Starting phenix.real_space_refine on Sat Sep 12 14:35:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.map" model { file = "/net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z3u_6882/09_2026/5z3u_6882.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.30, per 1000 atoms: 0.20 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: 1.34 Conformation dependent library (CDL) restraints added in 276.7 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: 2.13 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: 4.49 Time building geometry restraints manager: 1.63 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=" C3' DG I 101 " pdb=" O3' DG I 101 " ideal model delta sigma weight residual 1.435 1.368 0.067 1.30e-02 5.92e+03 2.62e+01 bond pdb=" C3' DA I 29 " pdb=" O3' DA I 29 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.94e+01 ... (remaining 17645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 24918 4.10 - 8.19: 146 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=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.41e+01 angle pdb=" O4' DG J 55 " pdb=" C4' DG J 55 " pdb=" C3' DG J 55 " ideal model delta sigma weight residual 106.00 102.54 3.46 6.00e-01 2.78e+00 3.33e+01 angle pdb=" O4' DA J 100 " pdb=" C4' DA J 100 " pdb=" C3' DA J 100 " ideal model delta sigma weight residual 106.00 102.60 3.40 6.00e-01 2.78e+00 3.20e+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: 1741 0.048 - 0.097: 840 0.097 - 0.145: 232 0.145 - 0.194: 37 0.194 - 0.242: 6 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=" C3' DT J 50 " pdb=" C4' DT J 50 " pdb=" O3' DT J 50 " pdb=" C2' DT J 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.32e+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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.620 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.232 17650 Z= 0.837 Angle : 1.061 20.487 25082 Z= 0.752 Chirality : 0.059 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/Z covalent geometry : bond 0.01175 / 0.84 (17650) covalent geometry : angle 1.06126 / 0.75 (25082) hydrogen bonds : bond 0.11866 / 7.66 ( 961) hydrogen bonds : angle 9.14371 / 6.37 ( 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 : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 769 ASP cc_start: 0.7632 (p0) cc_final: 0.7302 (t0) REVERT: O 790 LEU cc_start: 0.6813 (tp) cc_final: 0.6413 (mp) REVERT: O 803 ILE cc_start: 0.8338 (mt) cc_final: 0.7910 (mt) REVERT: O 810 TYR cc_start: 0.5672 (m-80) cc_final: 0.5366 (m-80) REVERT: O 812 MET cc_start: 0.7655 (mtm) cc_final: 0.7421 (tpp) REVERT: O 854 ARG cc_start: 0.6229 (mtm-85) cc_final: 0.4888 (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: 0.4888 (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: 0.7169 (t-170) REVERT: O 930 ASN cc_start: 0.7820 (m-40) cc_final: 0.7371 (t0) REVERT: O 932 PRO cc_start: 0.6273 (Cg_exo) cc_final: 0.5925 (Cg_endo) REVERT: O 1015 MET cc_start: 0.5562 (tpt) cc_final: 0.5336 (tmm) REVERT: O 1116 MET cc_start: 0.8497 (ptm) cc_final: 0.7967 (mtt) REVERT: O 1183 THR cc_start: 0.7213 (m) cc_final: 0.6933 (p) REVERT: O 1293 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6833 (mm-30) REVERT: O 1338 GLU cc_start: 0.3751 (tm-30) cc_final: 0.3147 (pm20) REVERT: A 52 ARG cc_start: 0.8493 (mtt90) cc_final: 0.7862 (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: 0.8295 (mt-10) REVERT: B 77 LYS cc_start: 0.9159 (mttt) cc_final: 0.8647 (mtmt) REVERT: C 84 GLN cc_start: 0.8441 (tp40) cc_final: 0.8220 (tp40) REVERT: C 95 LYS cc_start: 0.8822 (tptm) cc_final: 0.8320 (ttmm) REVERT: D 37 TYR cc_start: 0.8428 (m-80) cc_final: 0.8150 (m-10) REVERT: D 59 MET cc_start: 0.9241 (mmm) cc_final: 0.8978 (tpp) REVERT: D 82 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8647 (mttp) REVERT: D 90 GLU cc_start: 0.8341 (mp0) cc_final: 0.8037 (mp0) REVERT: E 49 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7943 (ttm-80) REVERT: E 68 GLN cc_start: 0.8297 (tt0) cc_final: 0.7976 (tm-30) REVERT: E 81 ASP cc_start: 0.9098 (m-30) cc_final: 0.8569 (t70) REVERT: F 79 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8196 (mptt) REVERT: F 88 TYR cc_start: 0.7820 (m-10) cc_final: 0.7433 (m-10) REVERT: F 91 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8761 (ttpt) REVERT: G 35 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8324 (mtm-85) REVERT: G 95 LYS cc_start: 0.8282 (tptm) cc_final: 0.7801 (tppt) REVERT: H 31 LYS cc_start: 0.8365 (tptt) cc_final: 0.7456 (mmtp) REVERT: H 33 SER cc_start: 0.8079 (p) cc_final: 0.7737 (m) REVERT: H 36 ILE cc_start: 0.9042 (pt) cc_final: 0.8753 (pt) REVERT: H 76 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.7260 (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: 0.8936 (p) REVERT: H 117 LYS cc_start: 0.8252 (tttp) cc_final: 0.8014 (ttmt) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.1821 time to fit residues: 86.8595 Evaluate side-chains 209 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 0.1980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 749 HIS O 890 HIS ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1025 GLN O1054 GLN O1104 HIS O1111 GLN O1189 GLN O1192 GLN A 68 GLN A 76 GLN B 25 ASN B 75 HIS B 93 GLN C 89 ASN D 46 HIS E 68 GLN F 75 HIS G 104 GLN H 46 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100508 restraints weight = 34114.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099346 restraints weight = 65688.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099805 restraints weight = 66028.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099932 restraints weight = 48369.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099736 restraints weight = 49847.033| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17650 Z= 0.172 Angle : 0.751 9.205 25082 Z= 0.423 Chirality : 0.049 0.437 2856 Planarity : 0.006 0.054 2163 Dihedral : 28.989 160.495 4678 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.09 % Allowed : 2.62 % Favored : 97.29 % 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: -1.56 (0.21), residues: 1313 helix: -0.33 (0.17), residues: 794 sheet: -2.38 (0.61), residues: 57 loop : -1.97 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 96 TYR 0.026 0.002 TYR O 810 PHE 0.032 0.002 PHE O 835 TRP 0.020 0.002 TRP O1083 HIS 0.011 0.002 HIS O 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (17650) covalent geometry : angle 0.75058 / 0.42 (25082) hydrogen bonds : bond 0.05689 / 3.75 ( 961) hydrogen bonds : angle 5.45647 / 3.76 ( 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 272 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8204 (tp) cc_final: 0.7483 (mp) REVERT: O 803 ILE cc_start: 0.8130 (mt) cc_final: 0.7842 (mt) REVERT: O 810 TYR cc_start: 0.4451 (m-80) cc_final: 0.3937 (m-80) REVERT: O 828 LEU cc_start: 0.7696 (tp) cc_final: 0.7433 (tp) REVERT: O 838 TRP cc_start: 0.5608 (m100) cc_final: 0.5037 (m100) REVERT: O 854 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.5323 (ttp-110) REVERT: O 876 ILE cc_start: 0.9012 (pt) cc_final: 0.8493 (tt) REVERT: O 980 ILE cc_start: 0.5833 (mt) cc_final: 0.5365 (mm) REVERT: O 1013 CYS cc_start: 0.6662 (m) cc_final: 0.6400 (m) REVERT: O 1338 GLU cc_start: 0.3281 (tm-30) cc_final: 0.2779 (pm20) REVERT: B 84 MET cc_start: 0.6553 (mmp) cc_final: 0.6329 (mtm) REVERT: C 79 ILE cc_start: 0.8988 (pt) cc_final: 0.8701 (pt) REVERT: C 89 ASN cc_start: 0.7956 (m110) cc_final: 0.7746 (m-40) REVERT: C 95 LYS cc_start: 0.8849 (tptm) cc_final: 0.8406 (ttmm) REVERT: E 62 ILE cc_start: 0.8939 (mt) cc_final: 0.8701 (mt) REVERT: E 81 ASP cc_start: 0.8312 (m-30) cc_final: 0.8062 (t70) REVERT: E 129 ARG cc_start: 0.7620 (tpt90) cc_final: 0.7393 (tpt170) REVERT: F 74 GLU cc_start: 0.7391 (tp30) cc_final: 0.7108 (tp30) REVERT: F 91 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8210 (tttt) REVERT: F 96 THR cc_start: 0.8630 (m) cc_final: 0.7981 (p) REVERT: G 89 ASN cc_start: 0.7943 (m-40) cc_final: 0.7676 (m110) REVERT: G 92 GLU cc_start: 0.5834 (mt-10) cc_final: 0.5240 (pt0) REVERT: G 95 LYS cc_start: 0.8307 (tptm) cc_final: 0.7762 (tppt) REVERT: H 31 LYS cc_start: 0.8402 (tptt) cc_final: 0.8027 (mttp) REVERT: H 56 MET cc_start: 0.8311 (tpp) cc_final: 0.8078 (tpp) REVERT: H 97 LEU cc_start: 0.8483 (mt) cc_final: 0.8013 (mt) REVERT: H 115 VAL cc_start: 0.9603 (t) cc_final: 0.9311 (p) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1565 time to fit residues: 61.4430 Evaluate side-chains 188 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 20.0000 chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 681 HIS ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 984 HIS A 68 GLN B 27 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 104 GLN H 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100566 restraints weight = 34506.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099354 restraints weight = 65454.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099973 restraints weight = 64326.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099631 restraints weight = 49472.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099752 restraints weight = 52441.202| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17650 Z= 0.166 Angle : 0.707 9.574 25082 Z= 0.399 Chirality : 0.045 0.276 2856 Planarity : 0.005 0.080 2163 Dihedral : 28.853 161.934 4678 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.09 % Allowed : 2.62 % Favored : 97.29 % 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: -0.54 (0.23), residues: 1313 helix: 0.53 (0.18), residues: 803 sheet: -1.72 (0.61), residues: 57 loop : -1.72 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 854 TYR 0.025 0.002 TYR O 810 PHE 0.022 0.002 PHE O 835 TRP 0.011 0.001 TRP O 838 HIS 0.008 0.001 HIS O1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (17650) covalent geometry : angle 0.70671 / 0.40 (25082) hydrogen bonds : bond 0.05294 / 3.45 ( 961) hydrogen bonds : angle 4.93657 / 3.40 ( 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 226 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8236 (tp) cc_final: 0.7480 (mp) REVERT: O 810 TYR cc_start: 0.4173 (m-80) cc_final: 0.3565 (m-80) REVERT: O 876 ILE cc_start: 0.8978 (pt) cc_final: 0.8526 (tt) REVERT: O 980 ILE cc_start: 0.5876 (mt) cc_final: 0.5431 (mm) REVERT: B 84 MET cc_start: 0.6680 (mmp) cc_final: 0.6265 (mtm) REVERT: C 24 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7983 (mm-40) REVERT: C 95 LYS cc_start: 0.8789 (tptm) cc_final: 0.8438 (ttmm) REVERT: E 49 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7555 (mtp85) REVERT: F 79 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8622 (mptt) REVERT: F 88 TYR cc_start: 0.7583 (m-10) cc_final: 0.7337 (m-10) REVERT: F 91 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8156 (tttt) REVERT: F 96 THR cc_start: 0.8437 (m) cc_final: 0.8189 (p) REVERT: G 95 LYS cc_start: 0.8254 (tptm) cc_final: 0.7739 (tppt) REVERT: H 31 LYS cc_start: 0.8307 (tptt) cc_final: 0.8042 (mttp) REVERT: H 56 MET cc_start: 0.8197 (tpp) cc_final: 0.7809 (tpp) REVERT: H 98 LEU cc_start: 0.8867 (mm) cc_final: 0.8645 (mm) REVERT: H 115 VAL cc_start: 0.9542 (t) cc_final: 0.9297 (p) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1547 time to fit residues: 50.7224 Evaluate side-chains 178 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 0.7980 chunk 101 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 102 optimal weight: 0.0470 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN B 25 ASN B 27 GLN E 68 GLN E 113 HIS G 24 GLN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099035 restraints weight = 34295.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097786 restraints weight = 69377.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098355 restraints weight = 66614.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098426 restraints weight = 50431.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098444 restraints weight = 47135.945| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17650 Z= 0.153 Angle : 0.665 8.456 25082 Z= 0.377 Chirality : 0.044 0.290 2856 Planarity : 0.005 0.050 2163 Dihedral : 28.781 162.699 4678 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.00 (0.23), residues: 1313 helix: 1.01 (0.19), residues: 804 sheet: -1.42 (0.58), residues: 68 loop : -1.63 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 77 TYR 0.025 0.002 TYR O 810 PHE 0.017 0.002 PHE O1159 TRP 0.012 0.001 TRP O 838 HIS 0.006 0.001 HIS O1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (17650) covalent geometry : angle 0.66472 / 0.38 (25082) hydrogen bonds : bond 0.04769 / 3.11 ( 961) hydrogen bonds : angle 4.51643 / 3.12 ( 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 238 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8251 (tp) cc_final: 0.7476 (mp) REVERT: O 810 TYR cc_start: 0.3994 (m-80) cc_final: 0.3572 (m-80) REVERT: O 876 ILE cc_start: 0.9100 (pt) cc_final: 0.8652 (tt) REVERT: O 980 ILE cc_start: 0.5909 (mt) cc_final: 0.5428 (mm) REVERT: O 1055 LEU cc_start: 0.8166 (mt) cc_final: 0.7959 (mt) REVERT: B 84 MET cc_start: 0.6578 (mmp) cc_final: 0.6054 (mtm) REVERT: C 16 THR cc_start: 0.8592 (p) cc_final: 0.8348 (p) REVERT: C 24 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8163 (mm-40) REVERT: C 95 LYS cc_start: 0.8814 (tptm) cc_final: 0.8428 (ttmm) REVERT: F 79 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8502 (mttp) REVERT: F 88 TYR cc_start: 0.7670 (m-10) cc_final: 0.7273 (m-10) REVERT: F 91 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8251 (tttt) REVERT: G 23 LEU cc_start: 0.8550 (mm) cc_final: 0.8249 (mt) REVERT: G 95 LYS cc_start: 0.8260 (tptm) cc_final: 0.7882 (tppt) REVERT: H 31 LYS cc_start: 0.8269 (tptt) cc_final: 0.8044 (mttp) REVERT: H 98 LEU cc_start: 0.8902 (mm) cc_final: 0.8680 (mm) REVERT: H 115 VAL cc_start: 0.9503 (t) cc_final: 0.9276 (p) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1410 time to fit residues: 50.0616 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 : 0.507 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 20.0000 chunk 97 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 146 optimal weight: 40.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 68 GLN E 125 GLN H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097007 restraints weight = 34164.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095968 restraints weight = 54429.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096058 restraints weight = 51689.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095724 restraints weight = 43545.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095699 restraints weight = 42682.711| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17650 Z= 0.152 Angle : 0.649 8.395 25082 Z= 0.369 Chirality : 0.043 0.298 2856 Planarity : 0.005 0.049 2163 Dihedral : 28.731 164.300 4678 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.21 (0.23), residues: 1313 helix: 1.15 (0.19), residues: 816 sheet: -1.15 (0.60), residues: 68 loop : -1.59 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.024 0.002 TYR O 810 PHE 0.015 0.001 PHE O1159 TRP 0.009 0.001 TRP O 838 HIS 0.004 0.001 HIS O1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (17650) covalent geometry : angle 0.64920 / 0.37 (25082) hydrogen bonds : bond 0.04698 / 3.06 ( 961) hydrogen bonds : angle 4.38274 / 3.02 ( 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 : 0.505 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: 0.8239 (tp) cc_final: 0.7430 (mp) REVERT: O 876 ILE cc_start: 0.9092 (pt) cc_final: 0.8710 (tt) REVERT: O 891 MET cc_start: 0.8104 (tmm) cc_final: 0.7865 (tmm) REVERT: O 980 ILE cc_start: 0.5945 (mt) cc_final: 0.5506 (mm) REVERT: B 84 MET cc_start: 0.6813 (mmp) cc_final: 0.6264 (mtm) REVERT: C 24 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8023 (mm-40) REVERT: C 95 LYS cc_start: 0.8843 (tptm) cc_final: 0.8423 (ttmm) REVERT: D 37 TYR cc_start: 0.7868 (m-80) cc_final: 0.7645 (m-10) REVERT: F 73 THR cc_start: 0.9082 (p) cc_final: 0.8881 (p) REVERT: F 74 GLU cc_start: 0.7559 (tp30) cc_final: 0.7285 (tp30) REVERT: F 79 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8390 (mttp) REVERT: F 80 THR cc_start: 0.9408 (t) cc_final: 0.9205 (t) REVERT: F 91 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8201 (tttt) REVERT: G 23 LEU cc_start: 0.8651 (mm) cc_final: 0.8316 (mt) REVERT: G 95 LYS cc_start: 0.8342 (tptm) cc_final: 0.7805 (tppt) REVERT: H 31 LYS cc_start: 0.8371 (tptt) cc_final: 0.7992 (mttp) REVERT: H 81 ASN cc_start: 0.8444 (m-40) cc_final: 0.8043 (t0) REVERT: H 115 VAL cc_start: 0.9474 (t) cc_final: 0.9226 (p) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1438 time to fit residues: 48.9586 Evaluate side-chains 179 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 0.0270 chunk 130 optimal weight: 40.0000 chunk 8 optimal weight: 20.0000 chunk 133 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 139 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 144 optimal weight: 50.0000 chunk 58 optimal weight: 4.9990 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098708 restraints weight = 34294.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097667 restraints weight = 61568.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097900 restraints weight = 64381.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097745 restraints weight = 46996.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097883 restraints weight = 46693.262| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 17650 Z= 0.192 Angle : 0.675 8.621 25082 Z= 0.379 Chirality : 0.044 0.303 2856 Planarity : 0.005 0.047 2163 Dihedral : 28.768 164.956 4678 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.23), residues: 1313 helix: 1.09 (0.18), residues: 819 sheet: -1.06 (0.61), residues: 68 loop : -1.63 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 32 TYR 0.022 0.002 TYR O1226 PHE 0.033 0.002 PHE C 25 TRP 0.007 0.001 TRP O 838 HIS 0.011 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (17650) covalent geometry : angle 0.67490 / 0.38 (25082) hydrogen bonds : bond 0.04904 / 3.20 ( 961) hydrogen bonds : angle 4.38819 / 3.04 ( 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 213 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8275 (tp) cc_final: 0.7404 (mp) REVERT: O 876 ILE cc_start: 0.9084 (pt) cc_final: 0.8748 (tt) REVERT: O 980 ILE cc_start: 0.5959 (mt) cc_final: 0.5556 (mm) REVERT: B 84 MET cc_start: 0.6825 (mmp) cc_final: 0.6165 (mtm) REVERT: C 16 THR cc_start: 0.8600 (p) cc_final: 0.8394 (p) REVERT: C 24 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8340 (mm-40) REVERT: C 95 LYS cc_start: 0.8851 (tptm) cc_final: 0.8456 (ttmm) REVERT: F 73 THR cc_start: 0.9186 (p) cc_final: 0.8957 (p) REVERT: F 74 GLU cc_start: 0.7616 (tp30) cc_final: 0.7325 (tp30) REVERT: F 79 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8425 (mttp) REVERT: F 91 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8161 (tttt) REVERT: G 23 LEU cc_start: 0.8574 (mm) cc_final: 0.8136 (mt) REVERT: G 95 LYS cc_start: 0.8370 (tptm) cc_final: 0.7842 (tppt) REVERT: H 31 LYS cc_start: 0.8343 (tptt) cc_final: 0.8051 (mmtp) REVERT: H 115 VAL cc_start: 0.9547 (t) cc_final: 0.9331 (p) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1426 time to fit residues: 45.5375 Evaluate side-chains 180 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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: 5.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 25 optimal weight: 50.0000 chunk 106 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 100 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100081 restraints weight = 33980.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099470 restraints weight = 52663.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099482 restraints weight = 53277.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098745 restraints weight = 50035.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.098919 restraints weight = 46157.715| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17650 Z= 0.142 Angle : 0.640 9.728 25082 Z= 0.363 Chirality : 0.043 0.308 2856 Planarity : 0.004 0.048 2163 Dihedral : 28.653 166.550 4678 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % 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: 0.40 (0.24), residues: 1313 helix: 1.29 (0.19), residues: 819 sheet: -0.94 (0.61), residues: 68 loop : -1.55 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 35 TYR 0.024 0.002 TYR F 88 PHE 0.020 0.002 PHE O1159 TRP 0.009 0.001 TRP O1185 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17650) covalent geometry : angle 0.63998 / 0.36 (25082) hydrogen bonds : bond 0.04523 / 2.97 ( 961) hydrogen bonds : angle 4.19704 / 2.90 ( 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 224 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8288 (tp) cc_final: 0.7428 (mp) REVERT: O 876 ILE cc_start: 0.9034 (pt) cc_final: 0.8668 (tt) REVERT: A 73 GLU cc_start: 0.7934 (pt0) cc_final: 0.7683 (pt0) REVERT: B 84 MET cc_start: 0.6784 (mmp) cc_final: 0.6319 (mtm) REVERT: C 16 THR cc_start: 0.8722 (p) cc_final: 0.8461 (p) REVERT: C 24 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7970 (mm-40) REVERT: C 95 LYS cc_start: 0.8818 (tptm) cc_final: 0.8406 (ttmm) REVERT: C 107 VAL cc_start: 0.8921 (t) cc_final: 0.8647 (t) REVERT: F 73 THR cc_start: 0.9068 (p) cc_final: 0.8845 (p) REVERT: F 74 GLU cc_start: 0.7462 (tp30) cc_final: 0.7176 (tp30) REVERT: F 79 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8475 (mttp) REVERT: F 91 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8112 (tttt) REVERT: G 95 LYS cc_start: 0.8266 (tptm) cc_final: 0.7783 (tppt) REVERT: H 31 LYS cc_start: 0.8414 (tptt) cc_final: 0.7942 (mttp) REVERT: H 49 THR cc_start: 0.8815 (m) cc_final: 0.8406 (m) REVERT: H 115 VAL cc_start: 0.9491 (t) cc_final: 0.9244 (p) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1402 time to fit residues: 47.0804 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 : 0.492 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 144 optimal weight: 50.0000 chunk 122 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 130 optimal weight: 40.0000 chunk 45 optimal weight: 7.9990 chunk 154 optimal weight: 30.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.128675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097161 restraints weight = 34377.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096566 restraints weight = 65466.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096345 restraints weight = 66987.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096307 restraints weight = 53056.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096186 restraints weight = 54941.459| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17650 Z= 0.205 Angle : 0.709 8.462 25082 Z= 0.393 Chirality : 0.045 0.310 2856 Planarity : 0.005 0.053 2163 Dihedral : 28.788 166.534 4678 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.14 (0.23), residues: 1313 helix: 1.06 (0.18), residues: 819 sheet: -1.09 (0.60), residues: 68 loop : -1.58 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 29 TYR 0.029 0.002 TYR F 88 PHE 0.017 0.002 PHE O1159 TRP 0.012 0.002 TRP O 888 HIS 0.011 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (17650) covalent geometry : angle 0.70855 / 0.39 (25082) hydrogen bonds : bond 0.05147 / 3.36 ( 961) hydrogen bonds : angle 4.38434 / 3.04 ( 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 219 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8350 (tp) cc_final: 0.7436 (mp) REVERT: O 831 TRP cc_start: 0.7924 (m100) cc_final: 0.7583 (m100) REVERT: O 876 ILE cc_start: 0.9109 (pt) cc_final: 0.8754 (tt) REVERT: O 899 MET cc_start: 0.8316 (mmm) cc_final: 0.7701 (tpp) REVERT: A 73 GLU cc_start: 0.7949 (pt0) cc_final: 0.7727 (pt0) REVERT: B 84 MET cc_start: 0.6814 (mmp) cc_final: 0.6337 (mtm) REVERT: C 16 THR cc_start: 0.8739 (p) cc_final: 0.8495 (p) REVERT: C 24 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8031 (mm-40) REVERT: C 95 LYS cc_start: 0.8789 (tptm) cc_final: 0.8395 (ttmm) REVERT: D 118 TYR cc_start: 0.9158 (t80) cc_final: 0.8891 (t80) REVERT: F 79 LYS cc_start: 0.8932 (mmtp) cc_final: 0.8552 (mttp) REVERT: F 91 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8178 (tttt) REVERT: G 23 LEU cc_start: 0.8774 (mt) cc_final: 0.8558 (mt) REVERT: G 95 LYS cc_start: 0.8283 (tptm) cc_final: 0.7816 (tppt) REVERT: H 31 LYS cc_start: 0.8402 (tptt) cc_final: 0.8010 (mmtp) REVERT: H 49 THR cc_start: 0.8920 (m) cc_final: 0.8477 (m) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1531 time to fit residues: 49.1534 Evaluate side-chains 180 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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: 1.9990 chunk 148 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 127 optimal weight: 0.0470 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 152 optimal weight: 40.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.128752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098095 restraints weight = 34469.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097001 restraints weight = 58944.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096833 restraints weight = 60079.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096240 restraints weight = 50243.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096352 restraints weight = 47917.810| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17650 Z= 0.201 Angle : 0.697 8.512 25082 Z= 0.388 Chirality : 0.044 0.312 2856 Planarity : 0.005 0.051 2163 Dihedral : 28.780 166.928 4678 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.10 (0.23), residues: 1313 helix: 1.02 (0.18), residues: 815 sheet: -1.08 (0.61), residues: 68 loop : -1.56 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 994 TYR 0.034 0.002 TYR F 88 PHE 0.018 0.002 PHE O1159 TRP 0.009 0.001 TRP O 888 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (17650) covalent geometry : angle 0.69719 / 0.39 (25082) hydrogen bonds : bond 0.05111 / 3.36 ( 961) hydrogen bonds : angle 4.40006 / 3.05 ( 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 218 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8356 (tp) cc_final: 0.7449 (mp) REVERT: O 831 TRP cc_start: 0.7978 (m100) cc_final: 0.7591 (m100) REVERT: O 876 ILE cc_start: 0.9133 (pt) cc_final: 0.8796 (tt) REVERT: O 899 MET cc_start: 0.8343 (mmm) cc_final: 0.7757 (tpp) REVERT: A 73 GLU cc_start: 0.7934 (pt0) cc_final: 0.7694 (pt0) REVERT: B 84 MET cc_start: 0.6619 (mmp) cc_final: 0.6223 (mtm) REVERT: C 16 THR cc_start: 0.8736 (p) cc_final: 0.8505 (p) REVERT: C 24 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7996 (mm-40) REVERT: C 95 LYS cc_start: 0.8853 (tptm) cc_final: 0.8396 (ttmm) REVERT: D 118 TYR cc_start: 0.9208 (t80) cc_final: 0.8940 (t80) REVERT: F 79 LYS cc_start: 0.9021 (mmtp) cc_final: 0.8566 (mttp) REVERT: F 91 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8145 (tttt) REVERT: G 95 LYS cc_start: 0.8221 (tptm) cc_final: 0.7747 (tppt) REVERT: H 31 LYS cc_start: 0.8460 (tptt) cc_final: 0.8045 (mmtp) REVERT: H 49 THR cc_start: 0.8909 (m) cc_final: 0.8598 (m) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1463 time to fit residues: 47.5065 Evaluate side-chains 177 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 5.9990 chunk 54 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1171 ASN E 68 GLN G 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.129680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102182 restraints weight = 34099.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.100793 restraints weight = 66820.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101019 restraints weight = 69932.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100350 restraints weight = 54840.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100399 restraints weight = 52665.867| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17650 Z= 0.163 Angle : 0.672 8.708 25082 Z= 0.378 Chirality : 0.043 0.313 2856 Planarity : 0.005 0.053 2163 Dihedral : 28.696 167.383 4678 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % 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: 0.26 (0.24), residues: 1313 helix: 1.15 (0.18), residues: 817 sheet: -1.09 (0.61), residues: 68 loop : -1.49 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.032 0.002 TYR F 88 PHE 0.020 0.001 PHE O1159 TRP 0.009 0.001 TRP O 888 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (17650) covalent geometry : angle 0.67220 / 0.38 (25082) hydrogen bonds : bond 0.04867 / 3.22 ( 961) hydrogen bonds : angle 4.27201 / 2.96 ( 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 225 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 790 LEU cc_start: 0.8378 (tp) cc_final: 0.7472 (mp) REVERT: O 831 TRP cc_start: 0.7889 (m100) cc_final: 0.7541 (m100) REVERT: O 876 ILE cc_start: 0.9039 (pt) cc_final: 0.8717 (tt) REVERT: O 899 MET cc_start: 0.8240 (mmm) cc_final: 0.7560 (tpp) REVERT: B 84 MET cc_start: 0.6754 (mmp) cc_final: 0.6211 (mtm) REVERT: C 24 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7928 (mm-40) REVERT: C 92 GLU cc_start: 0.8117 (mp0) cc_final: 0.7464 (mp0) REVERT: C 93 LEU cc_start: 0.9317 (mt) cc_final: 0.9106 (mt) REVERT: C 95 LYS cc_start: 0.8912 (tptm) cc_final: 0.8370 (ttmm) REVERT: D 56 MET cc_start: 0.8166 (tpp) cc_final: 0.7850 (tpp) REVERT: D 118 TYR cc_start: 0.9213 (t80) cc_final: 0.8951 (t80) REVERT: F 79 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8548 (mttp) REVERT: G 95 LYS cc_start: 0.8239 (tptm) cc_final: 0.7747 (tppt) REVERT: H 31 LYS cc_start: 0.8437 (tptt) cc_final: 0.8088 (mmtp) REVERT: H 49 THR cc_start: 0.8970 (m) cc_final: 0.8512 (m) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1449 time to fit residues: 48.3516 Evaluate side-chains 179 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 928 GLN D 92 GLN E 68 GLN G 89 ASN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100067 restraints weight = 34138.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098701 restraints weight = 56781.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098555 restraints weight = 59496.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098080 restraints weight = 47151.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.098146 restraints weight = 45221.193| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17650 Z= 0.144 Angle : 0.641 8.448 25082 Z= 0.363 Chirality : 0.042 0.314 2856 Planarity : 0.004 0.053 2163 Dihedral : 28.608 167.968 4678 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.49 (0.24), residues: 1313 helix: 1.35 (0.19), residues: 817 sheet: -1.00 (0.61), residues: 68 loop : -1.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 96 TYR 0.025 0.002 TYR F 88 PHE 0.019 0.002 PHE O1159 TRP 0.010 0.001 TRP O 888 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (17650) covalent geometry : angle 0.64095 / 0.36 (25082) hydrogen bonds : bond 0.04603 / 3.04 ( 961) hydrogen bonds : angle 4.14522 / 2.86 ( 2491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.61 seconds wall clock time: 41 minutes 2.51 seconds (2462.51 seconds total)