Starting phenix.real_space_refine on Fri Jul 3 18:47:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.map" model { file = "/net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jn3_22400/07_2026/7jn3_22400.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.062 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 64 5.49 5 Mg 4 5.21 5 S 48 5.16 5 Cl 2 4.86 5 C 9707 2.51 5 N 2932 2.21 5 O 2905 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15666 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 252} Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 201} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1658 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "D" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1676 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2099 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 252} Chain: "F" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1651 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1651 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 326 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'ZZX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'ZZX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 283 SG CYS A 37 59.013 114.196 48.713 1.00 75.59 S ATOM 306 SG CYS A 40 60.630 110.781 49.457 1.00 74.68 S ATOM 7403 SG CYS E 37 57.824 78.837 94.043 1.00 67.66 S ATOM 7426 SG CYS E 40 60.411 81.423 92.837 1.00 66.26 S Time building chain proxies: 3.48, per 1000 atoms: 0.22 Number of scatterers: 15666 At special positions: 0 Unit cell: (111.1, 199.1, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 48 16.00 P 64 15.00 Mg 4 11.99 F 2 9.00 O 2905 8.00 N 2932 7.00 C 9707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 702.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 37 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 37 " Number of angles added : 4 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 37.4% alpha, 16.6% beta 21 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.666A pdb=" N VAL A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 153 through 174 Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.572A pdb=" N ARG B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 174 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.559A pdb=" N LEU B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'C' and resid 69 through 72 removed outlier: 3.639A pdb=" N ALA C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 97 through 112 Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 154 through 175 Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.564A pdb=" N ALA D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 139 Processing helix chain 'D' and resid 153 through 175 Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 23 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.582A pdb=" N VAL E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 153 through 173 Processing helix chain 'E' and resid 184 through 199 removed outlier: 3.676A pdb=" N PHE E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'F' and resid 69 through 72 removed outlier: 3.740A pdb=" N ALA F 72 " --> pdb=" O PRO F 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 72' Processing helix chain 'F' and resid 97 through 113 removed outlier: 3.739A pdb=" N VAL F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 153 through 174 removed outlier: 3.688A pdb=" N GLU F 157 " --> pdb=" O GLN F 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 99 through 113 Processing helix chain 'G' and resid 124 through 127 Processing helix chain 'G' and resid 128 through 139 Processing helix chain 'G' and resid 155 through 174 Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 97 through 113 removed outlier: 3.776A pdb=" N ALA H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 138 removed outlier: 3.622A pdb=" N ALA H 136 " --> pdb=" O ARG H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 175 removed outlier: 3.661A pdb=" N ALA H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N MET H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 183 No H-bonds generated for 'chain 'H' and resid 181 through 183' Processing helix chain 'H' and resid 184 through 196 Processing helix chain 'H' and resid 261 through 263 No H-bonds generated for 'chain 'H' and resid 261 through 263' Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 93 removed outlier: 3.778A pdb=" N TRP A 76 " --> pdb=" O HIS A 93 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 64 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 81 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP A 61 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 143 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 120 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 6.598A pdb=" N TYR A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP A 242 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 248 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY A 236 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 224 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.744A pdb=" N TRP B 61 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.501A pdb=" N ASP B 64 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 78 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 91 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 247 through 251 removed outlier: 6.917A pdb=" N ALA B 248 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 238 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS B 235 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 226 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 92 removed outlier: 3.540A pdb=" N VAL C 89 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TRP C 61 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE C 118 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 237 through 242 removed outlier: 6.936A pdb=" N ALA C 248 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP C 242 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 82 removed outlier: 5.834A pdb=" N TRP D 61 " --> pdb=" O LYS D 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 261 removed outlier: 3.628A pdb=" N VAL D 249 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP D 237 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 88 through 93 removed outlier: 3.735A pdb=" N TRP E 76 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 81 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TRP E 61 " --> pdb=" O LYS E 119 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR E 143 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 120 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 257 through 261 removed outlier: 6.503A pdb=" N TYR E 246 " --> pdb=" O TRP E 242 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP E 242 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA E 248 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY E 236 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL E 224 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 88 through 93 removed outlier: 3.566A pdb=" N TRP F 76 " --> pdb=" O HIS F 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR F 63 " --> pdb=" O LYS F 119 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE F 118 " --> pdb=" O THR F 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 233 through 234 Processing sheet with id=AB6, first strand: chain 'F' and resid 237 through 242 removed outlier: 7.018A pdb=" N ALA F 248 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP F 242 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR F 246 " --> pdb=" O TRP F 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.773A pdb=" N VAL G 79 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP G 64 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR G 63 " --> pdb=" O LYS G 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 257 through 261 removed outlier: 6.788A pdb=" N TYR G 246 " --> pdb=" O TRP G 242 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP G 242 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA G 248 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS G 235 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE G 226 " --> pdb=" O LYS G 235 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP G 237 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 88 through 89 removed outlier: 6.125A pdb=" N TRP H 61 " --> pdb=" O LYS H 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 66 through 67 removed outlier: 3.907A pdb=" N THR H 66 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 257 through 258 removed outlier: 6.964A pdb=" N ALA H 248 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY H 236 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL H 224 " --> pdb=" O GLY H 236 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4272 1.33 - 1.45: 3133 1.45 - 1.57: 8568 1.57 - 1.69: 128 1.69 - 1.81: 84 Bond restraints: 16185 Sorted by residual: bond pdb=" CAN ZZX E 302 " pdb=" CAU ZZX E 302 " ideal model delta sigma weight residual 1.507 1.390 0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" CAS ZZX E 302 " pdb=" CAY ZZX E 302 " ideal model delta sigma weight residual 1.466 1.350 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" CAS ZZX A 302 " pdb=" CAY ZZX A 302 " ideal model delta sigma weight residual 1.466 1.350 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" CAN ZZX A 302 " pdb=" CAU ZZX A 302 " ideal model delta sigma weight residual 1.507 1.395 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CAZ ZZX A 302 " pdb=" CBA ZZX A 302 " ideal model delta sigma weight residual 1.421 1.320 0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 16180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 21614 2.01 - 4.03: 553 4.03 - 6.04: 64 6.04 - 8.06: 23 8.06 - 10.07: 5 Bond angle restraints: 22259 Sorted by residual: angle pdb=" N VAL A 33 " pdb=" CA VAL A 33 " pdb=" C VAL A 33 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N VAL A 96 " pdb=" CA VAL A 96 " pdb=" C VAL A 96 " ideal model delta sigma weight residual 111.91 107.02 4.89 8.90e-01 1.26e+00 3.01e+01 angle pdb=" N VAL E 96 " pdb=" CA VAL E 96 " pdb=" C VAL E 96 " ideal model delta sigma weight residual 111.91 107.46 4.45 8.90e-01 1.26e+00 2.50e+01 angle pdb=" O4' DA I 2 " pdb=" C4' DA I 2 " pdb=" C3' DA I 2 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT K 8 " pdb=" C4 DT K 8 " pdb=" O4 DT K 8 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 22254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.11: 8688 26.11 - 52.21: 742 52.21 - 78.31: 85 78.31 - 104.42: 14 104.42 - 130.52: 2 Dihedral angle restraints: 9531 sinusoidal: 4396 harmonic: 5135 Sorted by residual: dihedral pdb=" CA ARG A 227 " pdb=" C ARG A 227 " pdb=" N ILE A 228 " pdb=" CA ILE A 228 " ideal model delta harmonic sigma weight residual 180.00 132.84 47.16 0 5.00e+00 4.00e-02 8.89e+01 dihedral pdb=" CA ARG E 227 " pdb=" C ARG E 227 " pdb=" N ILE E 228 " pdb=" CA ILE E 228 " ideal model delta harmonic sigma weight residual 180.00 135.78 44.22 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CA ALA A 43 " pdb=" C ALA A 43 " pdb=" N PRO A 44 " pdb=" CA PRO A 44 " ideal model delta harmonic sigma weight residual -180.00 -140.85 -39.15 0 5.00e+00 4.00e-02 6.13e+01 ... (remaining 9528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1567 0.038 - 0.077: 599 0.077 - 0.115: 224 0.115 - 0.153: 52 0.153 - 0.192: 8 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CB ILE D 109 " pdb=" CA ILE D 109 " pdb=" CG1 ILE D 109 " pdb=" CG2 ILE D 109 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA GLU E 32 " pdb=" N GLU E 32 " pdb=" C GLU E 32 " pdb=" CB GLU E 32 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 2447 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAS ZZX E 302 " 0.031 2.00e-02 2.50e+03 5.28e-02 6.98e+01 pdb=" CAW ZZX E 302 " 0.079 2.00e-02 2.50e+03 pdb=" CAX ZZX E 302 " -0.004 2.00e-02 2.50e+03 pdb=" CAY ZZX E 302 " -0.129 2.00e-02 2.50e+03 pdb=" CAZ ZZX E 302 " -0.001 2.00e-02 2.50e+03 pdb=" CBA ZZX E 302 " 0.000 2.00e-02 2.50e+03 pdb=" CBB ZZX E 302 " 0.010 2.00e-02 2.50e+03 pdb=" CBC ZZX E 302 " 0.050 2.00e-02 2.50e+03 pdb=" NBF ZZX E 302 " -0.038 2.00e-02 2.50e+03 pdb=" OAG ZZX E 302 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAS ZZX A 302 " -0.030 2.00e-02 2.50e+03 5.25e-02 6.90e+01 pdb=" CAW ZZX A 302 " -0.080 2.00e-02 2.50e+03 pdb=" CAX ZZX A 302 " 0.004 2.00e-02 2.50e+03 pdb=" CAY ZZX A 302 " 0.128 2.00e-02 2.50e+03 pdb=" CAZ ZZX A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CBA ZZX A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CBB ZZX A 302 " -0.008 2.00e-02 2.50e+03 pdb=" CBC ZZX A 302 " -0.050 2.00e-02 2.50e+03 pdb=" NBF ZZX A 302 " 0.037 2.00e-02 2.50e+03 pdb=" OAG ZZX A 302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 227 " -0.258 9.50e-02 1.11e+02 1.16e-01 8.33e+00 pdb=" NE ARG E 227 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 227 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 227 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 227 " -0.011 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 150 2.56 - 3.14: 12496 3.14 - 3.73: 25765 3.73 - 4.31: 33884 4.31 - 4.90: 54423 Nonbonded interactions: 126718 Sorted by model distance: nonbonded pdb=" OAG ZZX A 302 " pdb="MG MG A 303 " model vdw 1.973 2.170 nonbonded pdb=" OAG ZZX E 302 " pdb="MG MG E 304 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU E 157 " pdb="MG MG E 304 " model vdw 1.983 2.170 nonbonded pdb=" OE2 GLU A 157 " pdb="MG MG A 303 " model vdw 1.998 2.170 nonbonded pdb=" OD1 ASP A 64 " pdb="MG MG A 303 " model vdw 2.034 2.170 ... (remaining 126713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'C' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'D' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'F' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'G' and resid 57 through 269) selection = (chain 'H' and resid 57 through 269) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 individual isotropic 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.580 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 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 : 0.005 0.117 16193 Z= 0.303 Angle : 0.751 10.073 22263 Z= 0.456 Chirality : 0.048 0.192 2450 Planarity : 0.006 0.116 2577 Dihedral : 18.249 130.525 6207 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.24 % 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: -2.09 (0.20), residues: 1783 helix: -0.18 (0.21), residues: 609 sheet: -1.53 (0.27), residues: 363 loop : -2.25 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 227 TYR 0.015 0.002 TYR C 194 PHE 0.019 0.001 PHE A 126 TRP 0.029 0.001 TRP E 233 HIS 0.012 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.30 (16185) covalent geometry : angle 0.74893 / 0.46 (22259) hydrogen bonds : bond 0.19442 / 13.56 ( 636) hydrogen bonds : angle 7.64463 / 5.55 ( 1814) metal coordination : bond 0.02132 / 1.39 ( 8) metal coordination : angle 4.21737 / 3.22 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.384 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1124 time to fit residues: 24.9412 Evaluate side-chains 109 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 0.0770 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 122 ASN B 160 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.226251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.191922 restraints weight = 29877.001| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 4.51 r_work: 0.4070 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16193 Z= 0.147 Angle : 0.668 12.440 22263 Z= 0.359 Chirality : 0.047 0.172 2450 Planarity : 0.005 0.057 2577 Dihedral : 18.882 134.059 2776 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.87 % Allowed : 8.70 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.18 % 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: -1.85 (0.20), residues: 1783 helix: 0.08 (0.21), residues: 609 sheet: -1.41 (0.27), residues: 367 loop : -2.15 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 244 TYR 0.007 0.001 TYR C 194 PHE 0.008 0.001 PHE A 199 TRP 0.018 0.001 TRP H 134 HIS 0.011 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (16185) covalent geometry : angle 0.66448 / 0.36 (22259) hydrogen bonds : bond 0.05415 / 3.88 ( 636) hydrogen bonds : angle 5.87409 / 4.18 ( 1814) metal coordination : bond 0.01848 / 1.23 ( 8) metal coordination : angle 5.42237 / 4.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.4910 (t80) cc_final: 0.3706 (t80) REVERT: B 133 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: C 242 TRP cc_start: 0.7038 (t60) cc_final: 0.6748 (t60) REVERT: F 121 ASP cc_start: 0.6192 (p0) cc_final: 0.5990 (p0) REVERT: F 134 TRP cc_start: 0.6690 (t60) cc_final: 0.6353 (t60) REVERT: G 250 LYS cc_start: 0.6148 (tmtt) cc_final: 0.5899 (tmmt) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.1323 time to fit residues: 28.3350 Evaluate side-chains 122 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 154 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN C 185 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN H 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.222723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.184704 restraints weight = 29001.706| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 4.17 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16193 Z= 0.214 Angle : 0.700 10.579 22263 Z= 0.374 Chirality : 0.047 0.174 2450 Planarity : 0.006 0.065 2577 Dihedral : 18.926 129.367 2776 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.87 % Allowed : 12.25 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.06 % 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: -1.88 (0.20), residues: 1783 helix: 0.15 (0.20), residues: 610 sheet: -1.58 (0.27), residues: 357 loop : -2.17 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.007 0.002 TYR A 246 PHE 0.019 0.002 PHE A 65 TRP 0.020 0.002 TRP D 134 HIS 0.010 0.002 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (16185) covalent geometry : angle 0.69719 / 0.37 (22259) hydrogen bonds : bond 0.05507 / 3.91 ( 636) hydrogen bonds : angle 5.55486 / 3.96 ( 1814) metal coordination : bond 0.01936 / 1.26 ( 8) metal coordination : angle 4.91404 / 3.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7774 (ttpp) REVERT: C 242 TRP cc_start: 0.6958 (t60) cc_final: 0.6708 (t60) REVERT: G 250 LYS cc_start: 0.5806 (tmtt) cc_final: 0.5581 (tmmt) outliers start: 28 outliers final: 14 residues processed: 143 average time/residue: 0.1332 time to fit residues: 28.4086 Evaluate side-chains 121 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain G residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 41 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 chunk 177 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS D 153 GLN E 93 HIS ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.225712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.189735 restraints weight = 29070.255| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 4.04 r_work: 0.4045 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16193 Z= 0.132 Angle : 0.605 9.232 22263 Z= 0.326 Chirality : 0.045 0.167 2450 Planarity : 0.005 0.055 2577 Dihedral : 18.756 135.595 2776 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.14 % Allowed : 14.66 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.06 % 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: -1.61 (0.20), residues: 1783 helix: 0.35 (0.21), residues: 611 sheet: -1.42 (0.26), residues: 368 loop : -2.00 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 227 TYR 0.010 0.001 TYR E 246 PHE 0.009 0.001 PHE A 199 TRP 0.017 0.001 TRP D 134 HIS 0.007 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16185) covalent geometry : angle 0.60124 / 0.33 (22259) hydrogen bonds : bond 0.04599 / 3.33 ( 636) hydrogen bonds : angle 5.25013 / 3.74 ( 1814) metal coordination : bond 0.01757 / 1.18 ( 8) metal coordination : angle 4.92299 / 3.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.6876 (mtp) cc_final: 0.6675 (mtt) REVERT: A 67 LEU cc_start: 0.8335 (tp) cc_final: 0.8104 (tp) REVERT: A 126 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.2655 (t80) REVERT: G 250 LYS cc_start: 0.5932 (tmtt) cc_final: 0.5655 (tmmt) outliers start: 32 outliers final: 12 residues processed: 136 average time/residue: 0.1266 time to fit residues: 26.3857 Evaluate side-chains 115 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 4 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.225947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.190875 restraints weight = 29142.941| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 3.96 r_work: 0.4067 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16193 Z= 0.131 Angle : 0.594 8.662 22263 Z= 0.322 Chirality : 0.044 0.168 2450 Planarity : 0.005 0.054 2577 Dihedral : 18.693 134.156 2776 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.54 % Allowed : 15.66 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -1.46 (0.20), residues: 1783 helix: 0.49 (0.21), residues: 611 sheet: -1.36 (0.27), residues: 366 loop : -1.92 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 263 TYR 0.013 0.001 TYR E 246 PHE 0.007 0.001 PHE E 126 TRP 0.017 0.001 TRP D 134 HIS 0.007 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (16185) covalent geometry : angle 0.59116 / 0.32 (22259) hydrogen bonds : bond 0.04391 / 3.17 ( 636) hydrogen bonds : angle 5.03970 / 3.59 ( 1814) metal coordination : bond 0.01589 / 1.07 ( 8) metal coordination : angle 4.34429 / 3.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8031 (ttpp) REVERT: A 27 MET cc_start: 0.6685 (mtp) cc_final: 0.6392 (mtt) REVERT: A 67 LEU cc_start: 0.8328 (tp) cc_final: 0.8072 (tp) REVERT: A 126 PHE cc_start: 0.5561 (OUTLIER) cc_final: 0.2604 (t80) REVERT: A 220 GLU cc_start: 0.7516 (pm20) cc_final: 0.7055 (tp30) REVERT: B 77 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 92 GLN cc_start: 0.3114 (tm-30) cc_final: 0.2906 (tm-30) REVERT: E 200 GLU cc_start: 0.7069 (pm20) cc_final: 0.6547 (pm20) REVERT: F 264 LYS cc_start: 0.7263 (tppt) cc_final: 0.6684 (mmtp) REVERT: G 185 GLN cc_start: 0.3341 (OUTLIER) cc_final: -0.2076 (pm20) REVERT: G 250 LYS cc_start: 0.5982 (tmtt) cc_final: 0.5745 (ttpt) outliers start: 38 outliers final: 19 residues processed: 146 average time/residue: 0.1250 time to fit residues: 27.5036 Evaluate side-chains 131 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 225 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 193 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 147 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 172 optimal weight: 0.3980 chunk 87 optimal weight: 0.0980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.224219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.186975 restraints weight = 28908.642| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 3.77 r_work: 0.4043 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16193 Z= 0.160 Angle : 0.609 9.374 22263 Z= 0.330 Chirality : 0.045 0.168 2450 Planarity : 0.005 0.054 2577 Dihedral : 18.799 133.321 2776 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.54 % Allowed : 16.13 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -1.42 (0.20), residues: 1783 helix: 0.52 (0.21), residues: 615 sheet: -1.39 (0.27), residues: 366 loop : -1.88 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 227 TYR 0.012 0.002 TYR E 246 PHE 0.015 0.002 PHE E 126 TRP 0.017 0.001 TRP D 134 HIS 0.008 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (16185) covalent geometry : angle 0.60603 / 0.33 (22259) hydrogen bonds : bond 0.04435 / 3.18 ( 636) hydrogen bonds : angle 4.98384 / 3.55 ( 1814) metal coordination : bond 0.01732 / 1.16 ( 8) metal coordination : angle 4.34112 / 3.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8059 (ttpp) REVERT: A 27 MET cc_start: 0.7063 (mtp) cc_final: 0.6859 (mtt) REVERT: A 126 PHE cc_start: 0.5586 (OUTLIER) cc_final: 0.2443 (t80) REVERT: D 81 VAL cc_start: 0.0873 (OUTLIER) cc_final: 0.0613 (t) REVERT: E 200 GLU cc_start: 0.7213 (pm20) cc_final: 0.6786 (pm20) REVERT: G 185 GLN cc_start: 0.3181 (OUTLIER) cc_final: -0.2002 (pp30) REVERT: G 250 LYS cc_start: 0.6012 (tmtt) cc_final: 0.5772 (ttpt) outliers start: 38 outliers final: 26 residues processed: 143 average time/residue: 0.1127 time to fit residues: 25.0546 Evaluate side-chains 135 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 193 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 130 optimal weight: 0.0470 chunk 86 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.224105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.186055 restraints weight = 28831.158| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.87 r_work: 0.4014 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16193 Z= 0.151 Angle : 0.607 9.538 22263 Z= 0.327 Chirality : 0.045 0.164 2450 Planarity : 0.005 0.055 2577 Dihedral : 18.798 134.670 2776 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.54 % Allowed : 16.33 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -1.31 (0.20), residues: 1783 helix: 0.67 (0.21), residues: 609 sheet: -1.36 (0.27), residues: 367 loop : -1.84 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 244 TYR 0.007 0.001 TYR E 246 PHE 0.013 0.001 PHE E 126 TRP 0.017 0.001 TRP D 134 HIS 0.007 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (16185) covalent geometry : angle 0.60395 / 0.33 (22259) hydrogen bonds : bond 0.04296 / 3.11 ( 636) hydrogen bonds : angle 4.90534 / 3.50 ( 1814) metal coordination : bond 0.01657 / 1.11 ( 8) metal coordination : angle 4.45921 / 3.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8042 (ttpp) REVERT: A 220 GLU cc_start: 0.7488 (pm20) cc_final: 0.7028 (tp30) REVERT: B 77 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 179 ARG cc_start: 0.6834 (tmt170) cc_final: 0.6280 (tmt170) REVERT: D 81 VAL cc_start: 0.0924 (OUTLIER) cc_final: 0.0676 (t) REVERT: E 12 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 200 GLU cc_start: 0.7225 (pm20) cc_final: 0.6797 (pm20) REVERT: G 105 TRP cc_start: -0.0550 (OUTLIER) cc_final: -0.0966 (m-10) REVERT: G 185 GLN cc_start: 0.3666 (OUTLIER) cc_final: -0.1580 (pp30) REVERT: G 250 LYS cc_start: 0.6089 (tmtt) cc_final: 0.5828 (ttpt) outliers start: 38 outliers final: 25 residues processed: 144 average time/residue: 0.1106 time to fit residues: 24.5978 Evaluate side-chains 139 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 105 TRP Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 41 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.225781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.188624 restraints weight = 29065.345| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 3.72 r_work: 0.4055 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16193 Z= 0.122 Angle : 0.574 8.525 22263 Z= 0.309 Chirality : 0.044 0.158 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.768 135.703 2776 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.28 % Allowed : 16.47 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -1.19 (0.20), residues: 1783 helix: 0.78 (0.21), residues: 610 sheet: -1.23 (0.27), residues: 377 loop : -1.81 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 263 TYR 0.005 0.001 TYR D 246 PHE 0.011 0.001 PHE E 126 TRP 0.016 0.001 TRP D 134 HIS 0.006 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16185) covalent geometry : angle 0.57089 / 0.31 (22259) hydrogen bonds : bond 0.04029 / 2.93 ( 636) hydrogen bonds : angle 4.78872 / 3.41 ( 1814) metal coordination : bond 0.01423 / 0.95 ( 8) metal coordination : angle 4.19670 / 2.92 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.7479 (pm20) cc_final: 0.6955 (tp30) REVERT: B 179 ARG cc_start: 0.6790 (tmt170) cc_final: 0.6272 (tmt170) REVERT: D 81 VAL cc_start: 0.0765 (OUTLIER) cc_final: 0.0513 (t) REVERT: F 264 LYS cc_start: 0.7414 (tppt) cc_final: 0.6814 (mmtp) REVERT: G 185 GLN cc_start: 0.3124 (OUTLIER) cc_final: -0.2015 (pp30) REVERT: G 250 LYS cc_start: 0.6031 (tmtt) cc_final: 0.5759 (ttpt) outliers start: 34 outliers final: 26 residues processed: 140 average time/residue: 0.1222 time to fit residues: 26.5371 Evaluate side-chains 138 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 7.9990 chunk 130 optimal weight: 0.0060 chunk 72 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.226136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.188803 restraints weight = 28970.246| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 3.64 r_work: 0.4084 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16193 Z= 0.120 Angle : 0.579 10.463 22263 Z= 0.309 Chirality : 0.044 0.162 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.757 135.061 2776 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.01 % Allowed : 17.20 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -1.12 (0.20), residues: 1783 helix: 0.84 (0.21), residues: 610 sheet: -1.19 (0.27), residues: 378 loop : -1.77 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.006 0.001 TYR D 246 PHE 0.010 0.001 PHE E 126 TRP 0.016 0.001 TRP D 134 HIS 0.006 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16185) covalent geometry : angle 0.57630 / 0.31 (22259) hydrogen bonds : bond 0.03939 / 2.87 ( 636) hydrogen bonds : angle 4.71971 / 3.36 ( 1814) metal coordination : bond 0.01522 / 1.02 ( 8) metal coordination : angle 4.00468 / 2.74 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8073 (ttpp) REVERT: A 220 GLU cc_start: 0.7564 (pm20) cc_final: 0.7022 (tp30) REVERT: B 179 ARG cc_start: 0.6752 (tmt170) cc_final: 0.6231 (tmt170) REVERT: D 81 VAL cc_start: 0.0795 (OUTLIER) cc_final: 0.0552 (t) REVERT: E 2 LEU cc_start: 0.8000 (pp) cc_final: 0.7543 (tt) REVERT: F 134 TRP cc_start: 0.6996 (t60) cc_final: 0.6066 (t60) REVERT: F 264 LYS cc_start: 0.7592 (tppt) cc_final: 0.7017 (mmtp) REVERT: G 185 GLN cc_start: 0.3043 (OUTLIER) cc_final: -0.2008 (pp30) REVERT: G 250 LYS cc_start: 0.6015 (tmtt) cc_final: 0.5735 (ttpt) outliers start: 30 outliers final: 25 residues processed: 139 average time/residue: 0.1149 time to fit residues: 24.7233 Evaluate side-chains 140 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 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 = 0.4872 r_free = 0.4872 target = 0.226333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.188007 restraints weight = 29002.038| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 3.64 r_work: 0.4056 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16193 Z= 0.120 Angle : 0.571 9.669 22263 Z= 0.305 Chirality : 0.044 0.187 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.750 134.721 2776 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.07 % Allowed : 17.34 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -1.02 (0.21), residues: 1783 helix: 0.92 (0.21), residues: 608 sheet: -1.10 (0.27), residues: 388 loop : -1.73 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 263 TYR 0.006 0.001 TYR D 246 PHE 0.006 0.001 PHE G 65 TRP 0.016 0.001 TRP D 134 HIS 0.006 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16185) covalent geometry : angle 0.56874 / 0.31 (22259) hydrogen bonds : bond 0.03901 / 2.85 ( 636) hydrogen bonds : angle 4.68123 / 3.34 ( 1814) metal coordination : bond 0.01484 / 1.00 ( 8) metal coordination : angle 3.92784 / 2.67 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.7534 (pm20) cc_final: 0.6995 (tp30) REVERT: B 179 ARG cc_start: 0.6753 (tmt170) cc_final: 0.6276 (tmt170) REVERT: C 193 MET cc_start: -0.1756 (mtp) cc_final: -0.2851 (ttt) REVERT: D 81 VAL cc_start: 0.0932 (OUTLIER) cc_final: 0.0692 (t) REVERT: E 2 LEU cc_start: 0.7942 (pp) cc_final: 0.7526 (tt) REVERT: F 264 LYS cc_start: 0.7595 (tppt) cc_final: 0.7117 (mmtp) REVERT: G 105 TRP cc_start: -0.0316 (OUTLIER) cc_final: -0.0757 (m-10) REVERT: G 185 GLN cc_start: 0.3400 (OUTLIER) cc_final: -0.1735 (pp30) REVERT: G 250 LYS cc_start: 0.5953 (tmtt) cc_final: 0.5667 (ttpt) outliers start: 31 outliers final: 25 residues processed: 144 average time/residue: 0.1178 time to fit residues: 26.3100 Evaluate side-chains 140 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 105 TRP Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 18 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 160 optimal weight: 0.0370 chunk 60 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 ASN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.226501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.188204 restraints weight = 28684.396| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 3.63 r_work: 0.4079 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16193 Z= 0.119 Angle : 0.572 9.730 22263 Z= 0.306 Chirality : 0.044 0.174 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.740 134.601 2776 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.01 % Allowed : 17.67 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1783 helix: 0.98 (0.21), residues: 606 sheet: -1.02 (0.27), residues: 387 loop : -1.76 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.006 0.001 TYR D 246 PHE 0.006 0.001 PHE E 65 TRP 0.041 0.001 TRP B 105 HIS 0.005 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (16185) covalent geometry : angle 0.56994 / 0.31 (22259) hydrogen bonds : bond 0.03855 / 2.81 ( 636) hydrogen bonds : angle 4.68723 / 3.34 ( 1814) metal coordination : bond 0.01486 / 1.00 ( 8) metal coordination : angle 3.71963 / 2.51 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5372.60 seconds wall clock time: 92 minutes 26.74 seconds (5546.74 seconds total)