt170) REVERT: F 74 GLU cc_start: 0.7459 (tp30) cc_final: 0.7177 (tp30) REVERT: F 91 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8263 (tttt) REVERT: F 96 THR cc_start: 0.8678 (m) cc_final: 0.8052 (p) REVERT: G 92 GLU cc_start: 0.5841 (mt-10) cc_final: 0.5398 (pt0) REVERT: G 95 LYS cc_start: 0.8373 (tptm) cc_final: 0.7843 (tppt) REVERT: H 31 LYS cc_start: 0.8439 (tptt) cc_final: 0.8061 (mttp) REVERT: H 56 MET cc_start: 0.8059 (tpp) cc_final: 0.7745 (tpp) REVERT: H 98 LEU cc_start: 0.8890 (mm) cc_final: 0.8621 (mm) REVERT: H 115 VAL cc_start: 0.9504 (t) cc_final: 0.9243 (p) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.1811 time to fit residues: 73.6234 Evaluate side-chains 204 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 5 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 681 HIS O1104 HIS D 92 GLN G 89 ASN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099221 restraints weight = 34377.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098049 restraints weight = 58821.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097689 restraints weight = 58558.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097113 restraints weight = 51583.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097007 restraints weight = 52675.630| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17650 Z= 0.182 Angle : 0.638 8.566 25082 Z= 0.359 Chirality : 0.038 0.203 2856 Planarity : 0.004 0.046 2163 Dihedral : 28.445 160.806 4678 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1313 helix: 0.92 (0.18), residues: 816 sheet: -1.75 (0.59), residues: 63 loop : -1.73 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 42 TYR 0.027 0.002 TYR O 810 PHE 0.016 0.002 PHE O1122 TRP 0.009 0.001 TRP O1185 HIS 0.006 0.001 HIS O 913 Details of bonding type rmsd covalent geometry : bond 0.00402 (17650) covalent geometry : angle 0.63771 (25082) hydrogen bonds : bond 0.04458 ( 961) hydrogen bonds : angle 4.39670 ( 2491) *********************** 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 245 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8335 (tp) cc_final: 0.7494 (mp) REVERT: O 810 TYR cc_start: 0.3975 (m-80) cc_final: 0.3722 (m-80) REVERT: O 876 ILE cc_start: 0.8972 (pt) cc_final: 0.8706 (tt) REVERT: O 980 ILE cc_start: 0.5905 (mt) cc_final: 0.5704 (mt) REVERT: A 76 GLN cc_start: 0.8640 (pp30) cc_final: 0.8350 (pp30) REVERT: A 77 ASP cc_start: 0.7301 (m-30) cc_final: 0.7033 (m-30) REVERT: B 84 MET cc_start: 0.6830 (mmp) cc_final: 0.6333 (mtm) REVERT: C 16 THR cc_start: 0.8736 (p) cc_final: 0.8489 (p) REVERT: C 81 ARG cc_start: 0.8841 (tpt170) cc_final: 0.8471 (tpt170) REVERT: C 95 LYS cc_start: 0.8863 (tptm) cc_final: 0.8453 (ttmm) REVERT: D 68 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7863 (mm-30) REVERT: D 90 GLU cc_start: 0.8167 (mp0) cc_final: 0.7567 (mp0) REVERT: D 96 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7694 (ttp80) REVERT: E 93 GLN cc_start: 0.8525 (tt0) cc_final: 0.8315 (tt0) REVERT: F 88 TYR cc_start: 0.7566 (m-10) cc_final: 0.7263 (m-10) REVERT: F 91 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8180 (tttt) REVERT: F 96 THR cc_start: 0.8460 (m) cc_final: 0.8212 (p) REVERT: G 23 LEU cc_start: 0.8686 (mm) cc_final: 0.8330 (mt) REVERT: G 95 LYS cc_start: 0.8266 (tptm) cc_final: 0.7745 (tppt) REVERT: H 31 LYS cc_start: 0.8179 (tptt) cc_final: 0.7960 (mmtp) REVERT: H 56 MET cc_start: 0.8383 (tpp) cc_final: 0.8067 (tpp) REVERT: H 115 VAL cc_start: 0.9532 (t) cc_final: 0.9322 (p) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1607 time to fit residues: 56.4494 Evaluate side-chains 187 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 928 GLN O1104 HIS B 25 ASN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099368 restraints weight = 34427.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098103 restraints weight = 62446.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098591 restraints weight = 67374.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098111 restraints weight = 48260.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098228 restraints weight = 49016.510| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3576 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= 0.176 Angle : 0.617 7.851 25082 Z= 0.348 Chirality : 0.038 0.195 2856 Planarity : 0.004 0.047 2163 Dihedral : 28.287 162.833 4678 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1313 helix: 1.32 (0.18), residues: 813 sheet: -1.49 (0.62), residues: 63 loop : -1.53 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 77 TYR 0.027 0.002 TYR D 80 PHE 0.015 0.002 PHE O1159 TRP 0.008 0.001 TRP O1185 HIS 0.012 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00391 (17650) covalent geometry : angle 0.61708 (25082) hydrogen bonds : bond 0.04291 ( 961) hydrogen bonds : angle 4.09431 ( 2491) *********************** 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 237 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8342 (tp) cc_final: 0.7457 (mp) REVERT: O 876 ILE cc_start: 0.8958 (pt) cc_final: 0.8706 (tt) REVERT: O 944 LYS cc_start: 0.7032 (ttpt) cc_final: 0.6705 (mmmt) REVERT: A 76 GLN cc_start: 0.8766 (pp30) cc_final: 0.8437 (pp30) REVERT: A 77 ASP cc_start: 0.7360 (m-30) cc_final: 0.7083 (m-30) REVERT: B 84 MET cc_start: 0.6722 (mmp) cc_final: 0.6262 (mtm) REVERT: C 95 LYS cc_start: 0.8885 (tptm) cc_final: 0.8487 (ttmm) REVERT: D 68 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7724 (mm-30) REVERT: E 68 GLN cc_start: 0.7782 (tp40) cc_final: 0.7568 (tm-30) REVERT: E 125 GLN cc_start: 0.7767 (mt0) cc_final: 0.7558 (mt0) REVERT: F 74 GLU cc_start: 0.7481 (tp30) cc_final: 0.7160 (tp30) REVERT: F 91 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8201 (tttt) REVERT: F 96 THR cc_start: 0.8528 (m) cc_final: 0.8145 (p) REVERT: G 95 LYS cc_start: 0.8365 (tptm) cc_final: 0.7830 (tppt) REVERT: H 31 LYS cc_start: 0.8271 (tptt) cc_final: 0.7976 (mmtp) REVERT: H 49 THR cc_start: 0.8974 (m) cc_final: 0.8474 (m) REVERT: H 56 MET cc_start: 0.8357 (tpp) cc_final: 0.7911 (tpp) REVERT: H 115 VAL cc_start: 0.9597 (t) cc_final: 0.9373 (p) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1630 time to fit residues: 55.3084 Evaluate side-chains 183 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 73 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 122 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN D 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097024 restraints weight = 34436.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095890 restraints weight = 49531.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095995 restraints weight = 48878.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095634 restraints weight = 39872.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095647 restraints weight = 40739.287| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3914 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= 0.161 Angle : 0.600 7.748 25082 Z= 0.340 Chirality : 0.037 0.189 2856 Planarity : 0.004 0.050 2163 Dihedral : 28.198 163.658 4678 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1313 helix: 1.47 (0.18), residues: 816 sheet: -1.32 (0.62), residues: 62 loop : -1.48 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.022 0.002 TYR D 37 PHE 0.016 0.002 PHE O1159 TRP 0.007 0.001 TRP O 888 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00350 (17650) covalent geometry : angle 0.60031 (25082) hydrogen bonds : bond 0.04096 ( 961) hydrogen bonds : angle 3.99311 ( 2491) *********************** 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 229 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8283 (tp) cc_final: 0.7389 (mp) REVERT: O 876 ILE cc_start: 0.9024 (pt) cc_final: 0.8798 (tt) REVERT: O 891 MET cc_start: 0.8167 (tmm) cc_final: 0.7800 (tmm) REVERT: O 944 LYS cc_start: 0.7106 (ttpt) cc_final: 0.6777 (mmmt) REVERT: O 1294 MET cc_start: 0.5801 (tpt) cc_final: 0.5441 (tpp) REVERT: A 76 GLN cc_start: 0.8803 (pp30) cc_final: 0.8483 (pp30) REVERT: A 77 ASP cc_start: 0.7405 (m-30) cc_final: 0.7028 (m-30) REVERT: B 84 MET cc_start: 0.6702 (mmp) cc_final: 0.6231 (mtm) REVERT: C 95 LYS cc_start: 0.8797 (tptm) cc_final: 0.8435 (ttmm) REVERT: D 68 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7750 (mm-30) REVERT: E 59 GLU cc_start: 0.7933 (pt0) cc_final: 0.7666 (pt0) REVERT: E 68 GLN cc_start: 0.7951 (tp40) cc_final: 0.7600 (tm-30) REVERT: E 108 ASN cc_start: 0.8768 (t0) cc_final: 0.8525 (t0) REVERT: F 74 GLU cc_start: 0.7517 (tp30) cc_final: 0.7314 (tp30) REVERT: F 91 LYS cc_start: 0.8372 (ttmm) cc_final: 0.8157 (tttt) REVERT: F 96 THR cc_start: 0.8394 (m) cc_final: 0.8026 (p) REVERT: G 23 LEU cc_start: 0.8932 (mt) cc_final: 0.8698 (mt) REVERT: G 92 GLU cc_start: 0.6578 (mt-10) cc_final: 0.5712 (pt0) REVERT: G 95 LYS cc_start: 0.8352 (tptm) cc_final: 0.7938 (tppt) REVERT: H 31 LYS cc_start: 0.8334 (tptt) cc_final: 0.7844 (mmtp) REVERT: H 49 THR cc_start: 0.8942 (m) cc_final: 0.8115 (p) REVERT: H 115 VAL cc_start: 0.9489 (t) cc_final: 0.9250 (p) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1510 time to fit residues: 50.6670 Evaluate side-chains 182 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 34 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 84 GLN C 89 ASN E 68 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094356 restraints weight = 34530.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.093130 restraints weight = 61910.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093535 restraints weight = 62145.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.093218 restraints weight = 45395.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093198 restraints weight = 47776.370| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17650 Z= 0.263 Angle : 0.688 8.607 25082 Z= 0.383 Chirality : 0.041 0.212 2856 Planarity : 0.005 0.055 2163 Dihedral : 28.434 162.555 4678 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1313 helix: 1.10 (0.18), residues: 813 sheet: -1.35 (0.60), residues: 62 loop : -1.59 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 854 TYR 0.031 0.003 TYR F 88 PHE 0.016 0.002 PHE O1159 TRP 0.012 0.001 TRP O1083 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00603 (17650) covalent geometry : angle 0.68797 (25082) hydrogen bonds : bond 0.05121 ( 961) hydrogen bonds : angle 4.34293 ( 2491) *********************** 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 215 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 677 THR cc_start: 0.1889 (m) cc_final: 0.1628 (m) REVERT: O 790 LEU cc_start: 0.8382 (tp) cc_final: 0.7407 (mp) REVERT: O 876 ILE cc_start: 0.9119 (pt) cc_final: 0.8848 (tt) REVERT: B 84 MET cc_start: 0.6636 (mmp) cc_final: 0.6271 (mtm) REVERT: C 95 LYS cc_start: 0.8856 (tptm) cc_final: 0.8457 (ttmm) REVERT: D 90 GLU cc_start: 0.8080 (mp0) cc_final: 0.7777 (mp0) REVERT: E 93 GLN cc_start: 0.8773 (tt0) cc_final: 0.8170 (tt0) REVERT: E 125 GLN cc_start: 0.7787 (mt0) cc_final: 0.7498 (mt0) REVERT: F 74 GLU cc_start: 0.7632 (tp30) cc_final: 0.7401 (tp30) REVERT: F 96 THR cc_start: 0.8436 (m) cc_final: 0.8112 (p) REVERT: G 95 LYS cc_start: 0.8390 (tptm) cc_final: 0.7780 (tppt) REVERT: H 31 LYS cc_start: 0.8536 (tptt) cc_final: 0.7950 (mmtp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1464 time to fit residues: 46.7353 Evaluate side-chains 174 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN E 68 GLN F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097650 restraints weight = 34188.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096548 restraints weight = 59145.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096528 restraints weight = 60610.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096558 restraints weight = 47529.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096485 restraints weight = 46429.555| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17650 Z= 0.192 Angle : 0.632 9.549 25082 Z= 0.354 Chirality : 0.038 0.221 2856 Planarity : 0.004 0.054 2163 Dihedral : 28.306 162.984 4678 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1313 helix: 1.29 (0.18), residues: 816 sheet: -1.18 (0.66), residues: 57 loop : -1.55 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.025 0.002 TYR O 810 PHE 0.017 0.002 PHE O1159 TRP 0.017 0.001 TRP O 831 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00433 (17650) covalent geometry : angle 0.63226 (25082) hydrogen bonds : bond 0.04508 ( 961) hydrogen bonds : angle 4.03536 ( 2491) *********************** 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 217 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 677 THR cc_start: 0.1707 (m) cc_final: 0.1430 (m) REVERT: O 790 LEU cc_start: 0.8404 (tp) cc_final: 0.7513 (mp) REVERT: A 60 LEU cc_start: 0.9280 (mp) cc_final: 0.9031 (mp) REVERT: B 84 MET cc_start: 0.6619 (mmp) cc_final: 0.6237 (mtm) REVERT: C 95 LYS cc_start: 0.8859 (tptm) cc_final: 0.8452 (ttmm) REVERT: D 90 GLU cc_start: 0.8044 (mp0) cc_final: 0.7744 (mp0) REVERT: E 74 ILE cc_start: 0.9302 (mt) cc_final: 0.9087 (mm) REVERT: E 76 GLN cc_start: 0.7511 (pt0) cc_final: 0.7275 (pt0) REVERT: E 125 GLN cc_start: 0.7797 (mt0) cc_final: 0.7589 (mt0) REVERT: F 74 GLU cc_start: 0.7358 (tp30) cc_final: 0.7135 (tp30) REVERT: F 96 THR cc_start: 0.8446 (m) cc_final: 0.8139 (p) REVERT: G 71 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8267 (ttp80) REVERT: G 95 LYS cc_start: 0.8367 (tptm) cc_final: 0.7869 (tppt) REVERT: G 104 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8176 (mt0) REVERT: H 31 LYS cc_start: 0.8604 (tptt) cc_final: 0.8038 (mmtp) REVERT: H 49 THR cc_start: 0.9014 (m) cc_final: 0.8470 (t) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1534 time to fit residues: 48.3921 Evaluate side-chains 170 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 6 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1189 GLN E 68 GLN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.129311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099043 restraints weight = 34293.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098118 restraints weight = 67007.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098600 restraints weight = 65117.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098457 restraints weight = 49637.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098606 restraints weight = 52037.565| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17650 Z= 0.184 Angle : 0.625 7.657 25082 Z= 0.350 Chirality : 0.038 0.197 2856 Planarity : 0.004 0.056 2163 Dihedral : 28.279 162.811 4678 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.09 % Allowed : 0.96 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1313 helix: 1.35 (0.18), residues: 816 sheet: -1.11 (0.69), residues: 57 loop : -1.48 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.029 0.002 TYR D 37 PHE 0.018 0.002 PHE O1159 TRP 0.011 0.001 TRP O 831 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00414 (17650) covalent geometry : angle 0.62522 (25082) hydrogen bonds : bond 0.04509 ( 961) hydrogen bonds : angle 4.01946 ( 2491) *********************** 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 209 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 677 THR cc_start: 0.1504 (m) cc_final: 0.1240 (m) REVERT: O 790 LEU cc_start: 0.8395 (tp) cc_final: 0.7594 (mp) REVERT: O 923 THR cc_start: 0.7907 (t) cc_final: 0.7295 (m) REVERT: A 59 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7577 (pt0) REVERT: B 84 MET cc_start: 0.6584 (mmp) cc_final: 0.6086 (mtm) REVERT: C 95 LYS cc_start: 0.8799 (tptm) cc_final: 0.8428 (ttmm) REVERT: D 90 GLU cc_start: 0.8185 (mp0) cc_final: 0.7838 (mp0) REVERT: E 68 GLN cc_start: 0.8278 (tm130) cc_final: 0.8067 (tm-30) REVERT: E 74 ILE cc_start: 0.9298 (mt) cc_final: 0.9084 (mm) REVERT: E 76 GLN cc_start: 0.7771 (pt0) cc_final: 0.7395 (pt0) REVERT: E 125 GLN cc_start: 0.7784 (mt0) cc_final: 0.7520 (mt0) REVERT: F 96 THR cc_start: 0.8332 (m) cc_final: 0.8096 (p) REVERT: G 95 LYS cc_start: 0.8329 (tptm) cc_final: 0.7781 (tppt) REVERT: H 31 LYS cc_start: 0.8504 (tptt) cc_final: 0.7982 (mmtp) REVERT: H 36 ILE cc_start: 0.8873 (pt) cc_final: 0.8104 (mp) REVERT: H 49 THR cc_start: 0.9032 (m) cc_final: 0.8446 (t) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1441 time to fit residues: 44.9334 Evaluate side-chains 174 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 20 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 92 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101341 restraints weight = 34094.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100065 restraints weight = 55885.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100296 restraints weight = 58294.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099783 restraints weight = 45805.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099765 restraints weight = 47583.522| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4641 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= 0.148 Angle : 0.593 7.393 25082 Z= 0.334 Chirality : 0.036 0.193 2856 Planarity : 0.004 0.054 2163 Dihedral : 28.097 163.178 4678 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1313 helix: 1.54 (0.18), residues: 819 sheet: -1.02 (0.69), residues: 57 loop : -1.38 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.024 0.002 TYR O 810 PHE 0.018 0.001 PHE O1159 TRP 0.014 0.001 TRP O 831 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00319 (17650) covalent geometry : angle 0.59337 (25082) hydrogen bonds : bond 0.04072 ( 961) hydrogen bonds : angle 3.83790 ( 2491) *********************** 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 222 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8349 (tp) cc_final: 0.7582 (mp) REVERT: O 923 THR cc_start: 0.7939 (t) cc_final: 0.7210 (m) REVERT: O 944 LYS cc_start: 0.6854 (ttpt) cc_final: 0.6650 (mmmt) REVERT: A 133 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 84 MET cc_start: 0.6662 (mmp) cc_final: 0.6236 (mtm) REVERT: C 95 LYS cc_start: 0.8774 (tptm) cc_final: 0.8398 (ttmm) REVERT: D 90 GLU cc_start: 0.8167 (mp0) cc_final: 0.7738 (mp0) REVERT: E 48 LEU cc_start: 0.8668 (mp) cc_final: 0.8465 (mt) REVERT: E 76 GLN cc_start: 0.7487 (pt0) cc_final: 0.7077 (pt0) REVERT: E 108 ASN cc_start: 0.8868 (t0) cc_final: 0.8579 (t0) REVERT: F 74 GLU cc_start: 0.7235 (tp30) cc_final: 0.6988 (tp30) REVERT: F 96 THR cc_start: 0.8351 (m) cc_final: 0.8053 (p) REVERT: G 84 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8179 (tm-30) REVERT: G 95 LYS cc_start: 0.8360 (tptm) cc_final: 0.7820 (tppt) REVERT: H 31 LYS cc_start: 0.8467 (tptt) cc_final: 0.7932 (mttm) REVERT: H 36 ILE cc_start: 0.8624 (pt) cc_final: 0.8122 (mp) REVERT: H 49 THR cc_start: 0.9021 (m) cc_final: 0.8676 (m) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1494 time to fit residues: 48.8923 Evaluate side-chains 173 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.128529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095261 restraints weight = 34177.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093936 restraints weight = 59529.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.094215 restraints weight = 58196.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093811 restraints weight = 44916.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093922 restraints weight = 43522.442| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17650 Z= 0.224 Angle : 0.665 11.523 25082 Z= 0.368 Chirality : 0.039 0.177 2856 Planarity : 0.005 0.057 2163 Dihedral : 28.306 162.043 4678 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1313 helix: 1.33 (0.18), residues: 820 sheet: -0.98 (0.67), residues: 63 loop : -1.38 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.028 0.002 TYR O 810 PHE 0.017 0.002 PHE O1159 TRP 0.005 0.001 TRP O 777 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00511 (17650) covalent geometry : angle 0.66517 (25082) hydrogen bonds : bond 0.04863 ( 961) hydrogen bonds : angle 4.09951 ( 2491) ********************** 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 204 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8310 (tp) cc_final: 0.7418 (mp) REVERT: O 991 LEU cc_start: 0.7716 (mm) cc_final: 0.7488 (tt) REVERT: O 1026 MET cc_start: 0.4707 (mmt) cc_final: 0.4415 (mmt) REVERT: A 59 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7672 (pt0) REVERT: B 84 MET cc_start: 0.6609 (mmp) cc_final: 0.6094 (mtm) REVERT: C 95 LYS cc_start: 0.8846 (tptm) cc_final: 0.8436 (ttmm) REVERT: D 90 GLU cc_start: 0.8150 (mp0) cc_final: 0.7711 (mp0) REVERT: E 76 GLN cc_start: 0.7888 (pt0) cc_final: 0.7443 (pt0) REVERT: E 94 GLU cc_start: 0.7702 (tp30) cc_final: 0.7488 (mm-30) REVERT: F 96 THR cc_start: 0.8346 (m) cc_final: 0.8018 (p) REVERT: G 95 LYS cc_start: 0.8163 (tptm) cc_final: 0.7603 (tppt) REVERT: H 31 LYS cc_start: 0.8465 (tptt) cc_final: 0.7845 (mmtp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1410 time to fit residues: 43.0397 Evaluate side-chains 166 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 114 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 92 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.132227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100707 restraints weight = 33855.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100083 restraints weight = 56197.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100007 restraints weight = 52007.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099766 restraints weight = 45034.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099783 restraints weight = 43247.538| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4941 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= 0.140 Angle : 0.597 10.963 25082 Z= 0.333 Chirality : 0.036 0.185 2856 Planarity : 0.004 0.052 2163 Dihedral : 27.955 163.360 4678 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1313 helix: 1.70 (0.19), residues: 822 sheet: -0.54 (0.68), residues: 59 loop : -1.36 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.025 0.002 TYR O 810 PHE 0.018 0.002 PHE O1159 TRP 0.010 0.001 TRP O 831 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00296 (17650) covalent geometry : angle 0.59705 (25082) hydrogen bonds : bond 0.03887 ( 961) hydrogen bonds : angle 3.74372 ( 2491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.84 seconds wall clock time: 41 minutes 21.13 seconds (2481.13 seconds total)