Starting phenix.real_space_refine on Wed Feb 4 13:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvb_47199/02_2026/9dvb_47199_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvb_47199/02_2026/9dvb_47199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvb_47199/02_2026/9dvb_47199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvb_47199/02_2026/9dvb_47199.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvb_47199/02_2026/9dvb_47199_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvb_47199/02_2026/9dvb_47199_neut.cif" } resolution = 3.6 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= 0.000 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7005 2.51 5 N 1788 2.21 5 O 1987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10802 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "C" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 450 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "D" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain breaks: 1 Chain: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1641 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1627 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Chain: "N" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "O" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 2 Chain: "P" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain breaks: 3 Chain: "W" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "X" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1627 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10802 At special positions: 0 Unit cell: (84.7, 93.5, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1987 8.00 N 1788 7.00 C 7005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 150 " - pdb=" SG CYS W 206 " distance=1.85 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 135 " - pdb=" SG CYS X 195 " distance=2.04 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 Links applied TRANS " HIS B 80 " - " TYR D 79 " " ALA D 94 " - " THR B 196 " " HIS N 80 " - " TYR P 79 " " ALA P 94 " - " THR N 196 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 399.1 milliseconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2626 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 37.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 80 through 107 removed outlier: 3.562A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.593A pdb=" N LYS B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 removed outlier: 3.593A pdb=" N ASP B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 168 removed outlier: 3.566A pdb=" N ASP B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 196 removed outlier: 3.502A pdb=" N GLU B 179 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 removed outlier: 3.666A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.532A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 19 Processing helix chain 'D' and resid 30 through 41 removed outlier: 3.918A pdb=" N TRP D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 60 removed outlier: 3.654A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 Processing helix chain 'D' and resid 95 through 117 removed outlier: 3.536A pdb=" N TRP D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 removed outlier: 3.522A pdb=" N PHE D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.156A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 109 removed outlier: 4.050A pdb=" N TRP H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.612A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.593A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 107 removed outlier: 3.504A pdb=" N THR N 89 " --> pdb=" O ALA N 85 " (cutoff:3.500A) Proline residue: N 92 - end of helix removed outlier: 3.602A pdb=" N VAL N 103 " --> pdb=" O ASP N 99 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 130 removed outlier: 3.681A pdb=" N ALA N 130 " --> pdb=" O ASP N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 168 removed outlier: 3.555A pdb=" N PHE N 152 " --> pdb=" O PHE N 148 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE N 154 " --> pdb=" O HIS N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 196 removed outlier: 3.941A pdb=" N GLN N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU N 181 " --> pdb=" O ALA N 177 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR N 183 " --> pdb=" O GLU N 179 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR N 184 " --> pdb=" O GLN N 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 25 Processing helix chain 'O' and resid 48 through 63 Processing helix chain 'P' and resid 3 through 19 removed outlier: 3.588A pdb=" N PHE P 11 " --> pdb=" O VAL P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 41 removed outlier: 3.592A pdb=" N VAL P 32 " --> pdb=" O ASP P 28 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER P 40 " --> pdb=" O TRP P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 60 removed outlier: 3.675A pdb=" N ALA P 48 " --> pdb=" O LEU P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 79 Processing helix chain 'P' and resid 95 through 116 Processing helix chain 'P' and resid 129 through 140 removed outlier: 3.721A pdb=" N PHE P 138 " --> pdb=" O LEU P 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'W' and resid 104 through 109 removed outlier: 4.012A pdb=" N TRP W 108 " --> pdb=" O GLY W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 168 No H-bonds generated for 'chain 'W' and resid 166 through 168' Processing helix chain 'X' and resid 122 through 129 removed outlier: 3.708A pdb=" N LYS X 127 " --> pdb=" O ASP X 123 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER X 128 " --> pdb=" O GLU X 124 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY X 129 " --> pdb=" O GLN X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 184 through 190 removed outlier: 3.698A pdb=" N LYS X 189 " --> pdb=" O ALA X 185 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS X 190 " --> pdb=" O ASP X 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.692A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER H 57 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.507A pdb=" N SER H 130 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 153 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.507A pdb=" N SER H 130 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 153 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL H 179 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.697A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 217 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.687A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.747A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.680A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.834A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 3 through 7 removed outlier: 3.541A pdb=" N SER W 21 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 11 through 12 removed outlier: 3.500A pdb=" N THR W 118 " --> pdb=" O TYR W 94 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG W 38 " --> pdb=" O TRP W 47 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP W 47 " --> pdb=" O ARG W 38 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER W 57 " --> pdb=" O SER W 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 130 through 134 removed outlier: 3.749A pdb=" N GLY W 149 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR W 186 " --> pdb=" O ASP W 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 130 through 134 removed outlier: 3.749A pdb=" N GLY W 149 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR W 186 " --> pdb=" O ASP W 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER W 187 " --> pdb=" O VAL W 179 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL W 179 " --> pdb=" O SER W 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 161 through 164 removed outlier: 4.685A pdb=" N TYR W 204 " --> pdb=" O VAL W 221 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.513A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.686A pdb=" N THR X 98 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 115 through 119 removed outlier: 3.612A pdb=" N SER X 115 " --> pdb=" O ASN X 138 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER X 163 " --> pdb=" O SER X 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 154 through 156 removed outlier: 4.614A pdb=" N TRP X 149 " --> pdb=" O GLN X 156 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS X 195 " --> pdb=" O LYS X 208 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS X 208 " --> pdb=" O CYS X 195 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3369 1.34 - 1.46: 2752 1.46 - 1.58: 4919 1.58 - 1.70: 0 1.70 - 1.81: 28 Bond restraints: 11068 Sorted by residual: bond pdb=" CB PRO X 142 " pdb=" CG PRO X 142 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.75e-01 bond pdb=" CB PRO L 142 " pdb=" CG PRO L 142 " ideal model delta sigma weight residual 1.506 1.475 0.031 3.90e-02 6.57e+02 6.38e-01 bond pdb=" CB PRO X 8 " pdb=" CG PRO X 8 " ideal model delta sigma weight residual 1.506 1.477 0.029 3.90e-02 6.57e+02 5.57e-01 bond pdb=" CB VAL H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.32e-01 bond pdb=" CB VAL W 37 " pdb=" CG2 VAL W 37 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.32e-01 ... (remaining 11063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 14574 1.00 - 2.00: 383 2.00 - 2.99: 74 2.99 - 3.99: 24 3.99 - 4.99: 14 Bond angle restraints: 15069 Sorted by residual: angle pdb=" N ALA X 51 " pdb=" CA ALA X 51 " pdb=" CB ALA X 51 " ideal model delta sigma weight residual 113.65 110.58 3.07 1.47e+00 4.63e-01 4.35e+00 angle pdb=" C SER L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.32 -3.78 1.91e+00 2.74e-01 3.91e+00 angle pdb=" N VAL W 64 " pdb=" CA VAL W 64 " pdb=" C VAL W 64 " ideal model delta sigma weight residual 109.34 112.82 -3.48 2.08e+00 2.31e-01 2.80e+00 angle pdb=" CA PHE W 111 " pdb=" C PHE W 111 " pdb=" O PHE W 111 " ideal model delta sigma weight residual 122.36 120.34 2.02 1.21e+00 6.83e-01 2.79e+00 angle pdb=" CA TYR X 91 " pdb=" CB TYR X 91 " pdb=" CG TYR X 91 " ideal model delta sigma weight residual 113.90 116.69 -2.79 1.80e+00 3.09e-01 2.40e+00 ... (remaining 15064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.13: 6036 12.13 - 24.27: 351 24.27 - 36.40: 101 36.40 - 48.54: 23 48.54 - 60.67: 5 Dihedral angle restraints: 6516 sinusoidal: 2438 harmonic: 4078 Sorted by residual: dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 32.33 60.67 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS W 150 " pdb=" SG CYS W 150 " pdb=" SG CYS W 206 " pdb=" CB CYS W 206 " ideal model delta sinusoidal sigma weight residual 93.00 41.10 51.90 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CA ARG X 143 " pdb=" CB ARG X 143 " pdb=" CG ARG X 143 " pdb=" CD ARG X 143 " ideal model delta sinusoidal sigma weight residual -60.00 -112.73 52.73 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 6513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1090 0.028 - 0.055: 452 0.055 - 0.083: 78 0.083 - 0.110: 94 0.110 - 0.138: 13 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA ILE X 48 " pdb=" N ILE X 48 " pdb=" C ILE X 48 " pdb=" CB ILE X 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL H 93 " pdb=" N VAL H 93 " pdb=" C VAL H 93 " pdb=" CB VAL H 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1724 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO H 159 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU W 158 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO W 159 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO W 159 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO W 159 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 156 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO H 157 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.016 5.00e-02 4.00e+02 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1753 2.76 - 3.30: 9912 3.30 - 3.83: 16802 3.83 - 4.37: 19390 4.37 - 4.90: 35118 Nonbonded interactions: 82975 Sorted by model distance: nonbonded pdb=" OG SER H 52 " pdb=" OH TYR H 101 " model vdw 2.231 3.040 nonbonded pdb=" NE2 GLN X 90 " pdb=" O LEU X 96 " model vdw 2.258 3.120 nonbonded pdb=" O ALA N 107 " pdb=" NE2 GLN N 175 " model vdw 2.268 3.120 nonbonded pdb=" NE2 GLN L 90 " pdb=" O LEU L 96 " model vdw 2.268 3.120 nonbonded pdb=" O ALA B 107 " pdb=" NE2 GLN B 175 " model vdw 2.276 3.120 ... (remaining 82970 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 'B' selection = chain 'N' } ncs_group { reference = (chain 'C' and (resid 4 through 26 or resid 32 through 43 or resid 47 through 63 \ )) selection = chain 'O' } ncs_group { reference = (chain 'D' and (resid 2 through 21 or resid 25 through 118 or resid 128 through \ 142)) selection = chain 'P' } ncs_group { reference = (chain 'H' and (resid 1 through 136 or resid 145 through 223)) selection = (chain 'W' and (resid 1 through 136 or resid 145 through 223)) } ncs_group { reference = chain 'L' selection = chain 'X' } 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: 3.300 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.140 Find NCS groups from input model: 0.170 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 11080 Z= 0.152 Angle : 0.526 26.717 15097 Z= 0.259 Chirality : 0.037 0.138 1727 Planarity : 0.003 0.047 1882 Dihedral : 8.826 58.600 3854 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.52 % Allowed : 4.20 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.06 (0.24), residues: 1370 helix: 1.11 (0.24), residues: 464 sheet: 0.38 (0.26), residues: 395 loop : 0.84 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 66 TYR 0.015 0.001 TYR X 91 PHE 0.008 0.001 PHE X 140 TRP 0.009 0.001 TRP W 47 HIS 0.002 0.001 HIS W 174 Details of bonding type rmsd covalent geometry : bond 0.00295 (11068) covalent geometry : angle 0.43740 (15069) SS BOND : bond 0.06553 ( 8) SS BOND : angle 8.91657 ( 16) hydrogen bonds : bond 0.27025 ( 578) hydrogen bonds : angle 8.49010 ( 1692) link_TRANS : bond 0.00584 ( 4) link_TRANS : angle 1.35514 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.403 Fit side-chains REVERT: B 167 ASN cc_start: 0.8133 (t0) cc_final: 0.7859 (t0) REVERT: H 65 LYS cc_start: 0.7999 (tttp) cc_final: 0.7712 (ttpt) REVERT: H 87 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7396 (mtm110) REVERT: L 146 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8005 (ttpp) REVERT: L 148 GLN cc_start: 0.8095 (mt0) cc_final: 0.7839 (mt0) REVERT: L 150 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8089 (mttp) REVERT: L 170 LYS cc_start: 0.8473 (mttt) cc_final: 0.8269 (mmtt) REVERT: W 204 TYR cc_start: 0.8575 (m-80) cc_final: 0.8268 (m-80) REVERT: X 146 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8594 (ttpt) outliers start: 6 outliers final: 2 residues processed: 176 average time/residue: 0.1131 time to fit residues: 27.4710 Evaluate side-chains 131 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain W residue 131 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 181 GLN H 202 GLN L 79 GLN L 125 GLN W 84 ASN X 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105319 restraints weight = 12991.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106615 restraints weight = 11673.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107912 restraints weight = 8795.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109961 restraints weight = 6619.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110347 restraints weight = 5815.663| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11080 Z= 0.179 Angle : 0.602 10.446 15097 Z= 0.302 Chirality : 0.040 0.145 1727 Planarity : 0.004 0.048 1882 Dihedral : 3.687 15.724 1494 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.40 % Allowed : 9.10 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.40 (0.23), residues: 1370 helix: 1.62 (0.23), residues: 477 sheet: 0.57 (0.25), residues: 413 loop : 0.75 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 8 TYR 0.019 0.002 TYR L 91 PHE 0.011 0.001 PHE D 62 TRP 0.013 0.001 TRP P 106 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00415 (11068) covalent geometry : angle 0.60222 (15069) SS BOND : bond 0.00253 ( 8) SS BOND : angle 0.84085 ( 16) hydrogen bonds : bond 0.05099 ( 578) hydrogen bonds : angle 5.32610 ( 1692) link_TRANS : bond 0.00243 ( 4) link_TRANS : angle 0.52703 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.374 Fit side-chains REVERT: D 12 LEU cc_start: 0.8769 (mt) cc_final: 0.8457 (tt) REVERT: D 100 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7565 (tt) REVERT: H 65 LYS cc_start: 0.7970 (tttp) cc_final: 0.7631 (ttpt) REVERT: H 220 LYS cc_start: 0.9255 (tttp) cc_final: 0.9020 (tttm) REVERT: N 105 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7757 (tp30) REVERT: P 6 LEU cc_start: 0.8240 (tt) cc_final: 0.8012 (mt) REVERT: W 30 VAL cc_start: 0.9416 (m) cc_final: 0.9105 (t) REVERT: W 207 ASN cc_start: 0.8608 (p0) cc_final: 0.8309 (p0) outliers start: 16 outliers final: 6 residues processed: 139 average time/residue: 0.0884 time to fit residues: 18.0121 Evaluate side-chains 124 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain X residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.099935 restraints weight = 13007.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103365 restraints weight = 22376.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.103857 restraints weight = 14025.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.106404 restraints weight = 9408.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.106255 restraints weight = 7036.314| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11080 Z= 0.152 Angle : 0.539 8.725 15097 Z= 0.267 Chirality : 0.039 0.144 1727 Planarity : 0.004 0.044 1882 Dihedral : 3.649 15.802 1493 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.40 % Allowed : 10.59 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.49 (0.23), residues: 1370 helix: 1.87 (0.23), residues: 477 sheet: 0.52 (0.25), residues: 414 loop : 0.69 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 66 TYR 0.015 0.001 TYR L 91 PHE 0.011 0.001 PHE D 62 TRP 0.011 0.001 TRP P 106 HIS 0.003 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00353 (11068) covalent geometry : angle 0.53766 (15069) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.05485 ( 16) hydrogen bonds : bond 0.04219 ( 578) hydrogen bonds : angle 4.69470 ( 1692) link_TRANS : bond 0.00148 ( 4) link_TRANS : angle 0.58757 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.385 Fit side-chains REVERT: D 12 LEU cc_start: 0.8596 (mt) cc_final: 0.8334 (tt) REVERT: H 65 LYS cc_start: 0.7998 (tttp) cc_final: 0.7657 (ttpt) REVERT: H 214 ASN cc_start: 0.8731 (t0) cc_final: 0.8512 (t0) REVERT: L 17 ASP cc_start: 0.8008 (m-30) cc_final: 0.7798 (m-30) REVERT: L 101 GLN cc_start: 0.8264 (mp10) cc_final: 0.7944 (mp10) REVERT: N 101 LEU cc_start: 0.8302 (tp) cc_final: 0.8095 (tp) REVERT: P 49 LEU cc_start: 0.9147 (mm) cc_final: 0.8878 (mm) REVERT: W 30 VAL cc_start: 0.9465 (m) cc_final: 0.9142 (t) REVERT: W 204 TYR cc_start: 0.8591 (m-80) cc_final: 0.8119 (m-80) outliers start: 16 outliers final: 12 residues processed: 131 average time/residue: 0.0875 time to fit residues: 16.7599 Evaluate side-chains 125 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 0.6980 chunk 32 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109298 restraints weight = 12901.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108208 restraints weight = 10251.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109377 restraints weight = 8631.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110580 restraints weight = 6621.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111105 restraints weight = 6039.716| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11080 Z= 0.126 Angle : 0.506 8.803 15097 Z= 0.251 Chirality : 0.038 0.145 1727 Planarity : 0.004 0.044 1882 Dihedral : 3.583 15.842 1492 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.36 % Allowed : 9.97 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.60 (0.23), residues: 1370 helix: 2.11 (0.23), residues: 476 sheet: 0.49 (0.25), residues: 414 loop : 0.69 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 8 TYR 0.013 0.001 TYR L 91 PHE 0.008 0.001 PHE X 140 TRP 0.011 0.001 TRP P 106 HIS 0.002 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00291 (11068) covalent geometry : angle 0.50537 (15069) SS BOND : bond 0.00309 ( 8) SS BOND : angle 0.85335 ( 16) hydrogen bonds : bond 0.03587 ( 578) hydrogen bonds : angle 4.35480 ( 1692) link_TRANS : bond 0.00134 ( 4) link_TRANS : angle 0.48498 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.391 Fit side-chains REVERT: D 100 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7477 (tt) REVERT: H 65 LYS cc_start: 0.7916 (tttp) cc_final: 0.7577 (ttpt) REVERT: H 214 ASN cc_start: 0.8811 (t0) cc_final: 0.8556 (t0) REVERT: L 17 ASP cc_start: 0.8099 (m-30) cc_final: 0.7796 (m-30) REVERT: L 101 GLN cc_start: 0.8254 (mp10) cc_final: 0.7928 (mp10) REVERT: P 49 LEU cc_start: 0.9076 (mm) cc_final: 0.8834 (mm) REVERT: W 30 VAL cc_start: 0.9433 (m) cc_final: 0.9110 (t) REVERT: W 125 GLN cc_start: 0.8039 (pm20) cc_final: 0.7650 (pm20) REVERT: W 204 TYR cc_start: 0.8541 (m-80) cc_final: 0.8064 (m-80) outliers start: 27 outliers final: 11 residues processed: 147 average time/residue: 0.0947 time to fit residues: 20.2532 Evaluate side-chains 137 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 111 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109904 restraints weight = 12905.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108392 restraints weight = 10729.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109195 restraints weight = 11416.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110748 restraints weight = 7354.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111242 restraints weight = 6334.428| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11080 Z= 0.127 Angle : 0.502 9.267 15097 Z= 0.248 Chirality : 0.038 0.143 1727 Planarity : 0.003 0.044 1882 Dihedral : 3.559 15.759 1492 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.01 % Allowed : 10.41 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.64 (0.23), residues: 1370 helix: 2.22 (0.23), residues: 476 sheet: 0.49 (0.25), residues: 414 loop : 0.64 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 117 TYR 0.013 0.001 TYR L 91 PHE 0.008 0.001 PHE X 140 TRP 0.010 0.001 TRP P 106 HIS 0.003 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00298 (11068) covalent geometry : angle 0.50160 (15069) SS BOND : bond 0.00289 ( 8) SS BOND : angle 0.69055 ( 16) hydrogen bonds : bond 0.03439 ( 578) hydrogen bonds : angle 4.18479 ( 1692) link_TRANS : bond 0.00129 ( 4) link_TRANS : angle 0.48468 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.269 Fit side-chains REVERT: D 68 HIS cc_start: 0.8189 (m-70) cc_final: 0.7897 (m-70) REVERT: D 100 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7496 (tt) REVERT: H 65 LYS cc_start: 0.7896 (tttp) cc_final: 0.7546 (ttpt) REVERT: H 214 ASN cc_start: 0.8815 (t0) cc_final: 0.8529 (t0) REVERT: L 17 ASP cc_start: 0.8232 (m-30) cc_final: 0.7899 (m-30) REVERT: L 101 GLN cc_start: 0.8273 (mp10) cc_final: 0.7960 (mp10) REVERT: P 49 LEU cc_start: 0.9060 (mm) cc_final: 0.8811 (mm) REVERT: W 30 VAL cc_start: 0.9423 (m) cc_final: 0.9085 (t) REVERT: W 125 GLN cc_start: 0.8044 (pm20) cc_final: 0.7629 (pm20) REVERT: W 204 TYR cc_start: 0.8551 (m-80) cc_final: 0.8068 (m-80) outliers start: 23 outliers final: 13 residues processed: 141 average time/residue: 0.0975 time to fit residues: 19.9366 Evaluate side-chains 134 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109744 restraints weight = 12911.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108271 restraints weight = 11121.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109146 restraints weight = 11763.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111432 restraints weight = 7423.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111778 restraints weight = 6162.366| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11080 Z= 0.120 Angle : 0.500 9.249 15097 Z= 0.245 Chirality : 0.038 0.164 1727 Planarity : 0.003 0.044 1882 Dihedral : 3.520 15.663 1492 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.36 % Allowed : 10.32 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.74 (0.23), residues: 1370 helix: 2.38 (0.23), residues: 478 sheet: 0.51 (0.25), residues: 414 loop : 0.65 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 19 TYR 0.012 0.001 TYR L 91 PHE 0.012 0.001 PHE D 62 TRP 0.010 0.001 TRP P 106 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00280 (11068) covalent geometry : angle 0.50009 (15069) SS BOND : bond 0.00290 ( 8) SS BOND : angle 0.63945 ( 16) hydrogen bonds : bond 0.03274 ( 578) hydrogen bonds : angle 4.05656 ( 1692) link_TRANS : bond 0.00116 ( 4) link_TRANS : angle 0.45068 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.405 Fit side-chains REVERT: C 49 ARG cc_start: 0.8122 (tpt90) cc_final: 0.7867 (tpt170) REVERT: D 68 HIS cc_start: 0.8163 (m-70) cc_final: 0.7878 (m-70) REVERT: D 100 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7462 (tt) REVERT: H 65 LYS cc_start: 0.7944 (tttp) cc_final: 0.7570 (ttpt) REVERT: H 214 ASN cc_start: 0.8806 (t0) cc_final: 0.8500 (t0) REVERT: L 17 ASP cc_start: 0.8304 (m-30) cc_final: 0.7932 (m-30) REVERT: L 101 GLN cc_start: 0.8294 (mp10) cc_final: 0.7948 (mp10) REVERT: N 189 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7567 (mm110) REVERT: P 49 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8758 (mm) REVERT: W 125 GLN cc_start: 0.8049 (pm20) cc_final: 0.7611 (pm20) REVERT: W 204 TYR cc_start: 0.8553 (m-80) cc_final: 0.7994 (m-80) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 0.0955 time to fit residues: 19.5737 Evaluate side-chains 139 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 189 GLN Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 206 CYS Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 14 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 0.0370 chunk 122 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.097089 restraints weight = 12906.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.097333 restraints weight = 10509.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097874 restraints weight = 8807.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.098207 restraints weight = 7876.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098388 restraints weight = 7704.662| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11080 Z= 0.139 Angle : 0.519 9.668 15097 Z= 0.252 Chirality : 0.038 0.151 1727 Planarity : 0.003 0.044 1882 Dihedral : 3.553 15.808 1492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.45 % Allowed : 10.94 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.74 (0.23), residues: 1370 helix: 2.38 (0.22), residues: 480 sheet: 0.51 (0.25), residues: 414 loop : 0.63 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 26 TYR 0.015 0.001 TYR L 91 PHE 0.008 0.001 PHE X 140 TRP 0.010 0.001 TRP P 106 HIS 0.003 0.001 HIS W 174 Details of bonding type rmsd covalent geometry : bond 0.00330 (11068) covalent geometry : angle 0.51834 (15069) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.66075 ( 16) hydrogen bonds : bond 0.03309 ( 578) hydrogen bonds : angle 4.03558 ( 1692) link_TRANS : bond 0.00145 ( 4) link_TRANS : angle 0.50472 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.268 Fit side-chains REVERT: C 49 ARG cc_start: 0.8149 (tpt90) cc_final: 0.7866 (tpt170) REVERT: D 68 HIS cc_start: 0.8170 (m-70) cc_final: 0.7872 (m-70) REVERT: D 100 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7439 (tt) REVERT: H 65 LYS cc_start: 0.8065 (tttp) cc_final: 0.7688 (ttpt) REVERT: H 214 ASN cc_start: 0.8792 (t0) cc_final: 0.8469 (t0) REVERT: L 17 ASP cc_start: 0.8281 (m-30) cc_final: 0.7991 (m-30) REVERT: L 101 GLN cc_start: 0.8226 (mp10) cc_final: 0.7930 (mp10) REVERT: P 6 LEU cc_start: 0.7965 (mt) cc_final: 0.7530 (mp) REVERT: P 49 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8669 (mm) REVERT: W 125 GLN cc_start: 0.8030 (pm20) cc_final: 0.7602 (pm20) REVERT: W 204 TYR cc_start: 0.8624 (m-80) cc_final: 0.8136 (m-80) outliers start: 28 outliers final: 21 residues processed: 138 average time/residue: 0.0786 time to fit residues: 15.7592 Evaluate side-chains 138 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 206 CYS Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.093988 restraints weight = 12968.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095735 restraints weight = 9717.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.096831 restraints weight = 7955.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.097840 restraints weight = 6913.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.098373 restraints weight = 6249.691| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11080 Z= 0.151 Angle : 0.528 9.511 15097 Z= 0.257 Chirality : 0.039 0.159 1727 Planarity : 0.004 0.044 1882 Dihedral : 3.585 15.681 1492 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.45 % Allowed : 11.37 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.71 (0.23), residues: 1370 helix: 2.37 (0.23), residues: 480 sheet: 0.48 (0.26), residues: 414 loop : 0.61 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 66 TYR 0.016 0.001 TYR L 91 PHE 0.009 0.001 PHE X 140 TRP 0.010 0.001 TRP P 106 HIS 0.002 0.001 HIS W 174 Details of bonding type rmsd covalent geometry : bond 0.00362 (11068) covalent geometry : angle 0.52803 (15069) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.67106 ( 16) hydrogen bonds : bond 0.03347 ( 578) hydrogen bonds : angle 4.05514 ( 1692) link_TRANS : bond 0.00162 ( 4) link_TRANS : angle 0.53763 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.239 Fit side-chains REVERT: B 195 ARG cc_start: 0.7397 (ttp-170) cc_final: 0.6781 (ttm170) REVERT: C 49 ARG cc_start: 0.8052 (tpt90) cc_final: 0.7778 (tpt170) REVERT: D 68 HIS cc_start: 0.8150 (m-70) cc_final: 0.7861 (m-70) REVERT: D 100 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7321 (tt) REVERT: H 65 LYS cc_start: 0.8063 (tttp) cc_final: 0.7681 (ttpt) REVERT: H 214 ASN cc_start: 0.8833 (t0) cc_final: 0.8514 (t0) REVERT: L 17 ASP cc_start: 0.8365 (m-30) cc_final: 0.8085 (m-30) REVERT: L 101 GLN cc_start: 0.8251 (mp10) cc_final: 0.7973 (mp10) REVERT: N 189 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7657 (mm110) REVERT: P 6 LEU cc_start: 0.8094 (mt) cc_final: 0.7646 (mp) REVERT: P 49 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (mm) REVERT: W 125 GLN cc_start: 0.7994 (pm20) cc_final: 0.7183 (pm20) REVERT: W 204 TYR cc_start: 0.8644 (m-80) cc_final: 0.8154 (m-80) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.0898 time to fit residues: 18.1852 Evaluate side-chains 139 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 189 GLN Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 206 CYS Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.132719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.093540 restraints weight = 13017.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.095321 restraints weight = 9682.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.096538 restraints weight = 7881.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.097447 restraints weight = 6818.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.097754 restraints weight = 6177.995| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11080 Z= 0.155 Angle : 0.537 9.791 15097 Z= 0.260 Chirality : 0.039 0.145 1727 Planarity : 0.004 0.044 1882 Dihedral : 3.628 15.834 1492 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.27 % Allowed : 11.46 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.69 (0.23), residues: 1370 helix: 2.36 (0.23), residues: 480 sheet: 0.48 (0.26), residues: 414 loop : 0.56 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 66 TYR 0.016 0.001 TYR L 91 PHE 0.009 0.001 PHE X 140 TRP 0.010 0.001 TRP P 106 HIS 0.002 0.001 HIS W 174 Details of bonding type rmsd covalent geometry : bond 0.00370 (11068) covalent geometry : angle 0.53656 (15069) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.67025 ( 16) hydrogen bonds : bond 0.03375 ( 578) hydrogen bonds : angle 4.07383 ( 1692) link_TRANS : bond 0.00163 ( 4) link_TRANS : angle 0.55886 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.356 Fit side-chains REVERT: B 195 ARG cc_start: 0.7444 (ttp-170) cc_final: 0.6800 (ttm170) REVERT: C 49 ARG cc_start: 0.7995 (tpt90) cc_final: 0.7736 (tpt170) REVERT: D 68 HIS cc_start: 0.8144 (m-70) cc_final: 0.7859 (m-70) REVERT: D 100 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7273 (tt) REVERT: H 65 LYS cc_start: 0.8017 (tttp) cc_final: 0.7603 (ttpt) REVERT: H 214 ASN cc_start: 0.8857 (t0) cc_final: 0.8544 (t0) REVERT: L 17 ASP cc_start: 0.8315 (m-30) cc_final: 0.7945 (m-30) REVERT: L 101 GLN cc_start: 0.8313 (mp10) cc_final: 0.8028 (mp10) REVERT: N 189 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7601 (mm110) REVERT: P 6 LEU cc_start: 0.8130 (mt) cc_final: 0.7725 (mp) REVERT: P 49 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8709 (mm) REVERT: W 125 GLN cc_start: 0.7995 (pm20) cc_final: 0.7235 (pm20) REVERT: W 204 TYR cc_start: 0.8637 (m-80) cc_final: 0.8150 (m-80) outliers start: 26 outliers final: 23 residues processed: 135 average time/residue: 0.0956 time to fit residues: 18.4400 Evaluate side-chains 139 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 189 GLN Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 180 LEU Chi-restraints excluded: chain W residue 206 CYS Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.0970 chunk 51 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.096632 restraints weight = 12867.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.098048 restraints weight = 9577.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.099017 restraints weight = 7681.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100104 restraints weight = 6478.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.100353 restraints weight = 5912.638| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11080 Z= 0.097 Angle : 0.513 10.748 15097 Z= 0.245 Chirality : 0.038 0.142 1727 Planarity : 0.003 0.045 1882 Dihedral : 3.514 15.146 1492 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.10 % Allowed : 11.72 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.86 (0.23), residues: 1370 helix: 2.51 (0.23), residues: 482 sheet: 0.57 (0.26), residues: 413 loop : 0.64 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 98 TYR 0.009 0.001 TYR X 91 PHE 0.008 0.001 PHE X 140 TRP 0.010 0.001 TRP P 106 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00222 (11068) covalent geometry : angle 0.51320 (15069) SS BOND : bond 0.00286 ( 8) SS BOND : angle 0.61559 ( 16) hydrogen bonds : bond 0.02966 ( 578) hydrogen bonds : angle 3.88983 ( 1692) link_TRANS : bond 0.00069 ( 4) link_TRANS : angle 0.30797 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.346 Fit side-chains REVERT: D 68 HIS cc_start: 0.8138 (m-70) cc_final: 0.7853 (m-70) REVERT: D 100 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7235 (tt) REVERT: H 65 LYS cc_start: 0.7964 (tttp) cc_final: 0.7550 (ttpt) REVERT: H 214 ASN cc_start: 0.8806 (t0) cc_final: 0.8523 (t0) REVERT: L 17 ASP cc_start: 0.8402 (m-30) cc_final: 0.8010 (m-30) REVERT: L 101 GLN cc_start: 0.8283 (mp10) cc_final: 0.7993 (mp10) REVERT: N 189 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7572 (mm110) REVERT: P 6 LEU cc_start: 0.8127 (mt) cc_final: 0.7717 (mp) REVERT: P 49 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8637 (mm) REVERT: W 125 GLN cc_start: 0.7976 (pm20) cc_final: 0.7208 (pm20) REVERT: W 204 TYR cc_start: 0.8589 (m-80) cc_final: 0.8107 (m-80) REVERT: X 143 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.8003 (ttp80) outliers start: 24 outliers final: 19 residues processed: 130 average time/residue: 0.0833 time to fit residues: 15.8508 Evaluate side-chains 131 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 189 GLN Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain W residue 50 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain X residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 14 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.132677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.094231 restraints weight = 13136.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094915 restraints weight = 10018.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095688 restraints weight = 8528.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096970 restraints weight = 7217.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.097162 restraints weight = 6369.131| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11080 Z= 0.188 Angle : 0.559 10.375 15097 Z= 0.271 Chirality : 0.040 0.145 1727 Planarity : 0.004 0.045 1882 Dihedral : 3.672 16.069 1492 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.10 % Allowed : 11.90 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.69 (0.23), residues: 1370 helix: 2.39 (0.23), residues: 482 sheet: 0.46 (0.26), residues: 414 loop : 0.55 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 66 TYR 0.019 0.002 TYR L 91 PHE 0.010 0.001 PHE L 140 TRP 0.009 0.001 TRP W 47 HIS 0.003 0.001 HIS N 80 Details of bonding type rmsd covalent geometry : bond 0.00452 (11068) covalent geometry : angle 0.55843 (15069) SS BOND : bond 0.00286 ( 8) SS BOND : angle 0.74551 ( 16) hydrogen bonds : bond 0.03501 ( 578) hydrogen bonds : angle 4.08964 ( 1692) link_TRANS : bond 0.00213 ( 4) link_TRANS : angle 0.65333 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.29 seconds wall clock time: 26 minutes 47.59 seconds (1607.59 seconds total)