Starting phenix.real_space_refine on Sat Sep 12 11:44:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jn3_22400/09_2026/7jn3_22400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jn3_22400/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jn3_22400/09_2026/7jn3_22400.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jn3_22400/09_2026/7jn3_22400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jn3_22400/09_2026/7jn3_22400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jn3_22400/09_2026/7jn3_22400.map" model { file = "/net/cci-nas-00/data/ceres_data/7jn3_22400/09_2026/7jn3_22400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jn3_22400/09_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-2.2.1-6174/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: 3.54, per 1000 atoms: 0.23 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: 1.35 Conformation dependent library (CDL) restraints added in 573.1 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: 1.82 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: 2.51 Time building geometry restraints manager: 1.72 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: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.650 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.950 ------------------------------------------------------------------------------- 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 : 0.752 10.073 22263 Z= 0.458 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 0.75026 / 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 : 0.462 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1078 time to fit residues: 23.8708 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 : 0.541 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.226351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.192132 restraints weight = 29912.807| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 4.55 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16193 Z= 0.143 Angle : 0.670 12.125 22263 Z= 0.358 Chirality : 0.047 0.173 2450 Planarity : 0.005 0.056 2577 Dihedral : 18.858 133.751 2776 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.87 % Allowed : 8.77 % Favored : 90.36 % 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: -1.84 (0.20), residues: 1783 helix: 0.08 (0.20), residues: 609 sheet: -1.40 (0.27), residues: 367 loop : -2.14 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 244 TYR 0.009 0.002 TYR B 246 PHE 0.009 0.001 PHE A 199 TRP 0.019 0.001 TRP H 134 HIS 0.011 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16185) covalent geometry : angle 0.66631 / 0.36 (22259) hydrogen bonds : bond 0.05347 / 3.83 ( 636) hydrogen bonds : angle 5.85408 / 4.17 ( 1814) metal coordination : bond 0.01884 / 1.24 ( 8) metal coordination : angle 5.48552 / 4.36 ( 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 151 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.4663 (t80) cc_final: 0.3658 (t80) REVERT: C 242 TRP cc_start: 0.6751 (t60) cc_final: 0.6464 (t60) REVERT: F 121 ASP cc_start: 0.6000 (p0) cc_final: 0.5787 (p0) REVERT: F 134 TRP cc_start: 0.6770 (t60) cc_final: 0.6347 (t60) REVERT: G 250 LYS cc_start: 0.5884 (tmtt) cc_final: 0.5684 (tmmt) outliers start: 13 outliers final: 7 residues processed: 146 average time/residue: 0.1222 time to fit residues: 26.4186 Evaluate side-chains 124 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 61 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN 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** F 92 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4860 r_free = 0.4860 target = 0.224621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.187634 restraints weight = 29238.116| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 4.21 r_work: 0.4024 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16193 Z= 0.180 Angle : 0.659 10.253 22263 Z= 0.352 Chirality : 0.046 0.173 2450 Planarity : 0.005 0.060 2577 Dihedral : 18.803 129.595 2776 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.81 % Allowed : 11.65 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.12 % 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: -1.76 (0.20), residues: 1783 helix: 0.23 (0.21), residues: 610 sheet: -1.48 (0.26), residues: 368 loop : -2.11 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.006 0.002 TYR A 246 PHE 0.015 0.001 PHE A 65 TRP 0.019 0.002 TRP D 134 HIS 0.009 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (16185) covalent geometry : angle 0.65579 / 0.35 (22259) hydrogen bonds : bond 0.05199 / 3.73 ( 636) hydrogen bonds : angle 5.50032 / 3.93 ( 1814) metal coordination : bond 0.01637 / 1.08 ( 8) metal coordination : angle 4.69864 / 3.61 ( 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 147 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 TRP cc_start: 0.7021 (t60) cc_final: 0.6799 (t60) REVERT: F 121 ASP cc_start: 0.6329 (p0) cc_final: 0.6092 (p0) REVERT: G 250 LYS cc_start: 0.5945 (tmtt) cc_final: 0.5720 (ttpt) outliers start: 27 outliers final: 13 residues processed: 140 average time/residue: 0.1166 time to fit residues: 24.9918 Evaluate side-chains 122 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 207 THR 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 122 ASN 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 249 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: 0.6980 chunk 108 optimal weight: 0.9990 chunk 153 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 159 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- 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** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 HIS E 122 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.226661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.189935 restraints weight = 29115.269| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 3.78 r_work: 0.4068 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16193 Z= 0.129 Angle : 0.594 8.519 22263 Z= 0.320 Chirality : 0.044 0.161 2450 Planarity : 0.005 0.054 2577 Dihedral : 18.667 134.162 2776 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.94 % Allowed : 14.26 % Favored : 83.80 % 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: -1.55 (0.20), residues: 1783 helix: 0.39 (0.21), residues: 611 sheet: -1.33 (0.26), residues: 368 loop : -1.98 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 227 TYR 0.014 0.001 TYR E 246 PHE 0.006 0.001 PHE A 65 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 0.00266 / 0.13 (16185) covalent geometry : angle 0.59083 / 0.32 (22259) hydrogen bonds : bond 0.04448 / 3.21 ( 636) hydrogen bonds : angle 5.17150 / 3.70 ( 1814) metal coordination : bond 0.01740 / 1.16 ( 8) metal coordination : angle 4.72650 / 3.62 ( 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 147 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.2712 (t80) REVERT: G 250 LYS cc_start: 0.6002 (tmtt) cc_final: 0.5738 (tmmt) outliers start: 29 outliers final: 12 residues processed: 143 average time/residue: 0.1129 time to fit residues: 24.9333 Evaluate side-chains 125 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE 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 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 122 ASN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 257 VAL 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: 3.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4865 r_free = 0.4865 target = 0.225313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.186409 restraints weight = 28962.895| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 3.84 r_work: 0.4051 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16193 Z= 0.151 Angle : 0.607 8.879 22263 Z= 0.327 Chirality : 0.045 0.160 2450 Planarity : 0.005 0.054 2577 Dihedral : 18.734 131.806 2776 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.07 % Allowed : 15.19 % Favored : 82.73 % 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: -1.48 (0.20), residues: 1783 helix: 0.47 (0.21), residues: 611 sheet: -1.38 (0.27), residues: 366 loop : -1.93 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 227 TYR 0.014 0.001 TYR E 246 PHE 0.010 0.001 PHE A 65 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 0.00325 / 0.15 (16185) covalent geometry : angle 0.60431 / 0.33 (22259) hydrogen bonds : bond 0.04469 / 3.20 ( 636) hydrogen bonds : angle 5.04909 / 3.61 ( 1814) metal coordination : bond 0.01565 / 1.05 ( 8) metal coordination : angle 4.18712 / 3.06 ( 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 144 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.2692 (t80) REVERT: A 220 GLU cc_start: 0.7570 (pm20) cc_final: 0.7040 (tp30) REVERT: E 229 GLU cc_start: 0.7472 (pm20) cc_final: 0.7009 (pp20) REVERT: G 250 LYS cc_start: 0.6002 (tmtt) cc_final: 0.5777 (ttpt) outliers start: 31 outliers final: 18 residues processed: 140 average time/residue: 0.1128 time to fit residues: 24.2947 Evaluate side-chains 125 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 80 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 140 ILE 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 219 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 147 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 172 optimal weight: 0.0870 chunk 87 optimal weight: 0.0170 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.223960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.186509 restraints weight = 28874.987| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 3.74 r_work: 0.4044 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16193 Z= 0.170 Angle : 0.616 9.630 22263 Z= 0.333 Chirality : 0.045 0.160 2450 Planarity : 0.005 0.055 2577 Dihedral : 18.766 132.368 2776 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.34 % Allowed : 16.00 % Favored : 81.66 % 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: -1.49 (0.20), residues: 1783 helix: 0.48 (0.20), residues: 611 sheet: -1.43 (0.27), residues: 366 loop : -1.92 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.014 0.001 TYR E 246 PHE 0.011 0.001 PHE G 65 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 0.00372 / 0.17 (16185) covalent geometry : angle 0.61367 / 0.33 (22259) hydrogen bonds : bond 0.04468 / 3.22 ( 636) hydrogen bonds : angle 5.02812 / 3.61 ( 1814) metal coordination : bond 0.01712 / 1.15 ( 8) metal coordination : angle 4.28269 / 3.03 ( 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 148 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 PHE cc_start: 0.5578 (OUTLIER) cc_final: 0.2452 (t80) REVERT: A 220 GLU cc_start: 0.7562 (pm20) cc_final: 0.7143 (tp30) REVERT: D 81 VAL cc_start: 0.0836 (OUTLIER) cc_final: 0.0566 (t) REVERT: E 229 GLU cc_start: 0.7693 (pm20) cc_final: 0.7101 (pp20) REVERT: G 185 GLN cc_start: 0.3339 (OUTLIER) cc_final: -0.1834 (pp30) REVERT: G 250 LYS cc_start: 0.5983 (tmtt) cc_final: 0.5756 (ttpt) outliers start: 35 outliers final: 21 residues processed: 142 average time/residue: 0.1041 time to fit residues: 23.3061 Evaluate side-chains 129 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 167 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 255 ASP Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 140 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 130 optimal weight: 0.0870 chunk 86 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 160 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 153 GLN E 122 ASN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.226385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.189199 restraints weight = 28909.292| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 3.65 r_work: 0.4086 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16193 Z= 0.121 Angle : 0.578 8.463 22263 Z= 0.313 Chirality : 0.044 0.156 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.692 134.755 2776 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.07 % Allowed : 16.27 % Favored : 81.66 % 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: -1.29 (0.20), residues: 1783 helix: 0.69 (0.21), residues: 609 sheet: -1.27 (0.26), residues: 377 loop : -1.87 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 227 TYR 0.008 0.001 TYR E 246 PHE 0.006 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 0.00251 / 0.12 (16185) covalent geometry : angle 0.57565 / 0.31 (22259) hydrogen bonds : bond 0.04122 / 2.99 ( 636) hydrogen bonds : angle 4.88474 / 3.50 ( 1814) metal coordination : bond 0.01598 / 1.07 ( 8) metal coordination : angle 4.03539 / 2.86 ( 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 147 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7357 (mp) REVERT: B 242 TRP cc_start: 0.8351 (m100) cc_final: 0.8145 (m100) REVERT: D 81 VAL cc_start: 0.0843 (OUTLIER) cc_final: 0.0583 (t) REVERT: E 229 GLU cc_start: 0.7545 (pm20) cc_final: 0.7011 (pp20) REVERT: F 264 LYS cc_start: 0.7450 (tptt) cc_final: 0.6919 (mmtp) REVERT: G 185 GLN cc_start: 0.3472 (OUTLIER) cc_final: -0.1881 (pp30) REVERT: G 250 LYS cc_start: 0.5952 (tmtt) cc_final: 0.5712 (ttpt) outliers start: 31 outliers final: 20 residues processed: 143 average time/residue: 0.1145 time to fit residues: 25.3724 Evaluate side-chains 133 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS 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 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 D residue 81 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 41 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** 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 = 0.4873 r_free = 0.4873 target = 0.226214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.187798 restraints weight = 29148.895| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 3.73 r_work: 0.4065 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2488 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= 0.123 Angle : 0.574 8.003 22263 Z= 0.310 Chirality : 0.044 0.162 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.689 132.982 2776 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.07 % Allowed : 16.40 % Favored : 81.53 % 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: -1.15 (0.20), residues: 1783 helix: 0.81 (0.21), residues: 610 sheet: -1.19 (0.27), residues: 377 loop : -1.79 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 263 TYR 0.007 0.001 TYR B 246 PHE 0.007 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 0.00263 / 0.12 (16185) covalent geometry : angle 0.57209 / 0.31 (22259) hydrogen bonds : bond 0.04006 / 2.90 ( 636) hydrogen bonds : angle 4.76774 / 3.42 ( 1814) metal coordination : bond 0.01499 / 1.01 ( 8) metal coordination : angle 3.79757 / 2.56 ( 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 148 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7740 (mmp-170) cc_final: 0.7491 (mmm160) REVERT: A 220 GLU cc_start: 0.7468 (pm20) cc_final: 0.6811 (tp30) REVERT: B 77 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7375 (mp) REVERT: B 179 ARG cc_start: 0.6761 (tmt170) cc_final: 0.6246 (tmt170) REVERT: D 81 VAL cc_start: 0.0928 (OUTLIER) cc_final: 0.0679 (t) REVERT: G 250 LYS cc_start: 0.5962 (tmtt) cc_final: 0.5712 (ttpt) outliers start: 31 outliers final: 25 residues processed: 143 average time/residue: 0.1175 time to fit residues: 25.4421 Evaluate side-chains 139 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS 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 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 260 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 140 ILE 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 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 96 VAL 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: 9.9990 chunk 130 optimal weight: 0.0970 chunk 72 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** E 122 ASN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.226290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.188297 restraints weight = 29094.959| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 3.74 r_work: 0.4078 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16193 Z= 0.124 Angle : 0.572 7.823 22263 Z= 0.309 Chirality : 0.044 0.181 2450 Planarity : 0.005 0.066 2577 Dihedral : 18.677 133.370 2776 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.28 % Allowed : 16.87 % Favored : 80.86 % 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: -1.08 (0.21), residues: 1783 helix: 0.86 (0.21), residues: 610 sheet: -1.09 (0.27), residues: 387 loop : -1.78 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG H 244 TYR 0.006 0.001 TYR E 246 PHE 0.007 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 0.00264 / 0.12 (16185) covalent geometry : angle 0.57030 / 0.31 (22259) hydrogen bonds : bond 0.03963 / 2.87 ( 636) hydrogen bonds : angle 4.73396 / 3.40 ( 1814) metal coordination : bond 0.01470 / 0.98 ( 8) metal coordination : angle 3.74061 / 2.51 ( 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 146 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7719 (mmp-170) cc_final: 0.7474 (mmm160) REVERT: A 220 GLU cc_start: 0.7493 (pm20) cc_final: 0.6900 (tp30) REVERT: B 77 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7343 (mp) REVERT: B 179 ARG cc_start: 0.6759 (tmt170) cc_final: 0.6267 (tmt170) REVERT: D 81 VAL cc_start: 0.0857 (OUTLIER) cc_final: 0.0605 (t) REVERT: E 71 MET cc_start: 0.7972 (mmt) cc_final: 0.7656 (mmt) REVERT: F 264 LYS cc_start: 0.7361 (tptt) cc_final: 0.6681 (mmtp) REVERT: G 185 GLN cc_start: 0.3621 (OUTLIER) cc_final: -0.1508 (pp30) REVERT: G 250 LYS cc_start: 0.6000 (tmtt) cc_final: 0.5751 (ttpt) outliers start: 34 outliers final: 25 residues processed: 141 average time/residue: 0.1109 time to fit residues: 23.8619 Evaluate side-chains 139 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS 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 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 E residue 80 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 140 ILE 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 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 81 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 96 optimal weight: 0.0030 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- 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** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** 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 = 0.226163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.187806 restraints weight = 29089.403| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 3.65 r_work: 0.4074 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 16193 Z= 0.177 Angle : 0.771 59.200 22263 Z= 0.446 Chirality : 0.046 0.609 2450 Planarity : 0.005 0.061 2577 Dihedral : 18.680 133.292 2776 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 2.07 % Allowed : 17.14 % Favored : 80.79 % 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: -1.08 (0.20), residues: 1783 helix: 0.86 (0.21), residues: 610 sheet: -1.08 (0.27), residues: 387 loop : -1.78 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 244 TYR 0.006 0.001 TYR E 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 0.00359 / 0.18 (16185) covalent geometry : angle 0.76916 / 0.45 (22259) hydrogen bonds : bond 0.03969 / 2.87 ( 636) hydrogen bonds : angle 4.74634 / 3.41 ( 1814) metal coordination : bond 0.01465 / 0.98 ( 8) metal coordination : angle 3.74481 / 2.51 ( 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 142 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.7723 (mmp-170) cc_final: 0.7483 (mmm160) REVERT: A 220 GLU cc_start: 0.7485 (pm20) cc_final: 0.6888 (tp30) REVERT: B 77 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7345 (mp) REVERT: B 179 ARG cc_start: 0.6768 (tmt170) cc_final: 0.6265 (tmt170) REVERT: D 81 VAL cc_start: 0.0904 (OUTLIER) cc_final: 0.0657 (t) REVERT: F 264 LYS cc_start: 0.7402 (tptt) cc_final: 0.6713 (mmtp) REVERT: G 185 GLN cc_start: 0.3802 (OUTLIER) cc_final: -0.1247 (pp30) REVERT: G 250 LYS cc_start: 0.6012 (tmtt) cc_final: 0.5758 (ttpt) outliers start: 31 outliers final: 27 residues processed: 138 average time/residue: 0.1125 time to fit residues: 23.6560 Evaluate side-chains 141 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS 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 191 LYS 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 E residue 80 THR Chi-restraints excluded: chain E residue 140 ILE 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 219 THR Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 81 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 18 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 160 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 85 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** 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 = 0.226149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.187739 restraints weight = 28776.764| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 3.59 r_work: 0.4076 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 16193 Z= 0.177 Angle : 0.771 59.200 22263 Z= 0.446 Chirality : 0.046 0.609 2450 Planarity : 0.005 0.061 2577 Dihedral : 18.680 133.292 2776 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % 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 : 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: -1.08 (0.20), residues: 1783 helix: 0.86 (0.21), residues: 610 sheet: -1.08 (0.27), residues: 387 loop : -1.78 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 244 TYR 0.006 0.001 TYR E 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 0.00359 / 0.18 (16185) covalent geometry : angle 0.76916 / 0.45 (22259) hydrogen bonds : bond 0.03969 / 2.87 ( 636) hydrogen bonds : angle 4.74634 / 3.41 ( 1814) metal coordination : bond 0.01465 / 0.98 ( 8) metal coordination : angle 3.74481 / 2.51 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.14 seconds wall clock time: 85 minutes 39.36 seconds (5139.36 seconds total)