Starting phenix.real_space_refine on Fri Jul 3 09:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjb_65109/07_2026/9vjb_65109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjb_65109/07_2026/9vjb_65109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vjb_65109/07_2026/9vjb_65109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjb_65109/07_2026/9vjb_65109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vjb_65109/07_2026/9vjb_65109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjb_65109/07_2026/9vjb_65109.map" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 50 5.49 5 S 41 5.16 5 C 8289 2.51 5 N 2133 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13115 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1783 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 215} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1791 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1791 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1791 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "I" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2359 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain: "J" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2350 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "X" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "Y" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 525 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "N" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 219 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.94, per 1000 atoms: 0.22 Number of scatterers: 13115 At special positions: 0 Unit cell: (99.724, 115.568, 149.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 41 16.00 P 50 15.00 O 2596 8.00 N 2133 7.00 C 8289 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: 0.70 Conformation dependent library (CDL) restraints added in 528.9 milliseconds 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 16 sheets defined 48.5% alpha, 12.2% beta 25 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.580A pdb=" N LEU A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 113 removed outlier: 3.649A pdb=" N GLU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.131A pdb=" N TYR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.512A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 removed outlier: 4.200A pdb=" N GLU B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 72 through 90 removed outlier: 4.144A pdb=" N LYS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 114 removed outlier: 4.072A pdb=" N LYS C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.904A pdb=" N TYR C 172 " --> pdb=" O ALA C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.790A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 removed outlier: 3.578A pdb=" N LYS D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 174 through 189 Processing helix chain 'I' and resid 51 through 60 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 89 through 94 Processing helix chain 'I' and resid 98 through 123 Processing helix chain 'I' and resid 125 through 138 removed outlier: 3.623A pdb=" N ALA I 129 " --> pdb=" O TYR I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 161 Processing helix chain 'I' and resid 170 through 194 removed outlier: 3.600A pdb=" N ALA I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 217 Processing helix chain 'I' and resid 218 through 221 Processing helix chain 'I' and resid 222 through 230 removed outlier: 3.791A pdb=" N ASP I 226 " --> pdb=" O ARG I 222 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE I 228 " --> pdb=" O LEU I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 233 No H-bonds generated for 'chain 'I' and resid 231 through 233' Processing helix chain 'I' and resid 236 through 245 Processing helix chain 'I' and resid 260 through 277 Processing helix chain 'J' and resid 51 through 60 Processing helix chain 'J' and resid 86 through 95 Processing helix chain 'J' and resid 97 through 122 removed outlier: 3.754A pdb=" N GLN J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 4.338A pdb=" N ALA J 131 " --> pdb=" O GLN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 160 Processing helix chain 'J' and resid 170 through 194 removed outlier: 3.584A pdb=" N ALA J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 217 Processing helix chain 'J' and resid 218 through 220 No H-bonds generated for 'chain 'J' and resid 218 through 220' Processing helix chain 'J' and resid 221 through 232 removed outlier: 3.960A pdb=" N VAL J 225 " --> pdb=" O PHE J 221 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 245 Processing helix chain 'J' and resid 246 through 249 Processing helix chain 'J' and resid 260 through 277 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.932A pdb=" N VAL A 3 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 12 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.804A pdb=" N LEU A 164 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 195 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 166 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 18 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR A 206 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 19 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU A 208 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR A 21 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 217 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.552A pdb=" N LYS D 136 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.862A pdb=" N ILE B 12 " --> pdb=" O VAL B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.720A pdb=" N PHE B 60 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE B 167 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B 62 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 164 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU B 195 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 166 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 217 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 207 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 215 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.559A pdb=" N VAL C 3 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.349A pdb=" N LEU C 164 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU C 195 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE C 166 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 18 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 22 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ALA C 17 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N TYR C 206 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 19 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU C 208 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR C 21 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.692A pdb=" N LYS D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.949A pdb=" N PHE D 60 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE D 167 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL D 62 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 164 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU D 195 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE D 166 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE D 204 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D 19 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 4 through 7 removed outlier: 7.311A pdb=" N ARG I 4 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU I 40 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL I 6 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 63 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL I 64 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS I 76 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE I 66 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE J 66 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS J 76 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL J 64 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG J 4 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU J 41 " --> pdb=" O ARG J 4 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL J 6 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR J 5 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU N 106 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 7 " --> pdb=" O LEU N 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 29 through 33 removed outlier: 6.732A pdb=" N TYR I 16 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR J 16 " --> pdb=" O THR J 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 15 " --> pdb=" O VAL J 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 252 through 254 removed outlier: 3.558A pdb=" N MET I 259 " --> pdb=" O TYR I 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 252 through 253 591 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3062 1.33 - 1.45: 2916 1.45 - 1.58: 7289 1.58 - 1.70: 98 1.70 - 1.82: 74 Bond restraints: 13439 Sorted by residual: bond pdb=" C GLU J 219 " pdb=" N PRO J 220 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.62e+01 bond pdb=" C3' DT X 18 " pdb=" C2' DT X 18 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DT X 21 " pdb=" C2' DT X 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.52e+00 bond pdb=" N PHE J 260 " pdb=" CA PHE J 260 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.34e-02 5.57e+03 8.32e+00 bond pdb=" CG HIS N 89 " pdb=" CD2 HIS N 89 " ideal model delta sigma weight residual 1.354 1.325 0.029 1.10e-02 8.26e+03 6.91e+00 ... (remaining 13434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 18158 3.59 - 7.18: 172 7.18 - 10.78: 30 10.78 - 14.37: 11 14.37 - 17.96: 1 Bond angle restraints: 18372 Sorted by residual: angle pdb=" CA LYS D 160 " pdb=" CB LYS D 160 " pdb=" CG LYS D 160 " ideal model delta sigma weight residual 114.10 127.02 -12.92 2.00e+00 2.50e-01 4.17e+01 angle pdb=" C ASP B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N ILE B 65 " pdb=" CA ILE B 65 " pdb=" C ILE B 65 " ideal model delta sigma weight residual 112.29 107.20 5.09 9.40e-01 1.13e+00 2.94e+01 angle pdb=" C ASN J 18 " pdb=" N ASN J 19 " pdb=" CA ASN J 19 " ideal model delta sigma weight residual 122.46 129.90 -7.44 1.41e+00 5.03e-01 2.78e+01 angle pdb=" N PHE N 82 " pdb=" CA PHE N 82 " pdb=" C PHE N 82 " ideal model delta sigma weight residual 111.28 105.59 5.69 1.09e+00 8.42e-01 2.72e+01 ... (remaining 18367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6349 17.84 - 35.67: 1074 35.67 - 53.51: 447 53.51 - 71.35: 143 71.35 - 89.18: 25 Dihedral angle restraints: 8038 sinusoidal: 3663 harmonic: 4375 Sorted by residual: dihedral pdb=" CD ARG N 102 " pdb=" NE ARG N 102 " pdb=" CZ ARG N 102 " pdb=" NH1 ARG N 102 " ideal model delta sinusoidal sigma weight residual 0.00 -72.75 72.75 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA PRO A 56 " pdb=" C PRO A 56 " pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LYS B 90 " pdb=" C LYS B 90 " pdb=" N PRO B 91 " pdb=" CA PRO B 91 " ideal model delta harmonic sigma weight residual 180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 8035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1952 0.097 - 0.194: 154 0.194 - 0.291: 13 0.291 - 0.388: 0 0.388 - 0.485: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU B 107 " pdb=" CB LEU B 107 " pdb=" CD1 LEU B 107 " pdb=" CD2 LEU B 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CB ILE D 97 " pdb=" CA ILE D 97 " pdb=" CG1 ILE D 97 " pdb=" CG2 ILE D 97 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE B 65 " pdb=" CA ILE B 65 " pdb=" CG1 ILE B 65 " pdb=" CG2 ILE B 65 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2117 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 102 " -1.035 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG N 102 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG N 102 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG N 102 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG N 102 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 189 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN B 189 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 189 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL B 190 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 23 " 0.027 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE J 23 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE J 23 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE J 23 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE J 23 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE J 23 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 23 " 0.009 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 12 2.01 - 2.73: 853 2.73 - 3.45: 18242 3.45 - 4.18: 31381 4.18 - 4.90: 53201 Nonbonded interactions: 103689 Sorted by model distance: nonbonded pdb=" OD1 ASN J 18 " pdb=" OE2 GLU N 91 " model vdw 1.285 3.040 nonbonded pdb=" OD2 ASP B 118 " pdb=" OE2 GLU C 146 " model vdw 1.344 3.040 nonbonded pdb=" OG SER J 35 " pdb=" CG ASN N 94 " model vdw 1.558 3.270 nonbonded pdb=" OD1 ASP C 142 " pdb=" OE1 GLU C 146 " model vdw 1.585 3.040 nonbonded pdb=" OE1 GLU B 128 " pdb=" O ALA C 132 " model vdw 1.631 3.040 ... (remaining 103684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 301) selection = (chain 'B' and (resid 1 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 301)) selection = (chain 'C' and (resid 1 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 301)) selection = (chain 'D' and (resid 1 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 301)) } ncs_group { reference = (chain 'I' and resid 1 through 287) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.120 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.053 13439 Z= 0.306 Angle : 1.040 17.959 18372 Z= 0.600 Chirality : 0.055 0.485 2120 Planarity : 0.012 0.464 2160 Dihedral : 21.828 89.182 5200 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.37 % Favored : 95.15 % Rotamer: Outliers : 4.04 % Allowed : 33.88 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.19), residues: 1465 helix: -1.14 (0.17), residues: 673 sheet: -1.10 (0.42), residues: 157 loop : -1.99 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 92 TYR 0.028 0.002 TYR A 206 PHE 0.062 0.003 PHE J 23 TRP 0.038 0.003 TRP I 3 HIS 0.015 0.002 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.31 (13439) covalent geometry : angle 1.03966 / 0.60 (18372) hydrogen bonds : bond 0.15082 / 10.36 ( 641) hydrogen bonds : angle 6.02957 / 4.25 ( 1807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8330 (pptt) REVERT: A 138 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5638 (tm-30) REVERT: A 149 MET cc_start: 0.8383 (mmm) cc_final: 0.8100 (mmp) REVERT: A 164 LEU cc_start: 0.8321 (tp) cc_final: 0.7918 (mp) REVERT: A 206 TYR cc_start: 0.6942 (m-10) cc_final: 0.5561 (m-80) REVERT: C 107 LEU cc_start: 0.9127 (mt) cc_final: 0.8839 (mt) REVERT: C 137 ILE cc_start: 0.8163 (mt) cc_final: 0.7601 (mt) REVERT: D 42 ASN cc_start: 0.7623 (m110) cc_final: 0.6652 (m-40) REVERT: D 150 GLU cc_start: 0.8155 (tt0) cc_final: 0.7937 (tt0) REVERT: I 39 VAL cc_start: 0.9357 (t) cc_final: 0.8955 (t) REVERT: J 190 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8004 (mm-30) outliers start: 54 outliers final: 17 residues processed: 361 average time/residue: 0.0964 time to fit residues: 51.1064 Evaluate side-chains 193 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 215 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 168 ASN A 201 GLN A 202 ASN B 115 HIS B 168 ASN C 179 GLN D 106 GLN D 188 ASN J 9 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS J 258 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.098026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068181 restraints weight = 43103.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.069950 restraints weight = 24342.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071201 restraints weight = 16743.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.072110 restraints weight = 12901.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072454 restraints weight = 10708.999| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13439 Z= 0.221 Angle : 0.720 8.538 18372 Z= 0.387 Chirality : 0.045 0.262 2120 Planarity : 0.005 0.098 2160 Dihedral : 18.531 89.344 2221 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.62 % Favored : 96.11 % Rotamer: Outliers : 6.96 % Allowed : 29.84 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1465 helix: 0.34 (0.19), residues: 687 sheet: -1.01 (0.43), residues: 157 loop : -1.70 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 198 TYR 0.023 0.002 TYR A 206 PHE 0.034 0.002 PHE D 145 TRP 0.035 0.003 TRP I 3 HIS 0.009 0.002 HIS J 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (13439) covalent geometry : angle 0.72008 / 0.39 (18372) hydrogen bonds : bond 0.05153 / 3.44 ( 641) hydrogen bonds : angle 4.59116 / 3.23 ( 1807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 166 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8963 (tpp) cc_final: 0.8750 (tpp) REVERT: A 138 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5591 (pm20) REVERT: A 162 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8388 (mmmm) REVERT: A 164 LEU cc_start: 0.8779 (tp) cc_final: 0.8338 (mp) REVERT: B 44 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8650 (pt) REVERT: B 115 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: D 96 MET cc_start: 0.8990 (tpp) cc_final: 0.8680 (tpp) REVERT: D 118 ASP cc_start: 0.8435 (t0) cc_final: 0.7216 (t0) REVERT: D 150 GLU cc_start: 0.8917 (tt0) cc_final: 0.8659 (tt0) REVERT: D 196 GLU cc_start: 0.7405 (tt0) cc_final: 0.7049 (mt-10) REVERT: I 24 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8014 (tmtt) REVERT: I 155 TYR cc_start: 0.8494 (t80) cc_final: 0.8105 (t80) REVERT: I 159 LEU cc_start: 0.8795 (tp) cc_final: 0.6836 (tp) REVERT: I 218 MET cc_start: 0.7830 (ttp) cc_final: 0.7422 (ttp) REVERT: I 222 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8534 (ttm-80) REVERT: I 240 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9035 (mpp) REVERT: I 249 MET cc_start: 0.8914 (ptp) cc_final: 0.8692 (ptp) REVERT: J 135 MET cc_start: 0.8350 (ttm) cc_final: 0.8121 (ttt) REVERT: J 146 ASN cc_start: 0.9459 (t0) cc_final: 0.9212 (t0) REVERT: J 190 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8245 (mm-30) REVERT: J 240 MET cc_start: 0.9126 (mtm) cc_final: 0.8780 (mtp) outliers start: 93 outliers final: 38 residues processed: 247 average time/residue: 0.1006 time to fit residues: 37.2945 Evaluate side-chains 192 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 222 ARG Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN B 168 ASN B 211 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.065524 restraints weight = 44278.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067296 restraints weight = 24673.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068448 restraints weight = 16747.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069395 restraints weight = 13276.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069617 restraints weight = 10854.809| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13439 Z= 0.252 Angle : 0.675 6.816 18372 Z= 0.364 Chirality : 0.043 0.153 2120 Planarity : 0.004 0.050 2160 Dihedral : 18.450 88.852 2209 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.98 % Favored : 94.88 % Rotamer: Outliers : 5.01 % Allowed : 29.84 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1465 helix: 0.93 (0.20), residues: 684 sheet: -1.25 (0.43), residues: 161 loop : -1.57 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 166 TYR 0.018 0.002 TYR A 206 PHE 0.020 0.002 PHE N 82 TRP 0.033 0.003 TRP I 3 HIS 0.008 0.002 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (13439) covalent geometry : angle 0.67457 / 0.36 (18372) hydrogen bonds : bond 0.04764 / 3.19 ( 641) hydrogen bonds : angle 4.41665 / 3.11 ( 1807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 141 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8610 (mt) REVERT: A 138 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5907 (pt0) REVERT: B 44 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8676 (pt) REVERT: B 216 TYR cc_start: 0.9163 (t80) cc_final: 0.8752 (t80) REVERT: D 50 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8172 (tp-100) REVERT: D 96 MET cc_start: 0.9053 (tpp) cc_final: 0.8728 (tpp) REVERT: D 118 ASP cc_start: 0.8481 (t0) cc_final: 0.8030 (t0) REVERT: D 150 GLU cc_start: 0.9000 (tt0) cc_final: 0.8758 (tt0) REVERT: D 196 GLU cc_start: 0.7396 (tt0) cc_final: 0.6992 (mt-10) REVERT: I 24 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8061 (tmtt) REVERT: I 159 LEU cc_start: 0.8402 (tp) cc_final: 0.8096 (tp) REVERT: I 249 MET cc_start: 0.8911 (ptp) cc_final: 0.8672 (ptp) REVERT: J 146 ASN cc_start: 0.9569 (t0) cc_final: 0.9299 (t0) REVERT: J 190 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8217 (mm-30) outliers start: 67 outliers final: 39 residues processed: 198 average time/residue: 0.0927 time to fit residues: 28.4681 Evaluate side-chains 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 202 ASN B 115 HIS B 168 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 HIS J 277 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.095214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.064837 restraints weight = 44334.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066547 restraints weight = 24827.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067704 restraints weight = 16958.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068623 restraints weight = 13444.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068958 restraints weight = 11073.220| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13439 Z= 0.223 Angle : 0.639 7.203 18372 Z= 0.343 Chirality : 0.042 0.145 2120 Planarity : 0.004 0.044 2160 Dihedral : 18.471 88.590 2204 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 5.46 % Allowed : 29.99 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1465 helix: 1.19 (0.20), residues: 682 sheet: -1.21 (0.48), residues: 133 loop : -1.51 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 102 TYR 0.021 0.002 TYR A 216 PHE 0.025 0.002 PHE B 5 TRP 0.036 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (13439) covalent geometry : angle 0.63891 / 0.34 (18372) hydrogen bonds : bond 0.04377 / 2.91 ( 641) hydrogen bonds : angle 4.27959 / 2.99 ( 1807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8175 (mm) REVERT: A 138 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: B 36 TYR cc_start: 0.9032 (m-80) cc_final: 0.8787 (m-80) REVERT: B 44 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8698 (pt) REVERT: B 115 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7819 (t-90) REVERT: B 216 TYR cc_start: 0.9164 (t80) cc_final: 0.8735 (t80) REVERT: D 96 MET cc_start: 0.9068 (tpp) cc_final: 0.8745 (tpp) REVERT: D 150 GLU cc_start: 0.9006 (tt0) cc_final: 0.8759 (tt0) REVERT: D 196 GLU cc_start: 0.7342 (tt0) cc_final: 0.6936 (mt-10) REVERT: I 24 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7898 (tmtt) REVERT: I 159 LEU cc_start: 0.8527 (tp) cc_final: 0.8227 (tp) REVERT: I 242 ARG cc_start: 0.9133 (tpm170) cc_final: 0.8929 (tpm170) REVERT: I 249 MET cc_start: 0.8913 (ptp) cc_final: 0.8668 (ptp) REVERT: I 259 MET cc_start: 0.8508 (pmm) cc_final: 0.7510 (pmm) REVERT: J 190 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8905 (mm-30) REVERT: J 276 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8793 (tp) outliers start: 73 outliers final: 43 residues processed: 200 average time/residue: 0.0944 time to fit residues: 29.5202 Evaluate side-chains 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 188 ASN A 202 ASN B 115 HIS B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.065083 restraints weight = 44084.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066897 restraints weight = 24618.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068062 restraints weight = 16748.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068949 restraints weight = 13102.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069200 restraints weight = 10904.941| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13439 Z= 0.145 Angle : 0.601 9.488 18372 Z= 0.321 Chirality : 0.042 0.298 2120 Planarity : 0.003 0.040 2160 Dihedral : 18.427 88.976 2202 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.78 % Favored : 95.09 % Rotamer: Outliers : 4.56 % Allowed : 30.59 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1465 helix: 1.39 (0.20), residues: 684 sheet: -1.14 (0.49), residues: 133 loop : -1.48 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 203 TYR 0.019 0.001 TYR A 216 PHE 0.021 0.001 PHE B 5 TRP 0.035 0.002 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (13439) covalent geometry : angle 0.60104 / 0.32 (18372) hydrogen bonds : bond 0.04052 / 2.71 ( 641) hydrogen bonds : angle 4.12117 / 2.86 ( 1807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8989 (tpp) cc_final: 0.8746 (tpp) REVERT: A 113 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8266 (mt) REVERT: A 138 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6266 (pt0) REVERT: A 189 ASN cc_start: 0.8641 (p0) cc_final: 0.8390 (p0) REVERT: B 36 TYR cc_start: 0.9024 (m-80) cc_final: 0.8716 (m-80) REVERT: B 44 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8664 (pt) REVERT: B 149 MET cc_start: 0.9284 (mmm) cc_final: 0.8999 (mmm) REVERT: B 216 TYR cc_start: 0.9168 (t80) cc_final: 0.8746 (t80) REVERT: D 96 MET cc_start: 0.9067 (tpp) cc_final: 0.8711 (tpp) REVERT: D 150 GLU cc_start: 0.8987 (tt0) cc_final: 0.8739 (tt0) REVERT: D 196 GLU cc_start: 0.7292 (tt0) cc_final: 0.6922 (mt-10) REVERT: I 24 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.7956 (tmtt) REVERT: I 135 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (pmm) REVERT: I 242 ARG cc_start: 0.9158 (tpm170) cc_final: 0.8929 (tpm170) REVERT: I 249 MET cc_start: 0.8915 (ptp) cc_final: 0.8686 (ptp) REVERT: I 259 MET cc_start: 0.8489 (pmm) cc_final: 0.7590 (pmm) REVERT: J 41 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8919 (tt) REVERT: J 190 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8064 (tp30) REVERT: J 218 MET cc_start: 0.8501 (mmm) cc_final: 0.8289 (mmm) REVERT: J 276 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8713 (tp) outliers start: 61 outliers final: 34 residues processed: 188 average time/residue: 0.0981 time to fit residues: 28.2922 Evaluate side-chains 174 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 113 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 141 optimal weight: 50.0000 chunk 124 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN J 19 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** 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 = 0.3686 r_free = 0.3686 target = 0.096399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.066020 restraints weight = 43441.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067787 restraints weight = 24103.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068981 restraints weight = 16417.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069583 restraints weight = 12954.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070403 restraints weight = 11032.953| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13439 Z= 0.121 Angle : 0.587 8.999 18372 Z= 0.312 Chirality : 0.041 0.181 2120 Planarity : 0.003 0.039 2160 Dihedral : 18.388 89.507 2202 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 4.64 % Allowed : 30.67 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.22), residues: 1465 helix: 1.47 (0.20), residues: 684 sheet: -1.11 (0.49), residues: 133 loop : -1.38 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 147 TYR 0.033 0.001 TYR A 216 PHE 0.028 0.001 PHE A 204 TRP 0.042 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13439) covalent geometry : angle 0.58681 / 0.31 (18372) hydrogen bonds : bond 0.03822 / 2.55 ( 641) hydrogen bonds : angle 3.96861 / 2.74 ( 1807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6111 (pt0) REVERT: A 189 ASN cc_start: 0.8669 (p0) cc_final: 0.8455 (p0) REVERT: B 36 TYR cc_start: 0.9015 (m-80) cc_final: 0.8628 (m-80) REVERT: B 44 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8603 (pt) REVERT: B 149 MET cc_start: 0.9294 (mmm) cc_final: 0.9010 (mmm) REVERT: B 216 TYR cc_start: 0.9164 (t80) cc_final: 0.8755 (t80) REVERT: D 96 MET cc_start: 0.9063 (tpp) cc_final: 0.8698 (tpp) REVERT: D 150 GLU cc_start: 0.8978 (tt0) cc_final: 0.8723 (tt0) REVERT: D 196 GLU cc_start: 0.7225 (tt0) cc_final: 0.6919 (mt-10) REVERT: I 135 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8182 (pmm) REVERT: I 242 ARG cc_start: 0.9170 (tpm170) cc_final: 0.8933 (tpm170) REVERT: I 249 MET cc_start: 0.8939 (ptp) cc_final: 0.8714 (ptp) REVERT: I 259 MET cc_start: 0.8483 (pmm) cc_final: 0.7587 (pmm) REVERT: J 41 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8884 (tt) REVERT: J 190 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8161 (tp30) REVERT: J 218 MET cc_start: 0.8541 (mmm) cc_final: 0.8278 (mmm) REVERT: J 276 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8680 (tp) outliers start: 62 outliers final: 40 residues processed: 194 average time/residue: 0.1007 time to fit residues: 29.9927 Evaluate side-chains 182 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 132 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.095532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.065168 restraints weight = 44141.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066964 restraints weight = 24512.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068212 restraints weight = 16716.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069079 restraints weight = 12888.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069419 restraints weight = 10777.618| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13439 Z= 0.152 Angle : 0.596 8.515 18372 Z= 0.317 Chirality : 0.041 0.170 2120 Planarity : 0.003 0.039 2160 Dihedral : 18.378 89.527 2202 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 3.96 % Allowed : 31.41 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1465 helix: 1.52 (0.20), residues: 685 sheet: -1.11 (0.46), residues: 143 loop : -1.37 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 166 TYR 0.026 0.001 TYR A 216 PHE 0.027 0.001 PHE A 204 TRP 0.028 0.002 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (13439) covalent geometry : angle 0.59608 / 0.32 (18372) hydrogen bonds : bond 0.03848 / 2.57 ( 641) hydrogen bonds : angle 3.99702 / 2.77 ( 1807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8991 (tpp) cc_final: 0.8751 (tpp) REVERT: A 138 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6163 (pt0) REVERT: B 36 TYR cc_start: 0.9014 (m-80) cc_final: 0.8599 (m-80) REVERT: B 44 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8660 (pt) REVERT: B 149 MET cc_start: 0.9318 (mmm) cc_final: 0.9017 (mmm) REVERT: B 216 TYR cc_start: 0.9165 (t80) cc_final: 0.8752 (t80) REVERT: D 1 MET cc_start: 0.7514 (ttp) cc_final: 0.7280 (ttp) REVERT: D 96 MET cc_start: 0.9066 (tpp) cc_final: 0.8699 (tpp) REVERT: D 150 GLU cc_start: 0.8955 (tt0) cc_final: 0.8696 (tt0) REVERT: D 196 GLU cc_start: 0.7254 (tt0) cc_final: 0.6940 (mt-10) REVERT: I 135 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8192 (pmm) REVERT: I 190 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8185 (mt-10) REVERT: I 242 ARG cc_start: 0.9182 (tpm170) cc_final: 0.8937 (tpm170) REVERT: I 249 MET cc_start: 0.8942 (ptp) cc_final: 0.8727 (ptp) REVERT: I 259 MET cc_start: 0.8500 (pmm) cc_final: 0.7599 (pmm) REVERT: J 41 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8912 (tt) REVERT: J 146 ASN cc_start: 0.9396 (t0) cc_final: 0.9095 (t0) REVERT: J 190 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8172 (tp30) REVERT: J 276 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8667 (tp) outliers start: 53 outliers final: 41 residues processed: 183 average time/residue: 0.0941 time to fit residues: 26.7282 Evaluate side-chains 182 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.0050 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 202 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** 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 = 0.3674 r_free = 0.3674 target = 0.095721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.065611 restraints weight = 43575.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067339 restraints weight = 24103.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068614 restraints weight = 16558.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.069444 restraints weight = 12710.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070032 restraints weight = 10608.516| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13439 Z= 0.130 Angle : 0.584 9.127 18372 Z= 0.311 Chirality : 0.041 0.177 2120 Planarity : 0.003 0.038 2160 Dihedral : 18.371 89.590 2202 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Rotamer: Outliers : 4.11 % Allowed : 31.26 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.23), residues: 1465 helix: 1.65 (0.20), residues: 679 sheet: -1.06 (0.47), residues: 143 loop : -1.28 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 102 TYR 0.021 0.001 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.026 0.002 TRP I 3 HIS 0.008 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13439) covalent geometry : angle 0.58450 / 0.31 (18372) hydrogen bonds : bond 0.03706 / 2.49 ( 641) hydrogen bonds : angle 3.91915 / 2.71 ( 1807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6077 (pt0) REVERT: B 36 TYR cc_start: 0.9007 (m-80) cc_final: 0.8551 (m-80) REVERT: B 44 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8624 (pt) REVERT: B 149 MET cc_start: 0.9316 (mmm) cc_final: 0.8985 (mmm) REVERT: B 216 TYR cc_start: 0.9156 (t80) cc_final: 0.8755 (t80) REVERT: D 96 MET cc_start: 0.9070 (tpp) cc_final: 0.8700 (tpp) REVERT: D 150 GLU cc_start: 0.8976 (tt0) cc_final: 0.8747 (tt0) REVERT: D 196 GLU cc_start: 0.7243 (tt0) cc_final: 0.6948 (mt-10) REVERT: I 135 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8174 (pmm) REVERT: I 190 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8150 (mt-10) REVERT: I 242 ARG cc_start: 0.9183 (tpm170) cc_final: 0.8923 (tpm170) REVERT: I 249 MET cc_start: 0.8927 (ptp) cc_final: 0.8719 (ptp) REVERT: I 259 MET cc_start: 0.8529 (pmm) cc_final: 0.7634 (pmm) REVERT: J 41 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8906 (tt) REVERT: J 190 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8249 (mm-30) REVERT: J 249 MET cc_start: 0.8728 (mmm) cc_final: 0.8450 (mmm) REVERT: J 276 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8640 (tp) outliers start: 55 outliers final: 43 residues processed: 186 average time/residue: 0.0993 time to fit residues: 28.2784 Evaluate side-chains 184 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 25 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** 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 = 0.3695 r_free = 0.3695 target = 0.096895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066728 restraints weight = 43716.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068594 restraints weight = 24017.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069879 restraints weight = 16231.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070719 restraints weight = 12384.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071000 restraints weight = 10364.535| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13439 Z= 0.115 Angle : 0.599 9.685 18372 Z= 0.318 Chirality : 0.041 0.183 2120 Planarity : 0.003 0.037 2160 Dihedral : 18.267 89.950 2199 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.70 % Rotamer: Outliers : 3.14 % Allowed : 31.94 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.23), residues: 1465 helix: 1.68 (0.20), residues: 679 sheet: -1.04 (0.46), residues: 143 loop : -1.23 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 147 TYR 0.018 0.001 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.023 0.002 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (13439) covalent geometry : angle 0.59914 / 0.32 (18372) hydrogen bonds : bond 0.03588 / 2.39 ( 641) hydrogen bonds : angle 3.85346 / 2.66 ( 1807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8978 (tpp) cc_final: 0.8724 (tpp) REVERT: A 138 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6003 (pt0) REVERT: A 164 LEU cc_start: 0.8808 (tp) cc_final: 0.8494 (mp) REVERT: A 189 ASN cc_start: 0.8750 (p0) cc_final: 0.8526 (p0) REVERT: B 44 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8606 (pt) REVERT: B 149 MET cc_start: 0.9326 (mmm) cc_final: 0.9000 (mmm) REVERT: B 216 TYR cc_start: 0.9155 (t80) cc_final: 0.8749 (t80) REVERT: D 96 MET cc_start: 0.9063 (tpp) cc_final: 0.8689 (tpp) REVERT: D 131 LYS cc_start: 0.9559 (tppp) cc_final: 0.9346 (ttmm) REVERT: D 196 GLU cc_start: 0.7248 (tt0) cc_final: 0.6996 (mt-10) REVERT: I 135 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8175 (pmm) REVERT: I 190 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8223 (mm-30) REVERT: I 242 ARG cc_start: 0.9190 (tpm170) cc_final: 0.8914 (tpm170) REVERT: I 249 MET cc_start: 0.8930 (ptp) cc_final: 0.8720 (ptp) REVERT: I 259 MET cc_start: 0.8559 (pmm) cc_final: 0.7635 (pmm) REVERT: J 41 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8887 (tt) REVERT: J 190 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8209 (mm-30) REVERT: J 251 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8604 (t) REVERT: J 276 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8534 (tp) outliers start: 42 outliers final: 34 residues processed: 185 average time/residue: 0.1008 time to fit residues: 28.7076 Evaluate side-chains 182 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN J 9 ASN J 29 GLN ** N 89 HIS ** 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 = 0.3651 r_free = 0.3651 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.064613 restraints weight = 44795.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066366 restraints weight = 25407.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067592 restraints weight = 17503.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.068232 restraints weight = 13510.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068867 restraints weight = 11577.975| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13439 Z= 0.206 Angle : 0.627 9.798 18372 Z= 0.335 Chirality : 0.041 0.168 2120 Planarity : 0.003 0.039 2160 Dihedral : 18.265 89.510 2199 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 3.37 % Allowed : 32.01 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1465 helix: 1.69 (0.20), residues: 681 sheet: -1.05 (0.46), residues: 143 loop : -1.21 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 4 TYR 0.019 0.002 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.060 0.004 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (13439) covalent geometry : angle 0.62725 / 0.33 (18372) hydrogen bonds : bond 0.03924 / 2.64 ( 641) hydrogen bonds : angle 4.00644 / 2.78 ( 1807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9033 (tpp) cc_final: 0.8776 (tpp) REVERT: A 138 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6203 (pt0) REVERT: B 44 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8665 (pt) REVERT: B 149 MET cc_start: 0.9348 (mmm) cc_final: 0.9029 (mmm) REVERT: B 216 TYR cc_start: 0.9195 (t80) cc_final: 0.8777 (t80) REVERT: D 96 MET cc_start: 0.9095 (tpp) cc_final: 0.8769 (tpp) REVERT: D 196 GLU cc_start: 0.7299 (tt0) cc_final: 0.6964 (mt-10) REVERT: I 135 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8260 (pmm) REVERT: I 190 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8271 (mm-30) REVERT: I 259 MET cc_start: 0.8565 (pmm) cc_final: 0.7685 (pmm) REVERT: J 183 LEU cc_start: 0.9053 (tp) cc_final: 0.8821 (tt) REVERT: J 190 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8245 (mm-30) REVERT: J 218 MET cc_start: 0.8411 (tpt) cc_final: 0.7923 (tpt) REVERT: J 249 MET cc_start: 0.8707 (mmm) cc_final: 0.8488 (mmm) REVERT: J 276 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8648 (tp) outliers start: 45 outliers final: 36 residues processed: 172 average time/residue: 0.0882 time to fit residues: 23.7875 Evaluate side-chains 170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 142 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN J 9 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** 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 = 0.3666 r_free = 0.3666 target = 0.095856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.064986 restraints weight = 44174.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.066718 restraints weight = 25024.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067880 restraints weight = 17274.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068675 restraints weight = 13525.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.069297 restraints weight = 11347.050| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13439 Z= 0.151 Angle : 0.608 10.125 18372 Z= 0.325 Chirality : 0.041 0.179 2120 Planarity : 0.003 0.036 2160 Dihedral : 18.252 89.250 2199 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.97 % Rotamer: Outliers : 3.14 % Allowed : 32.09 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1465 helix: 1.67 (0.20), residues: 683 sheet: -1.04 (0.46), residues: 143 loop : -1.25 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 242 TYR 0.017 0.001 TYR A 216 PHE 0.026 0.001 PHE A 204 TRP 0.051 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (13439) covalent geometry : angle 0.60784 / 0.33 (18372) hydrogen bonds : bond 0.03702 / 2.49 ( 641) hydrogen bonds : angle 3.94001 / 2.73 ( 1807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.75 seconds wall clock time: 35 minutes 25.91 seconds (2125.91 seconds total)