Starting phenix.real_space_refine on Sat Jun 14 03:49:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ku7_23035/06_2025/7ku7_23035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ku7_23035/06_2025/7ku7_23035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ku7_23035/06_2025/7ku7_23035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ku7_23035/06_2025/7ku7_23035.map" model { file = "/net/cci-nas-00/data/ceres_data/7ku7_23035/06_2025/7ku7_23035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ku7_23035/06_2025/7ku7_23035.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.060 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 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15666 Number of models: 1 Model: "" Number of chains: 16 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZZX': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'ZZX': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 283 SG CYS A 37 63.203 103.901 50.908 1.00146.57 S ATOM 306 SG CYS A 40 64.442 100.194 51.131 1.00167.11 S ATOM 7403 SG CYS E 37 57.256 59.151 87.803 1.00157.49 S ATOM 7426 SG CYS E 40 60.025 61.807 87.401 1.00173.77 S Time building chain proxies: 11.46, per 1000 atoms: 0.73 Number of scatterers: 15666 At special positions: 0 Unit cell: (110, 172.7, 139.7, 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: 3.96 Conformation dependent library (CDL) restraints added in 1.9 seconds 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=" NE2 HIS E 9 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " Number of angles added : 3 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: 56 helices and 17 sheets defined 37.8% alpha, 18.3% beta 24 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 5.24 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 removed outlier: 3.526A pdb=" N ALA A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.683A 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 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'B' and resid 97 through 113 removed outlier: 4.166A pdb=" N TRP B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 107 " --> pdb=" O HIS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 Processing helix chain 'B' and resid 154 through 174 removed outlier: 4.657A pdb=" N ARG B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) 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: 3.534A 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 'C' and resid 69 through 72 removed outlier: 3.818A 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 removed outlier: 3.566A pdb=" N HIS C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 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 removed outlier: 3.806A pdb=" N ASN E 41 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.805A pdb=" N ALA E 106 " --> pdb=" O GLN E 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 107 " --> pdb=" O HIS E 103 " (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 198 Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'F' and resid 69 through 72 removed outlier: 3.652A 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: 3.890A 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 155 through 174 removed outlier: 3.597A pdb=" N ARG F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 199 removed outlier: 3.651A pdb=" N PHE F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 97 through 113 removed outlier: 3.676A pdb=" N VAL G 101 " --> pdb=" O THR G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 128 through 139 Processing helix chain 'G' and resid 155 through 175 Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'H' and resid 68 through 72 removed outlier: 3.506A pdb=" N ALA H 72 " --> pdb=" O PRO H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 113 removed outlier: 3.775A pdb=" N ALA H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 138 Processing helix chain 'H' and resid 149 through 175 removed outlier: 3.913A pdb=" N ALA H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 removed outlier: 4.601A pdb=" N GLY H 186 " --> pdb=" O THR H 182 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 212 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 92 removed outlier: 6.052A pdb=" N TRP A 61 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 118 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 6.454A pdb=" N TYR A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP A 242 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA A 248 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 236 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 224 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 93 removed outlier: 3.586A pdb=" N ASP B 64 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TRP B 61 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.890A pdb=" N TYR B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP B 242 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 248 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS B 235 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 226 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 88 through 92 removed outlier: 3.608A pdb=" N ALA C 78 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 66 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP C 61 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AA7, first strand: chain 'C' and resid 237 through 242 removed outlier: 7.055A pdb=" N ALA C 248 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TRP C 242 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR C 246 " --> pdb=" O TRP C 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 90 removed outlier: 3.524A pdb=" N VAL D 89 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 80 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TRP D 61 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP D 121 " --> pdb=" O TRP D 61 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR D 63 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 118 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR D 143 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR D 120 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 145 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 257 through 261 Processing sheet with id=AB1, first strand: chain 'E' and resid 88 through 93 removed outlier: 6.122A pdb=" N TRP E 61 " --> pdb=" O LYS E 119 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 143 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 257 through 261 removed outlier: 6.415A pdb=" N TYR E 246 " --> pdb=" O TRP E 242 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP E 242 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA E 248 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY E 236 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 224 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 88 through 93 Processing sheet with id=AB4, first strand: chain 'F' and resid 257 through 261 removed outlier: 6.685A pdb=" N ALA F 248 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS F 235 " --> pdb=" O ILE F 226 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE F 226 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP F 237 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 88 through 90 removed outlier: 3.963A pdb=" N ASP G 64 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 119 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 63 " --> pdb=" O LYS G 119 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE G 118 " --> pdb=" O THR G 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 257 through 261 removed outlier: 6.750A pdb=" N TYR G 246 " --> pdb=" O TRP G 242 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP G 242 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA G 248 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS G 235 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE G 226 " --> pdb=" O LYS G 235 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP G 237 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 88 through 89 removed outlier: 6.337A pdb=" N TRP H 61 " --> pdb=" O LYS H 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 257 through 260 removed outlier: 6.402A pdb=" N LYS H 250 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL H 239 " --> pdb=" O LYS H 250 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY H 236 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 224 " --> pdb=" O GLY H 236 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4577 1.34 - 1.46: 3351 1.46 - 1.58: 8043 1.58 - 1.70: 130 1.70 - 1.82: 84 Bond restraints: 16185 Sorted by residual: bond pdb=" CBC ZZX L 401 " pdb=" NBF ZZX L 401 " ideal model delta sigma weight residual 1.468 1.651 -0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" CAO ZZX L 401 " pdb=" CBC ZZX L 401 " ideal model delta sigma weight residual 1.521 1.345 0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" CAO ZZX J 401 " pdb=" CBC ZZX J 401 " ideal model delta sigma weight residual 1.521 1.351 0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" CBC ZZX J 401 " pdb=" NBF ZZX J 401 " ideal model delta sigma weight residual 1.468 1.630 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " ideal model delta sigma weight residual 1.461 1.325 0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 16180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.66: 22249 9.66 - 19.32: 4 19.32 - 28.97: 0 28.97 - 38.63: 4 38.63 - 48.29: 2 Bond angle restraints: 22259 Sorted by residual: angle pdb=" CBC ZZX J 401 " pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " ideal model delta sigma weight residual 112.49 160.78 -48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" CBC ZZX L 401 " pdb=" CAO ZZX L 401 " pdb=" NBD ZZX L 401 " ideal model delta sigma weight residual 112.49 159.79 -47.30 3.00e+00 1.11e-01 2.49e+02 angle pdb=" CAO ZZX L 401 " pdb=" CBC ZZX L 401 " pdb=" NBF ZZX L 401 " ideal model delta sigma weight residual 106.81 70.95 35.86 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " pdb=" CAS ZZX J 401 " ideal model delta sigma weight residual 121.21 85.53 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CAO ZZX L 401 " pdb=" NBD ZZX L 401 " pdb=" CAS ZZX L 401 " ideal model delta sigma weight residual 121.21 85.85 35.36 3.00e+00 1.11e-01 1.39e+02 ... (remaining 22254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 8826 29.84 - 59.68: 660 59.68 - 89.52: 35 89.52 - 119.36: 1 119.36 - 149.20: 9 Dihedral angle restraints: 9531 sinusoidal: 4396 harmonic: 5135 Sorted by residual: dihedral pdb=" CA ALA E 43 " pdb=" C ALA E 43 " pdb=" N PRO E 44 " pdb=" CA PRO E 44 " ideal model delta harmonic sigma weight residual -180.00 -145.48 -34.52 0 5.00e+00 4.00e-02 4.77e+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 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CAM ZZX J 401 " pdb=" CAO ZZX J 401 " pdb=" NBD ZZX J 401 " pdb=" CBC ZZX J 401 " ideal model delta sinusoidal sigma weight residual 146.26 -2.94 149.20 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 9528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2177 0.071 - 0.143: 268 0.143 - 0.214: 3 0.214 - 0.286: 0 0.286 - 0.357: 2 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CBC ZZX L 401 " pdb=" CAC ZZX L 401 " pdb=" CAO ZZX L 401 " pdb=" NBF ZZX L 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.87 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CBC ZZX J 401 " pdb=" CAC ZZX J 401 " pdb=" CAO ZZX J 401 " pdb=" NBF ZZX J 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.87 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB ILE G 226 " pdb=" CA ILE G 226 " pdb=" CG1 ILE G 226 " pdb=" CG2 ILE G 226 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 2447 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAS ZZX L 401 " -0.016 2.00e-02 2.50e+03 3.02e-02 2.29e+01 pdb=" CAW ZZX L 401 " 0.000 2.00e-02 2.50e+03 pdb=" CAX ZZX L 401 " -0.063 2.00e-02 2.50e+03 pdb=" CAY ZZX L 401 " -0.008 2.00e-02 2.50e+03 pdb=" CAZ ZZX L 401 " 0.010 2.00e-02 2.50e+03 pdb=" CBA ZZX L 401 " 0.008 2.00e-02 2.50e+03 pdb=" CBB ZZX L 401 " 0.067 2.00e-02 2.50e+03 pdb=" CBC ZZX L 401 " 0.011 2.00e-02 2.50e+03 pdb=" NBF ZZX L 401 " 0.000 2.00e-02 2.50e+03 pdb=" OAG ZZX L 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAS ZZX J 401 " -0.007 2.00e-02 2.50e+03 2.24e-02 1.26e+01 pdb=" CAW ZZX J 401 " -0.000 2.00e-02 2.50e+03 pdb=" CAX ZZX J 401 " -0.046 2.00e-02 2.50e+03 pdb=" CAY ZZX J 401 " -0.004 2.00e-02 2.50e+03 pdb=" CAZ ZZX J 401 " 0.009 2.00e-02 2.50e+03 pdb=" CBA ZZX J 401 " 0.006 2.00e-02 2.50e+03 pdb=" CBB ZZX J 401 " 0.051 2.00e-02 2.50e+03 pdb=" CBC ZZX J 401 " 0.005 2.00e-02 2.50e+03 pdb=" NBF ZZX J 401 " -0.001 2.00e-02 2.50e+03 pdb=" OAG ZZX J 401 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB ZZX J 401 " 0.028 2.00e-02 2.50e+03 3.03e-02 1.15e+01 pdb=" CAR ZZX J 401 " -0.040 2.00e-02 2.50e+03 pdb=" CAX ZZX J 401 " 0.006 2.00e-02 2.50e+03 pdb=" NAQ ZZX J 401 " -0.030 2.00e-02 2.50e+03 pdb=" OAD ZZX J 401 " 0.036 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 168 2.51 - 3.11: 11773 3.11 - 3.70: 26701 3.70 - 4.30: 35533 4.30 - 4.90: 56283 Nonbonded interactions: 130458 Sorted by model distance: nonbonded pdb="MG MG A 302 " pdb=" OAG ZZX J 401 " model vdw 1.912 2.170 nonbonded pdb=" OE2 GLU A 157 " pdb="MG MG A 302 " model vdw 1.916 2.170 nonbonded pdb="MG MG A 302 " pdb=" OAF ZZX J 401 " model vdw 1.918 2.170 nonbonded pdb=" CAO ZZX L 401 " pdb=" CAY ZZX L 401 " model vdw 1.934 2.792 nonbonded pdb="MG MG E 303 " pdb=" OAG ZZX L 401 " model vdw 1.934 2.170 ... (remaining 130453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'C' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'D' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'F' and (resid 57 through 212 or resid 221 through 269)) selection = (chain 'G' and resid 57 through 269) selection = (chain 'H' and resid 57 through 269) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.890 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 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 0.183 16193 Z= 0.260 Angle : 0.974 48.291 22262 Z= 0.423 Chirality : 0.045 0.357 2450 Planarity : 0.005 0.058 2577 Dihedral : 18.717 149.197 6207 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 2.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1783 helix: 0.33 (0.21), residues: 610 sheet: -1.22 (0.25), residues: 395 loop : -1.82 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 134 HIS 0.007 0.001 HIS D 93 PHE 0.011 0.001 PHE B 126 TYR 0.030 0.002 TYR A 246 ARG 0.007 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.22562 ( 664) hydrogen bonds : angle 7.71108 ( 1884) metal coordination : bond 0.00796 ( 8) metal coordination : angle 4.15780 ( 3) covalent geometry : bond 0.00540 (16185) covalent geometry : angle 0.97274 (22259) *********************** 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 343 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.8096 (mm) cc_final: 0.7786 (mm) REVERT: A 76 TRP cc_start: 0.7251 (m100) cc_final: 0.6760 (m100) REVERT: A 134 TRP cc_start: 0.6850 (t60) cc_final: 0.6574 (t60) REVERT: A 209 ILE cc_start: 0.7309 (mm) cc_final: 0.6396 (mm) REVERT: B 61 TRP cc_start: 0.6686 (m-10) cc_final: 0.6182 (m-10) REVERT: B 91 THR cc_start: 0.5980 (p) cc_final: 0.5639 (p) REVERT: B 126 PHE cc_start: 0.6552 (m-80) cc_final: 0.5338 (m-10) REVERT: B 176 PHE cc_start: 0.8181 (m-80) cc_final: 0.7141 (m-80) REVERT: C 81 VAL cc_start: 0.4182 (t) cc_final: 0.3561 (p) REVERT: C 83 THR cc_start: -0.0713 (m) cc_final: -0.1049 (p) REVERT: C 244 ARG cc_start: 0.6270 (mtp180) cc_final: 0.5834 (tpp80) REVERT: D 71 MET cc_start: -0.0945 (mmt) cc_final: -0.1317 (mmt) REVERT: E 91 THR cc_start: 0.7681 (m) cc_final: 0.7412 (p) REVERT: E 199 PHE cc_start: 0.6773 (m-80) cc_final: 0.5818 (m-80) REVERT: E 238 ASN cc_start: 0.7142 (m-40) cc_final: 0.6584 (m110) REVERT: F 76 TRP cc_start: 0.7975 (m100) cc_final: 0.7662 (m100) REVERT: F 131 THR cc_start: 0.8467 (m) cc_final: 0.8183 (p) REVERT: F 176 PHE cc_start: 0.6800 (m-10) cc_final: 0.6395 (m-80) REVERT: G 71 MET cc_start: -0.2635 (ttt) cc_final: -0.2887 (mtt) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3421 time to fit residues: 162.6174 Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 93 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 165 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS B 92 GLN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.165987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.120207 restraints weight = 46176.911| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 6.74 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16193 Z= 0.173 Angle : 0.694 12.208 22262 Z= 0.364 Chirality : 0.047 0.170 2450 Planarity : 0.006 0.060 2577 Dihedral : 18.721 118.697 2776 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.81 % Allowed : 12.45 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1783 helix: 0.36 (0.20), residues: 632 sheet: -1.16 (0.24), residues: 401 loop : -1.66 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 134 HIS 0.007 0.001 HIS B 198 PHE 0.011 0.001 PHE B 176 TYR 0.025 0.003 TYR D 246 ARG 0.005 0.001 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.05858 ( 664) hydrogen bonds : angle 5.91888 ( 1884) metal coordination : bond 0.01802 ( 8) metal coordination : angle 7.49329 ( 3) covalent geometry : bond 0.00375 (16185) covalent geometry : angle 0.68832 (22259) *********************** 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 212 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6642 (m-70) REVERT: A 135 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 193 MET cc_start: 0.7906 (ttm) cc_final: 0.7520 (ttm) REVERT: B 61 TRP cc_start: 0.6910 (m-10) cc_final: 0.6406 (m-10) REVERT: B 176 PHE cc_start: 0.8389 (m-80) cc_final: 0.7839 (m-80) REVERT: B 232 GLU cc_start: 0.7953 (pp20) cc_final: 0.7305 (mp0) REVERT: E 193 MET cc_start: 0.7196 (mmp) cc_final: 0.6709 (mtm) REVERT: F 174 ASP cc_start: 0.7750 (p0) cc_final: 0.7350 (t70) REVERT: F 238 ASN cc_start: 0.6828 (p0) cc_final: 0.6517 (p0) REVERT: H 246 TYR cc_start: 0.5871 (p90) cc_final: 0.5410 (p90) outliers start: 27 outliers final: 17 residues processed: 200 average time/residue: 0.3435 time to fit residues: 108.0854 Evaluate side-chains 168 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 268 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.166385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.120297 restraints weight = 46531.992| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 6.59 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16193 Z= 0.142 Angle : 0.620 8.415 22262 Z= 0.328 Chirality : 0.045 0.197 2450 Planarity : 0.005 0.062 2577 Dihedral : 18.488 114.618 2776 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.08 % Allowed : 15.33 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1783 helix: 0.62 (0.20), residues: 632 sheet: -0.77 (0.24), residues: 411 loop : -1.74 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 138 HIS 0.007 0.001 HIS E 198 PHE 0.012 0.001 PHE E 176 TYR 0.021 0.002 TYR D 246 ARG 0.005 0.000 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 664) hydrogen bonds : angle 5.25843 ( 1884) metal coordination : bond 0.01056 ( 8) metal coordination : angle 3.94609 ( 3) covalent geometry : bond 0.00303 (16185) covalent geometry : angle 0.61870 (22259) *********************** 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 216 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 188 LEU cc_start: 0.8053 (mm) cc_final: 0.7804 (mp) REVERT: B 176 PHE cc_start: 0.8353 (m-80) cc_final: 0.7783 (m-80) REVERT: D 71 MET cc_start: -0.0093 (ttp) cc_final: -0.4360 (mmt) REVERT: D 177 MET cc_start: 0.2885 (mmp) cc_final: 0.2453 (tpp) REVERT: E 32 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: E 200 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: F 238 ASN cc_start: 0.7020 (p0) cc_final: 0.6745 (p0) REVERT: H 92 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: H 246 TYR cc_start: 0.5472 (p90) cc_final: 0.5183 (p90) outliers start: 46 outliers final: 21 residues processed: 202 average time/residue: 0.4059 time to fit residues: 126.5197 Evaluate side-chains 184 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 19 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 94 optimal weight: 0.0470 chunk 147 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 210 GLN B 122 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 204 ASN C 62 GLN C 197 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 93 HIS E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.164764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.106577 restraints weight = 47074.238| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 6.46 r_work: 0.3544 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16193 Z= 0.182 Angle : 0.655 10.516 22262 Z= 0.348 Chirality : 0.045 0.252 2450 Planarity : 0.005 0.053 2577 Dihedral : 18.500 110.147 2776 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.55 % Allowed : 16.93 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1783 helix: 0.87 (0.20), residues: 628 sheet: -0.74 (0.25), residues: 397 loop : -1.70 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 242 HIS 0.008 0.002 HIS E 198 PHE 0.010 0.001 PHE B 126 TYR 0.023 0.002 TYR H 246 ARG 0.013 0.001 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 664) hydrogen bonds : angle 5.10826 ( 1884) metal coordination : bond 0.01432 ( 8) metal coordination : angle 6.09565 ( 3) covalent geometry : bond 0.00397 (16185) covalent geometry : angle 0.65166 (22259) *********************** 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 224 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.9011 (m) cc_final: 0.8761 (p) REVERT: A 41 ASN cc_start: 0.8054 (t0) cc_final: 0.7769 (t0) REVERT: A 193 MET cc_start: 0.8690 (ttm) cc_final: 0.8484 (ttm) REVERT: B 163 LEU cc_start: 0.9151 (tp) cc_final: 0.8876 (tt) REVERT: B 176 PHE cc_start: 0.8068 (m-80) cc_final: 0.7596 (m-80) REVERT: E 27 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6706 (mtt) REVERT: E 32 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: E 35 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: E 146 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6352 (mt) REVERT: E 189 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8758 (mt) REVERT: E 200 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: F 232 GLU cc_start: 0.7513 (mp0) cc_final: 0.7136 (mp0) REVERT: F 238 ASN cc_start: 0.7168 (p0) cc_final: 0.6869 (p0) outliers start: 68 outliers final: 38 residues processed: 206 average time/residue: 0.2498 time to fit residues: 79.0953 Evaluate side-chains 179 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 169 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 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 = 0.4571 r_free = 0.4571 target = 0.165067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.125064 restraints weight = 47280.259| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 5.66 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16193 Z= 0.134 Angle : 0.583 8.230 22262 Z= 0.310 Chirality : 0.043 0.169 2450 Planarity : 0.005 0.058 2577 Dihedral : 18.475 109.645 2776 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.21 % Allowed : 19.01 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1783 helix: 1.10 (0.20), residues: 627 sheet: -0.66 (0.24), residues: 400 loop : -1.59 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 259 HIS 0.006 0.001 HIS E 212 PHE 0.010 0.001 PHE B 65 TYR 0.016 0.002 TYR D 246 ARG 0.008 0.000 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 664) hydrogen bonds : angle 4.87343 ( 1884) metal coordination : bond 0.01033 ( 8) metal coordination : angle 4.51453 ( 3) covalent geometry : bond 0.00297 (16185) covalent geometry : angle 0.58099 (22259) *********************** 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 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.8626 (m) cc_final: 0.8392 (t) REVERT: A 41 ASN cc_start: 0.8047 (t0) cc_final: 0.6976 (t0) REVERT: A 62 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: B 163 LEU cc_start: 0.9084 (tp) cc_final: 0.8851 (tt) REVERT: B 176 PHE cc_start: 0.8162 (m-80) cc_final: 0.7728 (m-80) REVERT: C 193 MET cc_start: 0.3543 (mtt) cc_final: 0.3264 (mtm) REVERT: C 227 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7799 (ttm110) REVERT: D 71 MET cc_start: -0.2926 (ttt) cc_final: -0.5786 (mmt) REVERT: D 244 ARG cc_start: 0.4173 (mmp-170) cc_final: 0.2678 (mmm160) REVERT: E 32 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: E 200 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: F 232 GLU cc_start: 0.7319 (mp0) cc_final: 0.7061 (mp0) REVERT: F 252 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7399 (mtm-85) outliers start: 48 outliers final: 32 residues processed: 178 average time/residue: 0.2671 time to fit residues: 72.3402 Evaluate side-chains 171 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 143 optimal weight: 0.1980 chunk 89 optimal weight: 30.0000 chunk 164 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 210 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** 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 = 0.4581 r_free = 0.4581 target = 0.165513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.123112 restraints weight = 47007.599| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 6.09 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16193 Z= 0.118 Angle : 0.576 8.883 22262 Z= 0.301 Chirality : 0.043 0.171 2450 Planarity : 0.005 0.054 2577 Dihedral : 18.376 108.241 2776 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.48 % Allowed : 19.41 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1783 helix: 1.31 (0.21), residues: 627 sheet: -0.42 (0.24), residues: 414 loop : -1.56 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 259 HIS 0.004 0.001 HIS E 198 PHE 0.009 0.001 PHE B 65 TYR 0.015 0.001 TYR D 246 ARG 0.004 0.000 ARG C 244 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 664) hydrogen bonds : angle 4.82703 ( 1884) metal coordination : bond 0.01013 ( 8) metal coordination : angle 4.13036 ( 3) covalent geometry : bond 0.00257 (16185) covalent geometry : angle 0.57433 (22259) *********************** 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 198 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 THR cc_start: 0.8466 (m) cc_final: 0.8240 (t) REVERT: B 163 LEU cc_start: 0.9114 (tp) cc_final: 0.8887 (tt) REVERT: B 176 PHE cc_start: 0.8255 (m-80) cc_final: 0.7673 (m-80) REVERT: D 71 MET cc_start: -0.2917 (ttt) cc_final: -0.5698 (mmt) REVERT: D 244 ARG cc_start: 0.4071 (mmp-170) cc_final: 0.1307 (mmt-90) REVERT: E 32 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: F 156 VAL cc_start: 0.7034 (OUTLIER) cc_final: 0.6662 (p) REVERT: F 232 GLU cc_start: 0.7346 (mp0) cc_final: 0.7090 (mp0) REVERT: H 242 TRP cc_start: 0.4726 (t60) cc_final: 0.4331 (t60) outliers start: 52 outliers final: 34 residues processed: 185 average time/residue: 0.2405 time to fit residues: 68.7935 Evaluate side-chains 172 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 181 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.163748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.121454 restraints weight = 46621.231| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 5.41 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16193 Z= 0.147 Angle : 0.598 9.526 22262 Z= 0.314 Chirality : 0.043 0.230 2450 Planarity : 0.005 0.056 2577 Dihedral : 18.368 107.721 2776 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.21 % Allowed : 19.81 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1783 helix: 1.32 (0.21), residues: 627 sheet: -0.43 (0.24), residues: 406 loop : -1.54 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 259 HIS 0.005 0.001 HIS E 198 PHE 0.010 0.001 PHE B 65 TYR 0.014 0.001 TYR H 246 ARG 0.010 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 664) hydrogen bonds : angle 4.89178 ( 1884) metal coordination : bond 0.01743 ( 8) metal coordination : angle 4.85263 ( 3) covalent geometry : bond 0.00328 (16185) covalent geometry : angle 0.59542 (22259) *********************** 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 186 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: B 163 LEU cc_start: 0.9150 (tp) cc_final: 0.8903 (tt) REVERT: B 176 PHE cc_start: 0.8197 (m-80) cc_final: 0.7598 (m-80) REVERT: C 193 MET cc_start: 0.3743 (mtt) cc_final: 0.3431 (mtm) REVERT: D 71 MET cc_start: -0.3611 (ttt) cc_final: -0.5993 (mmt) REVERT: D 244 ARG cc_start: 0.4093 (mmp-170) cc_final: 0.2773 (mmm160) REVERT: E 32 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: F 232 GLU cc_start: 0.7216 (mp0) cc_final: 0.6914 (mp0) REVERT: G 71 MET cc_start: -0.4889 (ttp) cc_final: -0.5173 (mtt) REVERT: H 242 TRP cc_start: 0.5472 (t60) cc_final: 0.4771 (t60) outliers start: 48 outliers final: 38 residues processed: 171 average time/residue: 0.2798 time to fit residues: 73.2350 Evaluate side-chains 168 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain F residue 105 TRP Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 268 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 0.0050 chunk 35 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.161596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.106177 restraints weight = 46062.667| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 6.99 r_work: 0.3460 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16193 Z= 0.177 Angle : 0.623 11.401 22262 Z= 0.328 Chirality : 0.044 0.212 2450 Planarity : 0.005 0.057 2577 Dihedral : 18.414 110.038 2776 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.35 % Allowed : 19.95 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1783 helix: 1.19 (0.21), residues: 634 sheet: -0.43 (0.24), residues: 406 loop : -1.54 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 259 HIS 0.007 0.001 HIS E 198 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.002 TYR D 246 ARG 0.008 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 664) hydrogen bonds : angle 4.89244 ( 1884) metal coordination : bond 0.01708 ( 8) metal coordination : angle 6.42780 ( 3) covalent geometry : bond 0.00405 (16185) covalent geometry : angle 0.61865 (22259) *********************** 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 185 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9266 (mmpt) cc_final: 0.8853 (mptt) REVERT: A 62 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: A 155 MET cc_start: 0.8587 (mtt) cc_final: 0.8050 (mtt) REVERT: B 163 LEU cc_start: 0.9263 (tp) cc_final: 0.8978 (tt) REVERT: B 176 PHE cc_start: 0.8332 (m-80) cc_final: 0.7681 (m-80) REVERT: C 260 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7804 (m) REVERT: D 71 MET cc_start: -0.1556 (ttt) cc_final: -0.3971 (mmt) REVERT: D 244 ARG cc_start: 0.4862 (mmp-170) cc_final: 0.3245 (mmm160) REVERT: E 3 ARG cc_start: 0.7224 (ptm-80) cc_final: 0.6684 (tpt90) REVERT: E 32 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: E 187 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8188 (tm-30) REVERT: F 187 GLU cc_start: 0.7855 (mp0) cc_final: 0.7618 (mp0) REVERT: F 232 GLU cc_start: 0.7877 (mp0) cc_final: 0.7563 (mp0) REVERT: G 71 MET cc_start: -0.2755 (ttp) cc_final: -0.3216 (mtt) outliers start: 50 outliers final: 34 residues processed: 171 average time/residue: 0.2669 time to fit residues: 69.5177 Evaluate side-chains 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 105 TRP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain F residue 105 TRP Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN E 212 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 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 = 0.4542 r_free = 0.4542 target = 0.162254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.097673 restraints weight = 46717.129| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 5.43 r_work: 0.3487 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16193 Z= 0.136 Angle : 0.601 9.462 22262 Z= 0.315 Chirality : 0.043 0.153 2450 Planarity : 0.005 0.056 2577 Dihedral : 18.270 109.868 2776 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.54 % Allowed : 21.15 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1783 helix: 1.26 (0.21), residues: 634 sheet: -0.32 (0.24), residues: 404 loop : -1.49 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP C 259 HIS 0.005 0.001 HIS E 212 PHE 0.008 0.001 PHE B 199 TYR 0.013 0.002 TYR D 246 ARG 0.011 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 664) hydrogen bonds : angle 4.87941 ( 1884) metal coordination : bond 0.01331 ( 8) metal coordination : angle 5.83922 ( 3) covalent geometry : bond 0.00305 (16185) covalent geometry : angle 0.59727 (22259) *********************** 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 165 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9195 (mmpt) cc_final: 0.8840 (mptt) REVERT: B 71 MET cc_start: 0.7268 (pmm) cc_final: 0.7054 (pmm) REVERT: B 163 LEU cc_start: 0.9271 (tp) cc_final: 0.8975 (tt) REVERT: B 176 PHE cc_start: 0.7849 (m-80) cc_final: 0.7486 (m-80) REVERT: C 260 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (m) REVERT: D 71 MET cc_start: -0.0738 (ttt) cc_final: -0.2724 (mmt) REVERT: D 244 ARG cc_start: 0.4252 (mmp-170) cc_final: 0.3140 (mmm160) REVERT: E 32 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: E 187 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8065 (tm-30) REVERT: E 210 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8004 (pp30) REVERT: F 187 GLU cc_start: 0.7772 (mp0) cc_final: 0.7499 (mp0) REVERT: F 232 GLU cc_start: 0.7730 (mp0) cc_final: 0.7493 (mp0) REVERT: F 246 TYR cc_start: 0.8632 (m-80) cc_final: 0.8202 (m-80) REVERT: G 71 MET cc_start: -0.1407 (ttp) cc_final: -0.1621 (mtp) outliers start: 38 outliers final: 28 residues processed: 156 average time/residue: 0.2761 time to fit residues: 64.9375 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 : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 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 = 0.4552 r_free = 0.4552 target = 0.163202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.118152 restraints weight = 45974.816| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 6.51 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.7627 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= 0.125 Angle : 0.604 10.403 22262 Z= 0.316 Chirality : 0.042 0.146 2450 Planarity : 0.005 0.058 2577 Dihedral : 18.165 108.992 2776 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.21 % Allowed : 21.69 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1783 helix: 1.26 (0.21), residues: 634 sheet: -0.23 (0.25), residues: 404 loop : -1.46 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 259 HIS 0.004 0.001 HIS E 198 PHE 0.007 0.001 PHE E 176 TYR 0.016 0.002 TYR C 246 ARG 0.011 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 664) hydrogen bonds : angle 4.83245 ( 1884) metal coordination : bond 0.01041 ( 8) metal coordination : angle 5.27895 ( 3) covalent geometry : bond 0.00281 (16185) covalent geometry : angle 0.60088 (22259) ********************** 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 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8524 (mmp) cc_final: 0.8189 (tpp) REVERT: B 163 LEU cc_start: 0.9159 (tp) cc_final: 0.8890 (tt) REVERT: B 176 PHE cc_start: 0.8422 (m-80) cc_final: 0.7888 (m-80) REVERT: D 71 MET cc_start: -0.3673 (ttt) cc_final: -0.5351 (mmt) REVERT: D 244 ARG cc_start: 0.4401 (mmp-170) cc_final: 0.3571 (mmp-170) REVERT: E 32 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: E 187 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 210 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: F 232 GLU cc_start: 0.7553 (mp0) cc_final: 0.7268 (mp0) REVERT: F 246 TYR cc_start: 0.8453 (m-80) cc_final: 0.7999 (m-80) REVERT: G 71 MET cc_start: -0.4282 (ttp) cc_final: -0.4565 (mtp) REVERT: H 172 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.4292 (tp30) outliers start: 33 outliers final: 25 residues processed: 149 average time/residue: 0.2588 time to fit residues: 59.4401 Evaluate side-chains 141 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 20 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.0040 chunk 139 optimal weight: 0.0770 chunk 134 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 overall best weight: 0.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 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 = 0.4562 r_free = 0.4562 target = 0.163976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102708 restraints weight = 45241.290| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 5.67 r_work: 0.3520 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.7725 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= 0.117 Angle : 0.605 13.383 22262 Z= 0.313 Chirality : 0.042 0.150 2450 Planarity : 0.005 0.058 2577 Dihedral : 18.077 107.306 2776 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.94 % Allowed : 22.22 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1783 helix: 1.26 (0.21), residues: 634 sheet: -0.14 (0.25), residues: 404 loop : -1.42 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 259 HIS 0.003 0.001 HIS G 103 PHE 0.007 0.001 PHE E 176 TYR 0.018 0.002 TYR C 246 ARG 0.010 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 664) hydrogen bonds : angle 4.80416 ( 1884) metal coordination : bond 0.01133 ( 8) metal coordination : angle 4.85575 ( 3) covalent geometry : bond 0.00259 (16185) covalent geometry : angle 0.60201 (22259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12366.62 seconds wall clock time: 214 minutes 2.89 seconds (12842.89 seconds total)